S1_7_2: [5.111] just filling my pencil case with (?crackers) [laughs] [8.042] S2_7_2: [8.042] [?] S9_T1_7_2: [9.535] [??] will be about [??] (2) but as long as you can do it. it means you can do it whatever [?]. (4) right well who's first ?. record [?] S1_7_2: [29.220] ok so shall we start with em the what is dysmorphology S5? S5_7_2: [35.557] ok S1_7_2: [35.902] ok? [36.848] well you're not [?] [38.277] [laughter] [39.154] still [?] S5_7_2: [40.744] still working . ok paper ,(3) sorry for that the staples are really [?] [gives out handout] S1_7_2: [48.397] no mine are folded so the stapler's [?] left there not any staples left S5_7_2: [62.013] ok er just a definition what is [?], ah it comes from the Greek, which is means ah, it's not normal but we can say here in this case er , it's something that is abnormal in form, and for example we can that it's ah malformed ear or dysmorphic ear, er which would be ah , dysmorphic feature. and this term er, em was defined by doctor Smith , in the sixties to describe the study er of human er, congenital , malformations. (2) and well in this case i just add a little extra information just to have an overview of the of our case , ah and in, ah the case ah , of two Q thirty seven syndrome ahm, we know that there is a variety of the physical features but in general we can say that, er physical er er i divide the features in the most important, that we can see is ah obviously how the patients, er looks like and, in the head for example we can say that, we can find the sparse hair, er sparse arched , eyebrows also it can be possible to find a round face or full cheeks , which is common , ah , lips and deep set eyes, and also it's uh , one of the most common features is, something that is not normal in the nose. so, we can see a short nose, ah, deficient notched nares. the nares is the, cavity it's in the nose this part, [gestures/points to it on self] (2) um, low set columella, which is this part, and it's, it's going to be like, this. no- not up, just down. and , (2) also we can see the ah, around the the mouth, ah is a short philtrum, which is we know it's here yeah, um also there's something called, hypoplastic cupid bow which is this feature around here on the lips, the division. so it's it's not a, very notorious can be, flat sometimes. em, also eh , pinna anomalies ah which is ah the part of the ear that projects like a little wing from the head it's like that [gestures]. : [240.316] [group laughs] S5_7_2: [242.559] so, they are just to make it more clear . and oh well, this is not on the head but inverted nipples and , also ahm , small hands and feet which is called brachimetaphalangism , this is the the most general er, picture in the the patient. ahm and also we we have another abnormalities in the heart dextrocardia which is mean the, the heart is in the right side, and aortic coarctation , ah the aorta is a artery , one of the biggest, and ah coarctation is just that it's the the it's narrowing , [ gestures] there is ah , and sometimes it provokes high pressure. and , about neurology of central nervous system we can find , ah mental retardation which is em also very very common , autism of patients, and behavioural disorders. it can can, er include ah hyperactivity , and seizures as well, it's very common. [ turning pages ] and at the end the, ah variety we can find not in the whole patient but it's often, ah , it's a short stature , obesity eczema which is a kind of ah , disease in the skin, yeah it's it's red. asthma as well, ah recurrent infections Wilms tumor which is uh, one of the most common, er tumors , in the , er childhood, and it is, it's kind -it's cancer . and, cystic kidneys. ehm, which er , also provokes a mal function of the kidneys. and just to have an an overview , what i'm saying , er i , add some pictures so the , (3) ah some patients , um and you can see in the , patient in the picture A , the forehead , the eyebrows are characteristic well here is not clear but if you find carefully, you look at carefully , the eyebrows also there are [?]. [referring to pictures] ahm, also the nasal bridge , you can see it . it's dysmorphic , well em, (2) also as i say low set with prominent, columella , and in the lips ah also the poor development of cupid bow . it is around here sorry see that it's, it's flat it's completely flat so , this one there are, other other features but this is a general picture of how, we can see the the , the patient . em , what else? um, well i just presume that one thing on the paper and just in the in the, pictures that we see , and , also there are some features that er there's not mention like er, for example the B M I this is body mass index which is related with er , obesity , ahm, and also like ahm, the behavioural disorders , so i think that the girl in , F and G well this is the same girl , has ah , hyperactivity . and most of them they have ah , neurological features of like a mental retardation. and that's it . S1_7_2: [477.314] that's great. has anyone got any questions ? dysmorphology? [others shake heads] shall we continue with developmental delay then? (2) shall we continue developmental delay then ? (12) [8.08 s2 gives out handout : [487.442] [S4 gives out handouts] S7_7_2: [498.144] [?]just pass them to [?] S4_7_2: [500.054] do you want to [517.434] developmental delay ehm involves ehm a child may not have attained or, been able to get eh certain certain skills at a certain age point and it's ehm in different areas like social language ehm , behave- you know behavioural physical em i put on , (2) i put on a general kind of note , of just some general things next to them i've put on em, things that are specific to em, the cryptic ehm, a paracentric inversion of chromosome two aso- associated with a cryptic duplication of two Q fourteen and deletion of two Q thirty seven. (2) so em i think he the wee boy had em, eh was fascinated with electrical sockets and he was obsessed by searching these out when he arrived at a new place . ehm i think he he certain things he developed normally at and and but em, [cough] it he sort of came to his parents' attention when he was about eighteen months old and he was avoiding eye con- eye contact, and em he wasn't answering to his name. ehm he eventually got diagnosed with ehm autism , S1_7_2: [594.046] that's him there, we've got the same paper [referring to handout] S4_7_2: [596.285] oh right ok [597.462] [s1 & others laugh] [598.369] anyway he got diagnosed with autism and i think he ended up in , to going to a special kind of school an institution and ahm, a lot of em terminal deletions with two Q em, about i think about eighty to ninety percent all had developmental delay, and em about a quarter or so of those also had autistic behaviour associated, with it, so, it seems like a, there's you know it's, em quite commonly seen in [?deletions ] in that region of the chromosome, S1_7_2: [637.543] great. (3) shall we start going through our kind of diagnostic techniques? em so i think S9_T1_7_2: [645.134] see just , going back to deve- developmental delay in general , what are you actually what are you looking for [? that's quite a lot ]in this case, but what for a child what is the developmental delay what (2) what S4_7_2: [659.905] is it S9_T1_7_2: [660.122] what [??] S4_7_2: [661.091] i think it's by a certain , em age or turning point or i suppose just like i suppose feeding themselves or kind of words and language and , just response to certain stimuli or , that [noise of papers makes inaudible] , ehm you know just trying to get at S9_T1_7_2: [676.471] yeah so what what what , basic milestones would you expect? what i don't know maybe , for like what S5_7_2: [685.710] no i think what is related with directly with the age S9_T1_7_2: [689.132] uhum S5_7_2: [689.373] for example at what time they start to walk , or to say some words S9_T1_7_2: [692.067] yeah when when would you expect them to walk? what age would you expect them? S7_7_2: [692.424] yeah S3_7_2: [697.230] is it nineteen months? S4_7_2: [698.207] it's about eighteen months S8_7_2: [699.243] eighteen months? yeah S9_T1_7_2: [700.537] and if you look at children i don't know at about eighteen months , will they all be abnormal or? S7_7_2: [705.362] no S4_7_2: [705.698] no . but i think it's more the case of oh i should've said really , that it's not necessarily because it's one thing's occurred means that they've got developmental delay but rather maybe be in a combination , S8_7_2: [713.774] uhum [716.042] yeah S9_T1_7_2: [719.874] when would you expect a child to start speaking? S4_7_2: [723.310] i think they start [? at the same], i think they start using words and start making noises [?] i think it could be quite young you know, like less than one i'd say [??] making noises[?] anyway we need to get on with the, the inversion. (3) his speech (3) his speech and language devel-dev- development was delayed , he started using meaningful words at thirty months and phrases at sixty months, so it's five that's five years so that's very old not very old but yeah compared to a normal S8_7_2: [734.589] i [?] S3_7_2: [734.985] i think S9_T1_7_2: [758.087] but is it [759.697] well [761.739] yeah S8_7_2: [762.209] [?] table S1_7_2: [763.430] [??] S4_7_2: [767.084] it says it just says that ehm (3) during the first six months he was ehm hypoactive so i think he had, he wasn't very mobile or wasn't seeking things out [referring to article] (2) and he was he must have been coordinated enough or mobile enough because it says his motor milestones were normal, he sat at nine months and walked at fourteen months, [791.131] S9_T1_7_2: [791.750] so that was a [?] S4_7_2: [792.768] yeah so that was so he did have some normal, ehm S8_7_2: [793.086] [?] S3_7_2: [796.620] [?features] S4_7_2: [797.994] features. S9_T1_7_2: [800.301] yeah if you look at the overall picture rather than , just [?] a more specific thing S4_7_2: [804.467] yeah S9_T1_7_2: [804.938] and there is a big age obviously [?], some children walk at one some don't walk till, nineteen months and then you're looking at [??] S5_7_2: [810.651] yeah [815.996] yeah also it's important for example when they eat well, later on. er how , they take the spoon, S4_7_2: [824.370] how independent they are [826.021] how S5_7_2: [826.021] yeah independent , the speech i mean the first words that they learn is mum and dad , simple words and then the speech , becomes a bit more complex. so that's important [838.728] . S3_7_2: [841.264] ok S1_7_2: [846.010] anymore questions on developmental delay? (4) i think the first techniques i have down is FISH, S6_7_2: [857.079] yep S1_7_2: [857.652] do you want to S6 S6_7_2: [858.958] ok [gives H/Os] [879.329] ok? so ah, i'll just speak briefly about ah fluorescent in situ hybridisation technique, so the technique is ah ah used to identify any ah, the presence of er ah any chromosomes chromosomal regions abnormality like ah ah the presence of the, ah chromosome specific chromosomal regions or, chromosomes itself. ah and they er use fluorescent labelled ah organically tied probes, um to ah anneal to a specific target ah , specific DNA. so er they need to ah have um fluorescent er , fl- light markers code , er to, check the results , and, as you see in the figure uhm, on the right side of the figure there's a ah target DNA , and on the left those are the two actually there are three over here but mainly there we're going to use the two of them, two different probes one of them is er indirect labelling ah on the left with the haptens, and on the right it's a direct label with a with a fluorescent . so on step C , er with that's the step of the denaturation, er of the probes as well as the target DNA, and step D is the annealing step where the probe will anneal to our to our specific er, DNA target, and the step E is ah only an extra step for the ah labelling the indirect ah, probe with the er, whatever chromogene which is mainly fluorescent . (2) ahm , so there are different types of ah, probes used in ah FISH technique, centromeric probes are ah to detect specific repetitive ah DNA sequences, found either in the centromereah or just around it , and er it is very useful in ah the screening of ah trisomy thirteen eighteen and twenty one . (2) and, uhm same thing with the telomeric er probes which are also detect this repetitive er sequences, but the location of the telomeric er areas is usually at the end of the chromosome . locus specific probes are ah bind unique DNA sequence within the genome , to detect any small changes , micro deletion or micro duplication , er that cannot be detected by the conventional um er karyotyping . er subtelomeric er probes , ah can be used to identify er origin of extra materials found on G banded ah chromosome, um, and they are useful for, patients with mental retardation to determine er if subtelomeric deletions duplications are present, em er especially if nor- the karyotype were normal . uhm , lastly whole chromosome paint probes um er refers to the um hybridisation of fluorescently labelled chromosome specific composite probe , pools to cytological preparations which allows the visualisation chromosomes in metaphase or interphase cells . um and the identification of both numerical and structural chromosomes abbre-abbreci- aberrations erm in human pathology with high sensitivity and specificity. so um basically we are er painting those chromosome uh um different twenty four different colours, uhm so we can differentiate between each one of them . and there are two different types of ah ah, um er whole , paint whole chromosome paint probes ah, multi colour FISH and er eh spectral karyotyping. SKY . and er both of them both of them are used in diagnostic and research applications. so uhm , this table just show the, uh uh applications of FISH in the diagnostic part and the research, uhm ah, like in the diagnostic part as an example identification of specific chromosomes , or also can be used for cases that filled , in in finding any abnormalities in the karyotyping . while in research it's very useful in stuff like gene mapping. (2) ok? thank you (2) any questions? (2) lots of questions S3_7_2: [1107.120] aberrations : [1186.189] [group laughs] S1_7_2: [1192.931] ok? erm shall we go on to the subtelomeric, probes S7_7_2: [1197.097] yeah [1201.236] yeah ? ok in the beginning i will actually want to, er clear the point as to what is S1_7_2: [1206.009] do you want to pass your sheets? S7_7_2: [1207.528] so sorry S1_7_2: [1208.011] it's ok S7_7_2: [1208.755] actually er, we all of us we are actually wondering as to why would anybody go for a sub telomeric sequencing , so the answer for that is sub telomeres are regions er which are gene rich , and er subtelomeric regions have been evolved , which the evolution of er, er the human race, there've been multiple duplications , to er- that has been followed for millions of years which gave rise to the subtelomeres , and the subtelomeres are er specific to each chromosome . so er. as- as in this paper by Elena et al it is given that er , the human subtelomeres are polymorphic patchworks which answers the question as to why there's polymorphism in er the subtelomeres . then , er the deletions either a gain or loss or an alteration in subtelomeric regions , gives rise to potential phenotypic effect that's because , there are twenty five small, families of genes that are involved in subtelomeric regions , and ah , ah they , i mean almost eighteen families contain at least one subtelomeric member that encodes a potentially important protein , a functional protein. that's why we have er potential phenotypic effect, if there is a gain or a loss or an alteration in the subtelomeric region. (2) ah, we would, suggest subtelomeric sequencing for a case where , when when we don't know whether, er there has- when we don't know the root cause of mental retardation or any physical abnormality. er we really don't know what is gone wrong with the patient either with karyotyping or any other test when we don't know what is wrong , that's when we er anybody can suggest er, the case er for subtelomeric sequencing . and the probes . the probes are about , er, (2) they they comprise of a unique sequence, and suppressed repetitive DNA like i told it's been evolved because er, of the duplications of DNA . it is either recombinant or clo- cloned DNA . er the , comments of subtelomeric probes are that not all probes are chromosome specifically do , er give rise to you know cross hybridisation with other chromosomes , er only some of the probes detect polymorphism that is two Q seven P and X P , we can't , erm, expect that all the subtelomeric probes would detect polymorphisms, ah familial studies are really necessary to find out whether the chromosomal imbalance is true or a familial variant. individual subtelomeric probes have been used to focus on specific subtelomeric areas, er some probes have been developed recently , and er i did not go through recent papers because it was more technical and did not tell anything about the basic subtelomere what we ere looking for, and er, er probes are chosen from the unique distal sequence to [?] to provide the best chromosomal specificity possible, subtelomeric probes or sequencing is recommended for mental retardation and other syndromes of unknown origin like, [?] and like how even Dr. D, told us that nobody would , in the beginning they wouldn't suggest subtelomeric sequencing because it's not cost effective , and er , on the other side there's just, er er the end of the chromosome which shows the TTAGG repeat which is a common repeat in a subtelomeric region , and er there is a diagram it's it's in black and white so you can't read like all the probes, this is er the result of FISH, on er us- using subtelomeric specific probes on ah, derivative ah i mean terminal of T, er two P and terminal of two T Q . and that's it. (4) : [1224.141] [? evolved-?who] S1_7_2: [1450.385] anyone have any questions on? (3) S9_T1_7_2: [1456.208] are there any distance spans [?] to, subtelomeric screening , (2) or is there anything else any other techniques you could do, instead ? S7_7_2: [1467.085] well , like it's told over here it , could be some polymorphisms are detected , like [?] two chromosomes , so if there is polymorphisms in any other chromosome i don't think subtelomeric probes might detect them S9_T1_7_2: [1480.578] so that's a point what what what change what does a subtelomeric, polymorphism , mean in that context or is it (2) what's detected and does it mean that all other subtelomeric probes are useless? S1_7_2: [1495.734] no cos sometimes you don't want there to be polymorphism. you're trying to see that the region's present, and not deleted like in this case S9_T1_7_2: [1507.985] so would most [?] subtelomeric probes , pick up deletions or duplications? or [?all] the ones that are on chromosomes? two subtelomeric? S6_7_2: [1520.108] sorry i didn't hear you [?what's that?] S9_T1_7_2: [1520.967] just to say that there're a bit, some detect polymorphisms two seven and X S7_7_2: [1527.728] the two Q seven P and XP S9_T1_7_2: [1528.890] uhuh what- what does that mean ? S7_7_2: [1533.376] i didn't , like what i understood from from that paper was that, er , er when there's polymorphism on on these three chromosomes they've developed probes , that detect polymorphism only on these three chromosomes, so the research is on its way to detect polymorphism er to to create probes for the other chromosomes as well S9_T1_7_2: [1543.385] uh huh [1546.286] uhuh [1556.175] so that's something for polymorphisms, but presumably the probes do detect deletions though if they're there S7_7_2: [1565.013] yeah they should do S9_T1_7_2: [1566.675] or eh are, deletions or duplications on any chromosome not just, not just those specific ones it must just be like S7_7_2: [1569.976] on any chromosome [1573.508] yeah, [1574.270] so, it's easier because er for each chromosome we have a specific telomeric subtelomeric probe , so that way i think er the polymorphism shouldn't matter much because we have a specific er, subtelomeric probe for each chromosome , so that way if it didn't depending on whether it binds or not we can [? do something else ] (3) but it will [?? show] polymorphisms S9_T1_7_2: [1580.074] uhuh [1599.048] yeah I'm not sure S1_7_2: [1600.067] in the paper i've well i'm going to talk about later they actually there's a specific , subtelomeric probe set and that just happens to be i think it was, the two Q ones happened the probes they frequently used happened to be on polymorphic regions so they always have to add, a second non polymorphic probe , so it was like a, standard kit that they got in and this has just been shown that one of them S9_T1_7_2: [1621.985] it's part of a standard kit right S4_7_2: [1623.853] this is how [?] [to S4; concurrent inaudible] S7_7_2: [1624.978] is it er from S1_7_2: [1626.403] yeah the de Villard paper , so it was a specific kit and then they specifically mentioned they have to use some additional ones they've got from elsewhere , so i don't know if that's just a recent finding that they've got those polymorphisms S7_7_2: [1638.140] oh yeah maybe S9_T1_7_2: [1643.272] so what other types what what's a disadvantage other than polymorphisms which is a good point what's another disadvantage of ? S7_7_2: [1650.376] cross hybridisation S9_T1_7_2: [1652.272] uhuh cross hybridisation, yep , possibility. so other, you know kind of practical S1_7_2: [1660.576] it's pretty large scale you don't find small S9_T1_7_2: [1662.610] uhum [1663.715] uhum uhum certain S1_7_2: [1665.503] [?for] really small changes S9_T1_7_2: [1667.916] ok. (2) what about the cost of it? S7_7_2: [1671.143] it's, (2) it's not cost effective. it's really expensive S9_T1_7_2: [1674.417] uhum [1676.389] so is there anything else that's more cost effective that could be done and that's quite often done i think S7_7_2: [1681.302] uhum S3_7_2: [1682.119] [?probably? issues?] S2_7_2: [1684.414] did they mention it at a lecture? S3_7_2: [1686.458] is it MALPA S9_T1_7_2: [1687.413] yeah, uhuh, you can do that for subtelomeric regions as well S6_7_2: [1691.697] umm S9_T1_7_2: [1693.207] [?] S4_7_2: [1694.980] [??] oh we done an analysis about MLPA S7_7_2: [1698.079] yeah [?] S9_T1_7_2: [1698.103] oh right ok S4_7_2: [1699.583] but it wasn't for this it must be for the microarrays [?] S9_T1_7_2: [1702.931] oh right ok yeah S4_7_2: [1704.101] and it said that MLPA, wasn't useful S3_7_2: [1708.176] oh right, i don't [??] S1_7_2: [1709.639] [?] S9_T1_7_2: [1711.124] cos MLPA you can get like, [??] : [1711.124] [some concurrent here; overlaps and inaudible] S2_7_2: [1712.695] [?] the deletions are in [?] S5_7_2: [1715.326] [?]] S4_7_2: [1716.003] yeah [1717.275] i don't know can't remember S3_7_2: [1717.782] [??] S5_7_2: [1719.813] [?] S4_7_2: [1720.808] oh sorry S3_7_2: [1723.896] [??] S1_7_2: [1729.374] ok does S7_7_2: [1729.800] but i think there'd be very rare cases that, would be recommended for subtelomeric er sequencing or probing [direct to S9] S9_T1_7_2: [1735.827] in odd [?] S1_7_2: [1736.899] i think in the research though all the mental- there's lots of mental retardation researches S4_7_2: [1740.335] yeah S7_7_2: [1740.917] yeah, which does not have any i mean, for which they are not able to find any [?basis/bases] for S1_7_2: [1746.635] well that's i think that's why they're using the subtelo S7_7_2: [1749.117] yeah S1_7_2: [1749.858] telomeric probes it's almost like a screen S9_T1_7_2: [1753.328] what percentage does anyone have a rough, what percentage roughly of , cases of mental retardation you would actually pick up something in? S7_7_2: [1759.679] four to five percent S9_T1_7_2: [1760.970] uhum , i think it's about five percent [?] that, in cases of mental retardation sub telomeric pro- sub telomeric probes might be picked up yeah. (3) S1_7_2: [1775.776] ok so on to em , CGH S3_7_2: [1781.203] ok. CGH stands for comparative genomic hybridisation as we all know, em scientists discovered em, this technique by when they were er doing a study to investigate tumour cells in cancer , so they both er they in this experiment em , they use both different- differentially labelled er, er DNA sequence from , er reference sample , that is tenderised and from patient samples . and they co hybridise them , er and a meta-metaphase chromosome spread . whereby after after which, er from the intensity ratios , they detected the ah , DNA sequence and mapping any chromosomal abnormalities. em, (2) this was for the traditional , comparative genomic hybridisation , there are more er improved , er CGH procedures . so basically they, extract the genomic DNA from patients' peripheral blood lymphocytes or from skin fibroblasts or any other available tissue. and if you can see on page, two diagram , basically this is the [? ] DNA that i was telling you about and the test of DNA. in DNA labelling they usually mainly, they mainly usually use , er either Cy three , dye or Cy five dye. to differentiate between each reference or DNA tested er, test DNA er sequences. which by they co hyb- co hybridise them the to a slide , and the modern array of CGH they use a target genomic slide , that i'm going to talk to you about later on , and then , they , eh detect it through a computer software , and, eh from the data analysis softwares they deduce whether er, there was a deletion or duplication or, any chromosomal abnormalities . (2) em, so the resolution is really important in this technique and it covers a wide range of , ah me- mega bases , rather than FISH and karyotyping , em so and other thing that they've used is, they use either er bacterial or , [? cross] mate er for inserting DNA sequences , for the CGH for the past six years and it was successfully done, with a resolution of eh one mega bases, that detected several chromosome abnormalities, so imbalances up to one mega bases on the traditional CGH were detected only, but in the, mi- in the array which is microarray CGH em, the resolution was even higher, to like five megabases . and more advanced technologies are improving till present , and they use either CDNA arrays oligonuleotide and SNP arrays, that is the resolution five eh mega bases . em, on the other hand i've also ah had a table , er for er brief comparison, between karyotyping FISH and CGH. so, in , (2) the karyotyping cannot, it it does[n't?] detect chromosomal abnormalities and also FISH and CGH, for the microscopic DNA changes , in karyotyping it is unable to detect them , in FISH it only detect them at metaphases chromosomes , and in CGH it detects them , the DNA copy changes at multiple loci in a genome in karyotyping no eh , eh detection of DNA changes and also in FISH, but, the CGH technique can detect the DNA changes at multiple loci in the genome. and if you see the limit whether whether it is limited by probe number , in karyotyping there is no, probe numbers in the FISH, yes but in , the CGH it is limited by probe number. (2) and , move on ah, i've done some, er, i found some clinical applications of CGH in er, different fields , so , in our case like for mental retardation and dysmorphism, i found a paper that found two new micro deletion syndromes, that were discovered by this technique , and each associated with several abnormalities syndromes, on the other hand in prenatal diagnostic investigations, eh this technique works, eh on the DNA of single cell , and it was de- er extracted from CVS amniocytes, and it, eventually detected the microdeletion duplication in this syndrome. and this can be as well in future option, for diagnostic. er for translocation both affected patients and normal carrier patients where, balanced translocations shown to be, to have only insertions and duplication but also disrupted genes near the translocation regions, was found by this technique, er this technique was very very em, important in cancer investigations as i mentioned, eh they first found that ehm, discovery of this technique was based when they were looking in cancer investigation as we all know , that numerical and structural imbalances occur in the pre malignant cells, and by using this technique it discovered the nature of diagnostic for cancer cells such as , cutaneous beta cell lymphocytes. (2) em , for the traditional CGH em, eh, yeah for the trad- for the traditional , CGH there's a limit which is , the resolution was up to one er megabase , but for the em , array CGH , there's a limitation as it cannot detect either em , translocations, and insertion-inversion, inversions in some certain areas, and, hopefully in the future they will improve em this technique, and that's it. (2) S1_7_2: [2162.084] so is there a reason there's certain areas that they can't , use it for or is it just S3_7_2: [2166.958] yeah and they have to compare with by other techniques such as FISH, the reasons behind it i'm not still sure about it but, em the micro deletion, em microscopic er, abnormalities such as inversions and translocation, they're still working in it and investigating it, why it doesn't detect it, whereas in FISH they detected it. (3) S9_T1_7_2: [2195.285] what kind of inversions translocations would you detect you're right there're certain ones it won't detect S7_7_2: [2201.539] balance S9_T1_7_2: [2202.241] uhum yeah why wouldn't it detect balance? S1_7_2: [2205.248] because the same genome is present S5_7_2: [2207.908] yeah S7_7_2: [2207.908] umm S9_T1_7_2: [2208.433] yep. so there's nothing lost nothing gained S7_7_2: [2210.856] oh yeah yeah S9_T1_7_2: [2211.752] yeah so you're right it won't detect , balance the translocations and inversions but it will detect balance where there's been a S7_7_2: [2217.519] deletion or [?insertion] yeah S9_T1_7_2: [2219.036] good point. (2) see with regards to the resolutions on the first page S3_7_2: [2224.377] yeah S9_T1_7_2: [2225.210] any comments ? about [?] (2) S3_7_2: [2230.247] any sorry what? S9_T1_7_2: [2231.714] any comments? S1_7_2: [2233.133] i'd've thought the resolution would be better that we'd see smaller than a megabase S3_7_2: [2238.062] mm (3) S9_T1_7_2: [2241.609] so is a resolution , one megabase to start with , and then improved technologies, gave a resolution of five megabases but is that a better or worse resolution? (3) S3_7_2: [2254.975] i think it's better S9_T1_7_2: [2257.860] when compared by (2) S3_7_2: [2262.442] [?eh] S9_T1_7_2: [2262.442] what kind of resolution are you looking for? S3_7_2: [2265.516] [ehm?] S9_T1_7_2: [2265.924] as as small as you can possibly get , S3_7_2: [2268.268] ah S9_T1_7_2: [2268.513] so one mega –one megabase resolution's actually , pretty good what's the resolution on normal karyotyping S7_7_2: [2273.900] five S9_T1_7_2: [2274.496] abou- about five ish S7_7_2: [2275.166] five S3_7_2: [2278.988] but [?] are from like small kilobases up to five megabases or S9_T1_7_2: [2283.555] but kilo- but kilobases sometimes kilo bases [are a] really really good resolution S3_7_2: [2287.751] yeah S9_T1_7_2: [2288.225] it might be, cos obviously then you're looking at a tiny wee bit, compared to a five megabase where you're looking at a huge big chunk [?] karyotyping as well S1_7_2: [2298.202] yep S4_7_2: [2298.559] instead of SNP do they just do [?] one S9_T1_7_2: [2301.198] one S3_7_2: [2302.106] there [?] SNP. cos it says something about ten kilobases but i thought the five megabases were , em they were better ? i have this em , figure in one of the papers that i've read , and it, (22) yeah, it's on there , (2) it's like , the size of [?] genomic changes , (2) and so S9_T1_7_2: [2349.866] [??] S3_7_2: [2351.211] yeah, so this is the scan that only the nucleotide arrays can look at it starts from, hundred megabases up to one base pair , no up to ten base pairs, whereas for the MLPA it only detects it from like, hundred kilobases up to ten base pairs , and in FISH it's ehm , around five megabases up to hundred kilobases, and for signal sequencing it works , that way rather , but i found that oligo microarrays is the best one, for detecting er for the resolution , it's the most improved one, i don't know if you can see S9_T1_7_2: [2390.512] [??] S1_7_2: [2390.908] oh it's on a larger scale S3_7_2: [2392.574] yeah it's on a larger scale S5_7_2: [2393.440] [?] computer scan (2) S9_T1_7_2: [2396.645] the oligo- what's ol- the resolution of the oligo S3_7_2: [2399.818] [ [S3 looking through papers] it's [?], yeah, (2) down to five , megabases : [2401.662] [?S7 & S3 asides?] S5_7_2: [2405.826] [?? aside?] S9_T1_7_2: [2408.946] right oh right so, (2) so five megabases is its worst resolution then S7_7_2: [2413.319] umm S3_7_2: [2414.683] that's why i'm confused that's what you just said S7_7_2: [2415.886] no no no no , what is the least resolution? [? one end] S3_7_2: [2419.805] ehm , it's about, S6_7_2: [2421.706] [?] S4_7_2: [2422.172] yeah S3_7_2: [2422.298] yeah [?ten] S6_7_2: [2422.902] ten ten megabases S7_7_2: [2424.365] ten base pairs? S3_7_2: [2425.430] ten base pairs S9_T1_7_2: [2426.308] so you can actually get a very good resolution [??] S3_7_2: [2428.076] oh is that what it's mean , oh [?] S7_7_2: [2429.279] yeah [laughs] : [2429.944] [S3laughs][some others laugh] S9_T1_7_2: [2430.318] that's it. ten megabases is great resolution , five megabases [?you could do ] simply by eye, on a karyotype so the smaller you get the better. (6) S5_7_2: [2437.896] can i see? S2_7_2: [2445.820] can i just ask a questions it's not actually to do with this PBL but it was see in this morning's lecture uhm, L was saying that like see, you can like the microarrays you use for detecting duplications deletions, we're saying for DMD they wouldn't, they wouldn't do a test where they cut up the, the DNA sequence why is that? S9_T1_7_2: [2464.270] say again she wasn't ? S2_7_2: [2465.798] she said like for example like, for looking for the DMD mutation for deletions or duplications i would think that you could use microarrays but she was saying you wouldn't use a technique where you would have to cut up the DNA , like for microarrays you'd have to do a restriction, before you actually load the, the DNA onto the array S9_T1_7_2: [2482.234] uhuh why might you not why would you ? S1_7_2: [2484.274] i think she was talking about PCRing it, up, for sequencing in small segments S4_7_2: [2490.177] i think that's later on and i think [?overlap not clear] remember her saying something about that but i don't know what it was about S1_7_2: [2491.592] oh [?] discussion S2_7_2: [2492.163] yes ,(2) cos that, cos it she had like MLPA as one of the answers but i put microarrays and MLPA , you know i just put everything down but then i was she just said you wouldn't cut up, any of the DNA sequence for DMDs, like if you look for a DNA mutation i was just wondering if there's a reason or not S9_T1_7_2: [2495.652] [?] [2508.226] if if you're a new mutations was that or was it like a [?] mutation S2_7_2: [2511.793] ahm i don't know S6_7_2: [2513.070] yeah if you don't know the mutation , [?] the mutation S2_7_2: [2514.048] yeah if you don't know the mutation you just try to S9_T1_7_2: [2514.425] [?] S2_7_2: [2516.622] detect the deletion or S6_7_2: [2518.094] because you won't get any products, from , i mean the five products, as what she was saying, S7_7_2: [2524.426] that is a very different [?deletion] , and then if it is PCR then you will do it S3_7_2: [2525.246] [? that's a deletion] S4_7_2: [2528.362] that was ehm is it that was if it was a dele- eh if there was a deletion there then sequencing it straightway wasn't a good thing to do, like the whole thing was, you'd have to do a MLPA first to make sure there was no deletions or duplications , before you went on to sequencing , i think that's the [??] S5_7_2: [2542.440] umm S4_7_2: [2542.922] [?getting] that there S1_7_2: [2543.898] so i should be missing big sequence but S2_7_2: [2546.046] did you actually use microarrays then to detect the deletion in DMD? would you use it? S9_T1_7_2: [2551.070] it's not used , i don't think, at the moment , i guess if i'm trying to think if you digested it , [snaps fingers?] could you then lose cos there's such a small bit could you then actually lose, you wouldn't have enough resolution to detect it in the microarrays maybe that are being used? but if you do one that's , i don't see why you couldn't use a one where you had a, probe for different exons : [2554.946] [some laughs & smiles] S2_7_2: [2575.405] uhum S9_T1_7_2: [2578.107] but maybe you don't have one that's like that to [? ?] S2_7_2: [2582.530] [s2 laughs slightly] S9_T1_7_2: [2584.110] see how when you cut up the DNA you should have cutters , maybe that would, it would amplify it do a whole genomic amplification cut it up, and then, (2) [?] it on but, (2) and then have the right probes for specific [? exons]. i don't know i don't know why [??] S2_7_2: [2605.659] probably just a [?] S9_T1_7_2: [2606.919] i'll ask her what she meant S2_7_2: [2609.106] i was just wondering [?] S9_T1_7_2: [2609.488] i wasn't there so i don't know what she said but S1_7_2: [2613.862] ok ehm so, before we go on to the outcomes hermizygosity? : [2618.660] [handouts papers ] S6_7_2: [2638.330] thanks S8_7_2: [2642.375] well , uhm hemizygosity is a condition where you just have one allele and so , in a diploid organism you're supposed to be having two alleles you just have one allele , what i inferred er from K's case is that, he probably would be hemizygous if he had a deletion along with the paracentric inversion. er, so , the, part the region of deletion could cause hemizygosity in K. there's –there's an example um , like, the hemizygosity for peptide receptor gene which is em in the two Q thirty seven locus , er affects the signal transduction it's a peptide receptor gene and it em, because of its hemizygosity the signal transduction is , er affected , so probably , uh depending on, er the region, of deletion in K , and what genes are present in there , that could affect his phenotype, so hemizygosity in K is probably the result of the concurrent deletion, along with his paracentric inversion , and em , till now there to date about a hundred patients with terminal deletions with breakpoints at two Q thirty seven have been reported , and most common features of um, having a two Q thirty seven deletion were developmental delay and metal retardation , and abnormal behaviour like autism and, hypotonia and stuff, and as S7 said um the subtelomeric region has a lot of genes which are involved in the, CNS , so probably that's why he has got mental retardation and stuff , hemizygous so, the hemizygosity implies that he could express just one copy , and uhm , well if the one copy which is like not deleted , ah if that is defective or it's a [?recessive] phonotype –i mean a recessive type , then it could be even worse for him, and i think hemizygosity could also, uhm explain why his parents where having a normal phenotype , and he was having a, abormal phenotype (3) S1_7_2: [2781.178] great. (2) anyone got any questions? (2) em shall we move on to , outcomes? we've kind of both done the same thing because we thought we'd just both attack it all , em so we'll probably just , pass between each other so S2_7_2: [2798.266] yeah (3) S1_7_2: [2802.597] if the snow hadn't got in the way it might have been, different, afraid they're not stapled together so , there should be : [2803.143] passes out h/os] S2_7_2: [2817.753] [?? one more] S3_7_2: [2823.284] i [??] S1_7_2: [2824.839] yes [?indeed] i think i've just given away all my copies S2_7_2: [2827.915] that's [?how] i've got one (7) do you want me to go at the start? [to S1] [2838.779] [laughs] S1_7_2: [2841.090] i think there's two copies there because i've given away my one [?] (10) S2_7_2: [2855.412] ok i'll i'll just start off S1_7_2: [2856.497] yeah [2856.901] [laughs] S2_7_2: [2858.020] em , ok so basically we're looking at the different outcomes that , parents would've that've possibly [?] the parents would've had from testing, so the first one was the two Q thirty seven deletion , and i looked this one up in Gardener and Sutherland and they actually have it as a syndrome known as Albright-like Syndrome , which was characterised by short stature round faces short metacarpals, em and these symptoms are very similar to the Albright Hereditary Osteodystrophy , uhm where parents of this condition also have varying degrees of deve-developmental delay, em, there's also another, symptom related to this region um called, Brachydactyly-Mental Retardation, which included severe mental retardation or developmental delay hypotonia , eh brachymetaphalangy of digits, and dysmorphology of the face, so there's like varying , degrees of symptoms like some of them you can see in this case some you can't , em but i've said that since both parents seem to have a normal phenotype the probability of finding this results would be quite low , em as you can see at the bottom i've said , non-penetrance so basically they could have a a disease genotype, and no phenotypic effects , em at all this could result from, basically i've got epigenetic factors, or over expression of affected genes which em alter the gain of function , or loss of function or like silencing, of certain genes, em, and i've sort of as- asked the questions if there was non-penetrance and if it was related to epigenetic factors would, gene –em , would like FISH be able to pick it up or microarrays be able to pick it up , em, i've also said about balanced translocations , that was like another possibility , that i could um- , that the technician or the scientist was looking at , and that would reveal a normal phenotype in the parents and it would give rise to like various segregation patterns, but to perform any sort of analysis or any sort of uhm , pregnancy risk calculation for S's pregnancy we need to find out the other chromosome on which the translocation occurred so we could do like a HAL test on it or an empiric risk calculation , em , i've sort of mentioned, like em, about the best way to look at this would probably be if we were looking for a deletion to use microarrays, uhm because they'd be able to detect deletions duplications , as well as unbalanced translocations but they obviously wouldn't be able to detect any balanced translocations or inversions unless there was a deletion in the break point, em also the procedure for microarrays takes up to seven days so, it would be, an easy procedure to perform so you could do a prenatal test for S, em the thing with mircroarrays is though they don't report anything, significant unless it's over a hundred kilobases , em, that's what i learnt from downstairs cos they use oligonucleotides [?] S9_T1_7_2: [3032.594] why would they not , report everything? S2_7_2: [3035.168] i think to them it's just insignificant or it's like , there's like , a lot of the normal people just have small deletions and , they just don't see it as something they would follow up (2) S1_7_2: [3046.179] ok so i'll probably talk more about K with the with the two Q thirty seven deletion syndrome , ah fifteen to twenty percent of eh people who have it can have a normal karyotype so you won't actually see anything , uhm ahm and most of these deletions are de novo , and the parents will also have a normal karyotype , so it doesn't actually say in the scenario whether the parents have been , karyotyped or not so even if they may have a normal karyotype or they may, show em simil- em similar , em abnormality , em so the risk to em, the unborn well the sib , em if em both the parents have a normal karyotype , em the recurrence risk is low , but i think when it's in the papers i read when it said normal karyoptype , i think it also expected further investigation so you wouldn't just go on a karyotype alone , cos there could be ehm, other things such as a balanced translocation or inversion , and if one of the parents has one of these the risk is, higher of recurrence, even if the don't have the deletion themselves so they're more likely to have another child with a deletion but i couldn't find any figures at all for what the risk might be, it's just higher. em so the the case that we one of the cases that we've been discussing the de Villard one, em the the patient in that the fourteen year old boy has a paracentric inversion of the, chromosome between two Q fourteen and two Q thirty seven point three , and there's a deletion in this case which is also which is at ehm , Q thirty seven, and a dup- a duplication at the other break point, and, in this case the parent had a balanced tran- um , paracentric inversion but is phenotypically normal , and doesn't have the deletion or the duplication, S2_7_2: [3046.751] [laughs] S4_7_2: [3155.069] so she doesn't have a small deletion [?] S1_7_2: [3156.834] i think said she was normal, i thought but maybe i've S4_7_2: [3159.746] i don't know maybe i'm thinking of something else S1_7_2: [3161.813] but it- well in this one and in this case it seemed that she just had the balanced trans- balanced inversion but didn't have any em , any deletion , em so there was in they've did subtelomeric FISH and showed that it was a two Q region in the paper the patient in this study, and they propose that this was due to probably imbalance created by a cross over, uhm of the inversion loop of chromosome two during meiosis, and this figure's actually really nice for showing inversion but unfortunately em in black and white it doesn't look quite as well- as good but em , (2) so they think that there's ehm been a breakage of a, chromosome, dicentric chromosome em product and that's what the , the boy in the de Villard , paper [shows coloured copy] has inherited so , it's a bit clearer when you've got colours, cos you , it's kind of green an-, and blues, em so it could be possible that the parents have one of the parents has a em a paracentric inversion which , we haven't been able to, visualise S2_7_2: [3229.099] uhum (3) S3_7_2: [3232.774] you can see in the scenario that we had it was a para- paracentric S7_7_2: [3237.849] para? S1_7_2: [3238.787] paracentric S7_7_2: [3239.249] [?] chromosome [3242.290] i think [? show us?] S1_7_2: [3242.836] i think [3244.203] yeah i think it's quite difficult S9_T1_7_2: [3245.242] possible S1_7_2: [3246.311] i think we we kind of came to the conclusion that you needed more investigation we needed more information to be able to kind of , (2) at least know what the parents', karyotypes were like and to then go on to , (2) you're probably able to give a more accurate risk , once you've got some more information from further investigations (2) S9_T1_7_2: [3268.601] i'm not sure what's happening in that diagram there just , what or what ends up what would end up which one is it [??] i think if [?] i think so it ends up [?molecular] so what's (5) S1_7_2: [3279.455] yeah [3286.876] cos you've got the, em the inversion in the maternal chromosome , it pairs up differently during meiosis and you get a little loop , cos the inversion so the way it pairs up and then , ehm similar to kind of em, (3) so you get, kind of different, cross over is that right ? S7_7_2: [3308.235] yeah S1_7_2: [3308.508] with the non sister chromatids, [S7 nods] ehm so you're ending up with abnormal chromosome structures so this one, ehm the one that it's the stared one ends up being, eh dicentric chromosome and then you get acentric fra-fragments as well , (3) and so then they're pulled in different directions so you're getting , abnormal, chromosomes , (2) so that's what's generating the deletion, em at the one end and the duplication at the other, in the, this case S7_7_2: [3342.420] and the chromosome in Down Syndrome [??] S3_7_2: [3345.548] yeah [3346.047] because [?] they will be em , apart from each other, and they will be breaking broken S1_7_2: [3346.355] yeah cos it's not viable S7_7_2: [3354.687] yeah S3_7_2: [3365.587] what's this one here? S2_7_2: [3367.938] [?] S1_7_2: [3369.044] the- these are the meiosis products in the mother that are possible S3_7_2: [3372.579] uhuh (4) so this diagram doesn't include the deletion of the other , the paternal , right? S1_7_2: [3382.354] it's maternal in this one, it's only in the maternal , and they've got a normal paternal , so ehm in the there there's an inversion and at one end of the inversion, there is a duplication and at the other end there is a deletion , so it's on ehm it's the two Q thirty seven end there is a deletion and at the other end there em, is a is a small duplication S3_7_2: [3383.338] only maternal [3406.098] uhum (6) [?ok] (4) S9_T1_7_2: [3415.464] what's your strategy now for the boy then? what [?] for the mother really i suppose [?], what what's your next, step ? S1_7_2: [3425.847] i think you'd want to kary- karyotype both the parents, and then see what that reveals and if they were both normal, potentially going on to doing some microarray S2_7_2: [3429.624] karyotype [3437.519] uhuh S1_7_2: [3438.092] you'd also want to confirm in the boy, what because you don't have the results from the non polymorphic, so with that whether it's er em , whether it is a deletion or whether it is , just a , polymorphic area and if it isn't a deletion and it is just polymorphic you don't know what's caused it at all . S9_T1_7_2: [3459.389] so what might you do then? (4) S1_7_2: [3464.644] you could look for em, (2) something else [3469.107] [laughs + group laughter ] : [3469.128] [laughs + group laughter ] S9_T1_7_2: [3470.734] but what [?] S7_7_2: [3471.553] you could [??] S1_7_2: [3473.576] probably a microarray S9_T1_7_2: [3474.779] oh a microarray yeah (2) S1_7_2: [3478.395] but i don't know whether you'd probably have time, S9_T1_7_2: [3480.461] yes that's the S1_7_2: [3481.456] to do a full- S9_T1_7_2: [3482.823] [?] S1_7_2: [3483.762] full, screen S9_T1_7_2: [3484.667] [?] you you were saying what is it the the micoarrays take seven days just now? [to S2] S2_7_2: [3487.251] seven days days to do, like usually if for example if you do like a blood karyotype automatically while you are karyotyping that would go straight to microarrays at eh same time S9_T1_7_2: [3494.030] ahh right ok S2_7_2: [3495.834] so you wouldn't like wait for two weeks to do the karyotyping and then send it away , it'd go at the same time S9_T1_7_2: [3496.832] uhuh [3498.199] that's interesting [3499.330] you do it at the same time S2_7_2: [3500.495] and it would come as an urgent , because she's pregnant S9_T1_7_2: [3502.997] because she's pregnant [s2 nods] S1_7_2: [3503.783] but if if both the parents don't have any kind of , abnormalities the risk of occurrence's a lot lower, there's nothing if it's just a , de novo in the, in K S3_7_2: [3516.462] but the thing that microarray one of the limitation of that it can't detect inversions , advanced translocation S2_7_2: [3523.056] it can only detect it if there's a small deletion at the break, but usually no [?? [very quietly]] (20 [?] S7_7_2: [3530.556] but if K's case isn't de novo then is it necessary for prenatal diagnosis S9_T1_7_2: [3537.181] ah good point S4_7_2: [3540.014] i suppose you don't know if it's de novo until you've , investigated it maybe? S3_7_2: [3542.410] just to confirm S9_T1_7_2: [3545.820] i suppose what even if it they do it , you know like kind of blood i suppose what's the normal there's a small chance of, S1_7_2: [3550.918] gonadal mosaicism S9_T1_7_2: [3552.811] what [?], you might get [??] i suppose (5) S1_7_2: [3562.658] but if they have the same kind of size of inversion that's been obviously visualised in abnormal karyotype in K's so you'd expect one of the parents , might also have a inversion that you could visualise on the karyotype as well , even if the deletion's too small to be S3_7_2: [3577.787] uhm S1_7_2: [3579.307] to see S2_7_2: [3584.296] how old is K? [?] S7_7_2: [3585.788] four years old S4_7_2: [3587.110] four S7_7_2: [3587.413] uhum S6_7_2: [3588.168] ok (4) S1_7_2: [3592.507] so have we got anything else that we need? (5) S9_T1_7_2: [3600.535] you guys are happy, with that ? S3_7_2: [3602.092] [?] S9_T1_7_2: [3603.567] it's definitely the most complex of the, scenarios so that was good that wasn't a bad attempt at all , and we're not doing any individual feedback , to each other on it it's a Moodle form : [3614.075] [yeah & nods] S7_7_2: [3614.458] yeah S9_T1_7_2: [3614.941] apparently i don't -did you got a Moodle post yesterday about it? S1_7_2: [3616.585] yeah S4_7_2: [3617.562] what's that about but what is it? S9_T1_7_2: [3619.356] it's just a peer assessment on each member of the group on first term PBL, rather than sit and , you know each telling each other because i think we tried that one year and we found it nobody said anything other than yes your work was fine thank you [group laugh] , but [?] : [3634.094] [group laugh] S9_T1_7_2: [3637.013] but if you do it on a Moodle form, it tends to be more constructive so people do say, i think your diagrams help but your references weren't. you know what i mean that kind of thing whereas you wouldn't say that to somebody's face probably S1_7_2: [3647.388] yeah [3649.473] yeah, i think if you've got time to go through what you've got from other people as well , are we doing more cytogenetics after Christmas or is this, in PBL S9_T1_7_2: [3652.863] yeah [3654.005] [?that's fine] [3656.428] yeah [3658.518] yes there's another one, i think there's a PBLs [?is cytogenetics], oh but i'm not one hundred percent sure, it will either be that or but you won't have started biochemical , after Christmas but you [?] S1_7_2: [3668.279] but we don't have PBL till February now don't we S9_T1_7_2: [3670.511] or [?] maybe it will S1_7_2: [3671.604] because there's a couple of weeks before we get back into PBL S9_T1_7_2: [3672.588] right ok right [3674.884] i don't know it'll probably say have you got the next term's timetable, it'll probably say what the first PBL is called [?] S4_7_2: [3680.898] [?] S6_7_2: [3680.898] [?] : [3681.005] [some overlasp inaudible] S7_7_2: [3681.140] [?] S1_7_2: [3682.374] cos some of them are just numbered i don't know if i'm looking at the older version as well they're just numbered S3_7_2: [3683.248] [?] [3684.838] we havne't had [?] S9_T1_7_2: [3686.669] ah i'd better [?] S2_7_2: [3688.281] you started [?today] S3_7_2: [3690.468] you know how to [?] in the [?] S4_7_2: [3692.874] week two seventeenth of January S9_T1_7_2: [3695.145] oh right S1_7_2: [3695.999] is that another one? uh? S4_7_2: [3697.224] PBL 8 query AML [looking at timetable ] S9_T1_7_2: [3699.465] yeah it's a cyto one S1_7_2: [3700.559] ah S2_7_2: [3701.367] oh no S9_T1_7_2: [3701.871] and then is there another one after that ? S4_7_2: [3703.758] er pre-natal screening S2_7_2: [3705.526] that's biochemical S4_7_2: [3705.752] bochemical S9_T1_7_2: [3706.146] that's biochemical stuff, so you've one more cyto PBL. and then , and that's cancer [?cyto obviously] , [?both biochemical]. great. you guys thank you for , like [?] you know : [3724.785] [group laughs ] S9_T1_7_2: [3726.386] finish the sweets and i'll put them in the lecture theatre if anybody wants them S1_7_2: [3729.535] ah S4_7_2: [3730.101] [?] S6_7_2: [3733.671] [?] : [3735.038] [?] [3736.566] [background overlap chat inaudible] S1_7_2: [3748.107] i'll just take them all for myself what sweets? there was no sweets in the PBL actually and my locker's just there : [3750.324] [group laughs] : [6.417] [[?] S18_T2_9_2: [8.823] ok S14_9_2: [10.736] [?] S16_9_2: [13.797] [?] S18_T2_9_2: [16.284] pass it up S10: [18.184] [?] S18_T2_9_2: [22.227] [?] S16_9_2: [24.293] [?] : [26.488] [ students handing out papers and settling in- background noise -parts inaudible] S18_T2_9_2: [27.857] yesterday she [?] S14_9_2: [33.787] S8 come on [indicating place to sit] S10: [39.348] [?] S13_9_2: [41.681] no it doesn't matter, just pull in a chair [to S10] S14_9_2: [49.253] yeah it's ok [50.319] S10: [76.986] do you want anything? S14_9_2: [97.907] [?] [looking at S13's brochures] S10: [104.521] is that your pile there? [referring to collection of handouts] S13_9_2: [105.654] yeah S14_9_2: [119.395] this paper? S13_9_2: [123.226] [giggle] S17_9_2: [123.724] all right S18_T2_9_2: [126.129] are you all, have you all got [?] a copy? S14_9_2: [127.022] yeah S13_9_2: [127.865] yeah S16_9_2: [128.797] yeah S14_9_2: [129.845] for you [handing copies to observer] S13_9_2: [132.919] oh thank you S14_9_2: [136.999] yes thank you S18_T2_9_2: [139.459] [?this is the way] all the paper : [141.538] [group laughter] S17_9_2: [142.302] [?] S12_9_2: [144.379] so, [?] S17_9_2: [147.117] [?there's one here i think [149.662] S17 S13_9_2: [149.990] [?] S10: [153.001] did i give you one? S13_9_2: [153.379] have i given you one? S17_9_2: [154.181] yeah S10: [154.997] S17? S17_9_2: [155.568] [?] S10: [158.471] i have a [?] paper S17_9_2: [164.176] is this you? : [165.089] [? no] S12_9_2: [166.398] [?] S16_9_2: [168.839] oh look at this [referring to brochures by S13] S13_9_2: [170.374] [laughs] S16_9_2: [170.935] that's S12_9_2: [170.970] there are two S13_9_2: [171.691] yeah S8_9_2: [175.223] have i got do you separate [?] S14_9_2: [175.691] do you have a separate [?] S13_9_2: [176.839] i forgot to print so she can have these S17_9_2: [178.932] skip the [?] S14_9_2: [186.683] i don't [?] a pile of [?] have you got [passing back to S18_t2], S17's : [187.106] [? who ?] S18_T2_9_2: [190.195] no i've only got, i've got one two three four five and you makes it six, ahm, so who's missing? S14_9_2: [190.344] no? S8_9_2: [197.536] er, mine, S18_T2_9_2: [198.113] S17_9_2: [200.594] i have only eight here copies S16_9_2: [202.144] oh wait S17_9_2: [202.918] so, when i finish i will give my copy for, [206.036] C? then i will bring yours next week. S18_T2_9_2: [206.036] yeah that's fine [207.124] right ok will you give it well, ahm S10: [211.866] do you want to give [?] [to S13] S17_9_2: [211.896] do you want S13_9_2: [212.279] have you got [?]there S17_9_2: [214.708] that's fine S18_T2_9_2: [215.389] ok so you share you share with, you share with S15 [?] while S17's, talking about it, then i'll give you this back S14_9_2: [217.063] yeah S16_9_2: [222.092] i have one [?] S18_T2_9_2: [223.221] so who hasn't who doesn't have a copy from S13_9_2: [224.771] just pass you those S16_9_2: [225.974] me S18_T2_9_2: [227.024] you don't have a copy S17_9_2: [228.324] i don't have copy for you and for C S18_T2_9_2: [230.268] uhuh, oh so if i S8_9_2: [232.556] you can mail me a copy S16_9_2: [234.225] you are [?] S13_9_2: [239.607] i've got two of [?] S18_T2_9_2: [240.676] i've got two of yours S16_9_2: [242.353] you have two of mine? S13_9_2: [243.460] yeah [laughs] S18_T2_9_2: [243.652] two of yours uhuh. who hasn't got one from S17? who hasn't got S17's? S8_9_2: [244.921] i don't think i got [?that ] S16_9_2: [247.070] who hasn't got this? S12_9_2: [248.884] maybe me S14_9_2: [248.884] maybe me S18_T2_9_2: [250.968] whose that's a S16 copy. that's a copy for [?] S10: [253.793] ok S18_T2_9_2: [256.120] ahm S13_9_2: [256.133] umm S14_9_2: [256.133] [?] me. i don't have one from you S18_T2_9_2: [259.486] uhm i've got S16_9_2: [259.538] [?] this is extra copy S10: [261.528] i S16_9_2: [263.255] [? did i give you this?] S10: [263.980] yeah S13_9_2: [264.676] is that it? S18_T2_9_2: [265.346] i don't have anything from S12 yet S12_9_2: [267.125] yeah yeah. just. does everyone else have 2 copies of mine? S16_9_2: [270.868] i've given this [272.116] yeah S10: [272.394] i think so S12_9_2: [274.013] ah ok [S13 appears to have copies] S13_9_2: [274.350] [giggles] S12_9_2: [275.596] anyone else? S16_9_2: [276.416] i printed ten so there should be enough S14_9_2: [280.311] i don't have one S10: [283.137] [?oh sorry ??] is it? S13_9_2: [285.571] [laughs] S16_9_2: [286.458] yeah really S13_9_2: [287.869] just take them all[gestures about handing out copies] S16_9_2: [288.470] [? overlap inaudible] S10: [289.509] first of all [?] S12_9_2: [290.514] one two three four five six seven eight nine ten. can you check again please? cos i count ten copies S13_9_2: [290.665] S10: [291.675] [? aside about handouts] [298.782] i gave to [gesturing to tutor], S18_T1 S12_9_2: [301.010] ok that's S18_T2_9_2: [301.721] but i've got S12 S16 S15 S10 S12 S14, and [? a few ?] S12_9_2: [303.252] that's [305.001] two more S15_9_2: [307.294] yeah i have one of yours sorry S18_T2_9_2: [309.757] what [?] S13_9_2: [311.561] no i -i didn't do double sided so S18_T2_9_2: [314.106] [?] S14_9_2: [319.734] who will start [321.102] in order to organise it from the beginning S16_9_2: [323.192] shall i start? S10: [324.354] i suppose you go first, ok. that's, then maybe the two of us together? [to S15] the two of us can go together [?] S15_9_2: [334.423] [nods to S10] S14_9_2: [335.261] who's the chair? S12_9_2: [336.066] ok yeah S15_9_2: [337.387] i think [?] S12_9_2: [337.530] ok maybe you start, S16 you cover the classification and causes ? S16_9_2: [343.281] classification symptoms and causes S12_9_2: [345.816] ok we start with S16 then [348.596] maybe you S10 S10: [349.743] right S12_9_2: [350.635] incidence of spine [353.247] and S13_9_2: [353.961] [?] S10: [354.726] me and S15 are kind of similar but [357.113] isn't it? S15_9_2: [357.634] yeah S10: [357.962] he's not about to go before me? S12_9_2: [359.766] he will be second S15 you will be third S10: [361.844] ok S15_9_2: [361.980] ok S12_9_2: [363.433] then screening test S10: [365.957] it's S14 S12_9_2: [367.064] it's no it's me S14_9_2: [367.064] umm S12_9_2: [369.952] then [370.868] diagnostics test [gesture to S8] S8 S8_9_2: [371.578] diagnostics S12_9_2: [374.869] then the accuracy of the text S14 S10: [380.281] would you go first? S13_9_2: [381.963] no i'll go last [383.674] don't think i've much to say S16_9_2: [385.628] what can you say about [387.996] [?] S13_9_2: [389.520] i've put -i've misplaced something S14_9_2: [390.784] [?] S10: [393.080] well S14_9_2: [393.936] so S12_9_2: [394.466] S13 will be before the counselling is that right S8_9_2: [396.626] i suppose S13_9_2: [396.626] umm S16_9_2: [397.036] i got causes [397.885] of of S12_9_2: [398.995] oh! thanks [401.006] you have here [hands to observer] S14_9_2: [402.058] so S16 first and then S10: [404.094] and when's S17 S14_9_2: [404.662] these are the incidence S16_9_2: [406.144] [?] when is S17? S13_9_2: [407.905] we've got S12_9_2: [408.725] S17 it will be the last one S13_9_2: [409.818] the first one yeah? [to S14 checking order; concurrent] S14_9_2: [410.839] yeah S16_9_2: [410.910] no but S13_9_2: [411.349] first then S10 S14_9_2: [412.984] yes S10` S13_9_2: [414.028] S15 S16_9_2: [414.469] i think these are the last one S14_9_2: [415.530] S15 S16_9_2: [415.890] i think leaflets should be the last S12_9_2: [417.642] then ok counselling and leaflets S14_9_2: [419.389] yes this one [still to S13 checking order] S12_9_2: [421.126] so start S16 S14_9_2: [421.875] [?] [423.355] what about this? S16_9_2: [424.150] shall we S10: [425.677] is everyone [?] caught up here [432.318] are you going through the order again? [looking round; aware not all ready to start] S12_9_2: [433.894] no start S16 can start S14_9_2: [435.708] S10 S12_9_2: [436.620] S16 will start S10: [437.448] yeah [?] so S16 then me S13_9_2: [437.817] yeah S12_9_2: [440.091] then S15 S16_9_2: [440.876] S15 S10: [441.957] then S15 S12_9_2: [442.771] then me S8_9_2: [443.188] then you [443.730] and after S12_9_2: [444.226] then S8 S8_9_2: [444.523] then me [445.086] then S10: [445.323] S8 S12_9_2: [445.732] then S14 S8_9_2: [446.085] S14 S12_9_2: [447.386] S17 [448.381] then S13 S10: [449.306] yeah perfect S16_9_2: [453.059] shall we start? S12_9_2: [453.877] yeah go ahead S16_9_2: [456.006] right em [457.980] so today topic is going to be about Spin- Spina Bifida S14_9_2: [462.954] Spina [correcting pronunciation] S16_9_2: [463.317] Bifida [464.258] and um [466.627] it's a, it's a disease, it's not a disease but it is a defect from birth, which is caused by the er, because of the spinal cords fail to close, during early development of the embryo, and em, so, ah like, like er in, in chickens or like birds they they actually it's like they develop like a normal system where they, just like er work there ways and down but in, in er human in human and mammals they actually have different initials, starting places, so sometimes you can just have like either higher above or down below, and the way it's em, it closes, it's like it's like this [gestures with h/o] [?it's like] it started from like uh, flaps, and then it just rise up and like you get a gap and then they join together and form like the, so the the correspond to central nervous system and the bone, system, and em, but what happens is that sometimes they they are not closed, and em, you can have like membrane which is, membrane which has been pushed out, and em then sometime you get like nervous system, coming out as well, so there's three types of em, eh Bif eh Spina Bifida, so the first one is called, Spin Bifida oc -occulta ? Occulta S14_9_2: [554.886] Occulta S16_9_2: [555.558] yeah. so it's it's the most common out the three, and em, there is er it is it is caused by like a small gap between the two, vertebrae. vertebrae ? er but, because they they are so small and they do not have any symptom at all like you don't get any symptom at all so they're are not that, dangerous ehm they also are like, (2) [?foul like?] like i said they're quite common. er second one is called uhm, Spina Bifida Men- i i can't yeah Melancae? er it's a this one is ehm, it's the the gaps a lot bigger, and the membranes are pushed, outside, but em, but the nervous is still in side, and they do not ca- like, but you can actually remove it surgically, and normally they don't have any, long term effects or anything. and the the most dangerous and-, (2) and like well known is er Myelo Meningocele S10: [588.493] Mengocele S14_9_2: [622.580] Myelomeningocele S16_9_2: [624.372] yeah that. S13_9_2: [626.133] [laugh] S18_T2_9_2: [627.192] quite right. S16_9_2: [627.997] i can't say all of these terms S18_T2_9_2: [628.921] you don't have to most of us can't S13_9_2: [630.507] i can't say most of them S16_9_2: [630.780] yeah. uhm. well, it is the most dangerous and uhm. (2) and well it it, what happens is that the um the nerve the nerve cells are also being pushed out and they -they form a sac, er, at the back of the baby, and this this sac could be removed but sometimes they do give like eh, symptoms before it is being cut. a-and what happens is that because the sac is out like because nervous system is outside, it's it's more like it's prone for like infections, so, even in fact that there's like other, side effects that could affect the baby, so, they tend to get it cut. but er, but we ca- we can control the nervous systems so like as soon as you, kind of [?] then you may get like problems. er below is just a figure of like what's it look like, between the other two. so, symptom one is uhm, there's 3 symptoms that they've found m- mostly first one is mobility, so what happens is that, er, the higher the er, the sac on the er spinal, er then, the more danger it is because, imagine if you have like er, a wire and a [? nerve set on] right high above then it affect like more, system. and so like the lower it is the less, like dangerous it is. and it can cause problems like uhm, (2) like like no muscles control or, loss of muscle controls. and sometimes er, the muscle are not used so you also get different symptoms such as erm, dislocated joints or, misshaped bones and abnormal spine curve. and speaking about muscles controls, er some of them are not, are are non functional, and so you have problems with your bowel and, intestine, and, and like down below so. er it's called, sphincter muscle which help you to, well it contracts and relax to, to store your urine and stools, but sometimes it not well controlled so, when a baby has a, em it like he has or she has a, longer precipitation? not precipitation er [?anticipation ] time and sometime when it's, done they actually can get diarrhoea which is because they can't really control. uhm, (2) and the third one is called, it's uhm it's caused by the fluid build up in the brain, which is caused cerebral, no.i [?]. ah is it cerebral spinal fluid, er, what happens is that the fluid is build up inside the brain and it actually can, it can press or push the brain, which can damage the neurons and therefore affect, the learning abilities, so kids with, eh, Spina Bifida tend to have like diffic- like learning difficulties S18_T2_9_2: [835.245] tell that to M in medical medical genetics. she wouldn't like that S16_9_2: [841.689] (2) no but, well the seventy percent of them have that so, er the other thirty are not. [laughter] : [848.640] [laughter] S16_9_2: [849.999] er, so i i did some other research on the um, causes. but i won't go into detail cos i know most of the, it's also been covered. but like uhm, they believe that it is caused by er environmental factors and genetic factors, and uhm, they they found out that there are some drugs er which can actually, increase the er, the risk er, by certain degree and, er, like the previous lecture we just had, for Scotland the population is like two, two babies per one thousand, er pregnancies and like within a family if there's a, if there's a known cases about, the disease then the risk increase about ten percent, and em, and like pregnant women who are, who are or who have diabetes or obesity have a, a higher chance of like seventeen percent of carrying a baby with ah Spina Bifida. Bifida. er it's about it. [?] any questions? S8_9_2: [917.274] yeah i have one. so the first, the first, one is is not harmful right? S16_9_2: [924.107] yeah S8_9_2: [925.109] and which one is the open Spina Bifida? second or the third? S16_9_2: [929.104] third one [?there] S8_9_2: [929.663] the third one? ok. (40 S14_9_2: [935.460] i think the second and third one are open. the second one are open but the nerve, this is not outside. S12_9_2: [941.520] so S14_9_2: [941.601] third one, open and the nerve is outside.so there are two points. S13_9_2: [946.302] so you can repair the second one with surgery cos there's no nerves S14_9_2: [949.593] yeah. S16_9_2: [950.391] you could repair both with surgery but, it's more dangerous to repair the third one, because of because the nerves are outside. S8_9_2: [950.637] so you can repair both S14_9_2: [954.214] third one S13_9_2: [955.307] cos the nerves S14_9_2: [956.972] yeah S12_9_2: [958.915] but the spinal fluid will be from both. in case of both right? S16_9_2: [963.228] spi- spinal fluid? S12_9_2: [965.182] yeah S16_9_2: [965.684] what do you mean spinal fluid? S8_9_2: [966.723] the cerebrospinal. (2) this fluid S12_9_2: [970.003] fluid in the spine S8_9_2: [970.692] spinal, chord S12_9_2: [971.815] it will be leaking from the affected areas S16_9_2: [973.940] ok S12_9_2: [974.765] to the amniotic fluid right? [looks round room] S10: [976.487] yeah S13_9_2: [976.487] yeah?[nods from others] S8_9_2: [976.508] yeah S14_9_2: [977.834] what's your point? S12_9_2: [979.415] there will be S10: [979.699] there that would be eh [?] all those markers come out of the hole. through the cerebrospinal fluid [?leaking] S16_9_2: [984.415] but but S12_9_2: [985.385] but i think that, that's what i think S16_9_2: [985.420] but [987.008] no but, that's why there's more than one vertebrae so, normally you would only find it within the, the two closed vertebrae. some like some of them are found in the, like, it's not all them that are open it's only one or two, so some are still contained within the the spinal chord S12_9_2: [1005.166] the spinal [?] (6) S10: [1011.950] can i start? no more questions? ok. so i did em, Spina Bifida and went into kind of more, connected genetic factors and any incidents of the genes. em as a a kind of [?expected] then they're related. so the two major sub groups of neural tube defects are Spina Bifida and anencephaly, the difference being Spina Bifida is, where there's em, a failure to properly close the bottom of the spinal column or er along the legnth of the spinal column, whereas anencephaly is where it's at the very top, so that if you're born with anencephaly your missing a portion of your brain, at the back, ahm of your head. [gesturing here] so, and as well anencephaly they tend to, die either the first day, or within a couple of days of the birth and they're born blind deaf and they, they're not conscious at all. and so it's severe whereas spina bifida most, most of them survive. em, the etiology then of neural tube defects, or defects they are all complex and we know that they are, at least we think there's a combination of, genetic and environmental factors. erm, one of the things we know about, with respect to the environment is that, folic supplementation, before conception is one of the best, ahm, ways of tackling it or or at least reducing the risk significantly, it reduces it's thought to reduce, the risk of the effect to pregnancy by about seventy percent. and although we don't know, exactly the entire mechanism behind the relationship, em, nevertheless it has prompted a lot of research into the genes, that encode enzymes which are which em, like the enzymes that will either bind, transport or metabolise folate. and we're trying to see then, if we can find genes, that are, if we can find maybe variations in the genes in the populations, ehm that may give rise to let's say a less capable [?probe/approach] a less capable enzyme, then then we may find a more, kind of significant relationship. so first of all how do we know that there's, there's a genetic component in the first place? em, there's a couple of factors firstly that we know that neural tube defects, are associated with a lot of syndromes, so trisomy eighteen trisomy, thirteen and any chromo- chromosomal rearrangements as well, em, give rise to NTDs. so we know they must be lying in there somewhere, in some of the genetic material. em, we know as well that, people tend to have family histories of NTDs. or not all of them, i think most cases are sporadic but, a significant amount as well family history. the occurrence risk is interesting as well because, although the occurrence risk, the occurrence risk is estimated to be two to five per cent which seems kind of small if you think about it, two to five per cent is two to five in a hundred, which is twenty to fifty in a thousand. and and if the normal incidence is only about, one in a thousand, then it's a significant increase. and the variation in twenty would be well we just did it there in class, em, kind of, like, some populations as i say in the next part, will have like em, five per thousand. so it's, a five times increase and then we did there in class that, if you already have an affected child, then it's ten fold. and then if you're affected yourself, and have an affected child then it's, twice the tenfold. S12_9_2: [1012.831] yeah [1188.868] twice S13_9_2: [1188.868] twice S15_9_2: [1189.524] tenfold S10: [1190.235] so if you combine, if if you are for example a woman that has, one of the parents had Spina Bifida, you already have an affected child and you live, or you're from an ethic group, that can [1190.335] be up to fifty times, the population risk which is huge. em, and then as well as i said certain ethnic groups'd have a much greater prevalence. so em, they vary geographically then across the world, the highest incidences of Spina Bifida are in Ireland Wales and the north of England. or as said it would be about approximately five per thousand births which is live births, which is about one in two hundred. the incidence then is lower in other Caucasian populations like Australia north America, and lower again in African and Asian populations, however you still have some sub populations in all of them, across the entire, you know globe that would have maybe a little pocket of, high incidence. em, so i just had a table here then of, in in the US. and the kind of significance they did a large [?done a] study on eight hundred and sixty five individuals who had Spina Bifida, and took into account then, their, em, their kind of ethnic background, and you can see it's forty five point nine it's almost half of them, are Hispanic Mexican, em by descent, and thirty six point two are European Caucasian so just between those two sub populations itself, within the US, it accounts for almost four out of every five, em Spina Bifida cases so you can see there's, something there while, the African American or Asia Pacific, it's a even Asia Pacific there very very low prevalence. em, so then the next page, i scanned the entire internet to try and find a as i was saying, easy, ehm, i have a of a, a simple diagram for the folic pathway itself. this is actually the easiest one that i could found though, sorry it looks a bit complicated. but basically [smiles] just, just notice there's basically eleven main genes, and they encode enzymes and all the enzymes are there in circles, and then they are all converting, em a substrate to a product, which are shown in squares. so then, the research is trying to locate all of these eleven enzymes and see, if there's variation somewhere in the cycle, and if if you know if you take out that component then there's a build up of, a some type of substrate and there might be a kind of em, eh- a kind of like a reduced amount of a product that you really need. and the folate [?enzyme] pathway is really important because em, it's involved in amino acid and protein and DNA synthesis. you have for example, if you look at the top right hand circle you have HCY and, MET they're two amino acids homocysteine and methionine. em, so they're obviously involved in amino acid protein synthesis. and then the bottom side of it is involved in making thymidine, which is one of the DNA bases [?AT] CG so it's extremely important, so it's it's an important pathway. so then i just had a, i will explain, two of the em let's say mainly studied, enzymes of those or of the ones that they've found to be, most significant. so MTFHR, which is at the top, ehm cycle it stands for methyl -Methyltetrahydrofolate Reductase, so this is the the gene encoded in this enzyme is currently the best dyed, and the most widely acepted genetic risk factor. and it catalyses a reaction from, five ten Methylenetetrahydrofolate to five Methylenetetrahydrofolate, excuse me, and this is a major circulating form of folate in the blood. em, and basically as i was saying then with, of the diagram up above it's involved in converting Homocysteine to Methionine, and this is you can then of course use this to your advantage as well when you're testing for em, for Spina Bifida and stuff you can look at, levels of Homocysteine in the maternal blood, because if the enzyme isn't there you should have a higher a higher than normal level of Homocysteineem. em, and the most common variant then, with the-[? IS] or with the kind of standard nomenclature is called the A two two, two V. ehm which is adenine [?thymine] amino acid at position two two two, but the most- it's more commonly referred to by it's older name which is basically a C to T, em substitution in position six seven. and the problem with this particular polymorphism is, that it gives rise to, an enzyme which is fifty percent less activity, so it's much less capable of, metabolising folate, ehm in the first place. so then i kind of give the statistics on that particular enzyme [??] particular polymorphism. and, a study in Ireland em, on general [?genes of ] Spina Bifida patients found that this particular polymorphism was not on either of one or both alleles, and, in those pregnancies, in seventy percent of those pregnancies em, they put down that you know a folic reduced folic level might have been a contributing factor to the pregnancy. so if you can add those or put these two sixty sixes together, then you could see that up to half of the folic related, neural tube defect-defects may be explained by this single gene variation, and, the highest incidence of this particular polymorphism, in the world is in Hispanic ancestry, you've intermediate frequency in Caucasians and the lowest incidences amongst African populations, so this correlates then with table one, correlates with- the polymoprphism correlates with the, [?] incidence of the NTDs across those groups. em, and it's also, like as i was saying there's also pockets of em, around the globe which have, maybe higher incidence than the rest of the countries though, certain areas of Mexico and northern China, em, also have, this polymorphism particularly high, and they also have NTD rates so a kind of strengthening the hypothesis. [1506.278] however they know that it's not the only factor because other regions like southern Italy, have a high incidence of the polymorphism, but they have low NTDs. so we know [?exactly only genes] they must be –you know interacting with a couple of other, genes or, em, so another, another point is that DHFR, which is Dihydrofolate Reductase, and, em, what that converts, er DHF to THF, and as i was saying then in the diagram this is involved in DNA, it's involved in, it's like -it creates a precursor of of the DNA base Thymidine. and, if you think about it neural tube closure like you need, to get that as i was saying to to get the closure to get the growth on the column you need -you need an awful lot of cellular proliferation, so you need an awful lot of DNA synthesis as well. so if you're going to have, mutations in the gene, that is important in producing Thymadine, as as really, as a vital base, then it might need to stop it, a stopping of the DNA synthesis, and reduce the cellular proliferation sequences that have a connection between them. so it's it's another candidate gene so we don't really know, for sure really, or if the genes or anything is involve or the genetic form we know that there is a component, but we're still a, a year's research left to find, everything that's kind of involved. em, yep alright. [all turning of pages] (3) any questions ? S14_9_2: [1591.211] i have a question. (2) if those people who has gene variation, cannot metabolise, the folate if those people who had gene variation, mutation which makes them unable to metabolise folic acid, for family and homocystine, what the significance of, giving them folic acid? they already cannot, metabolise the folic acid because of their mutation S10: [1605.234] uhuh [1607.431] yeah [1614.374] well S14_9_2: [1615.358] yeah S10: [1615.890] well the thing is S16_9_2: [1616.287] well S10: [1616.713] this one like if you have the DHFR er as i was saying that [1620.621] or sorry who has the MTHFR, em, mutation right ? [looks at S14]you could still, produce the protein but it- it's fifty percent less activity, of that particular enzyme so, they- they're, half as capable of kind of metabolising it, so you could say if you could give them more, they'd still produce half but if you maybe double it, then it'd be half. and then it'd be the same amount as a normal individual's so, it would be beneficial but you know you'd have to think about, them being half as effec- efficient as as another person. S14_9_2: [1650.920] mhum S10: [1652.045] as opposed to it being completely, let's say pointless to, em administer. ok? S14_9_2: [1657.923] ok thank you. (4) S16_9_2: [1663.078] how, how relevant is, folic acid in, S10: [1669.387] the body? S16_9_2: [1669.908] like yeah. the, the i read somewhere it was the NHS, web site itself they, they wouldn't advise pregnant women, to actually have a, folic acid er diet. [1681.766] but there's cases where, even though they they follow the diet but they could still produce, offsprings, with Spina Bifida S13_9_2: [1690.365] well then it might be more like the genetic factors S15_9_2: [1692.224] there are other, other factors also as well which affect the, S10: [1696.072] [?which ??] S15_9_2: [1697.018] except, folic acid. there are a lot of other factors as well S16_9_2: [1699.834] well, they also did research on well it's included here on the diagram S15_9_2: [1702.976] here on the diagram S16_9_2: [1704.053] B twelve. there's there's a lot of there's they're thinking B twelve because he also has something [?]. about [?]. (3) S14_9_2: [1715.549] [?] they what? S16_9_2: [1717.240] B twelve deficiency, will also cause eh, sp- S15_9_2: [1721.010] yeah S8_9_2: [1722.542] Spina Bifida? S14_9_2: [1722.542] Spina Bifida S16_9_2: [1722.873] Spina Bifida yeah S10: [1724.614] i didn't go into that one but it's up there in the, top left hand circle. em, where it says MTR MTRR that's B twelve? i don't know if it's is folic B two? [?] thirty six 6? [?does anyone [?] ] S14_9_2: [1734.333] no er S15_9_2: [1736.047] B six i guess, i think. i think but i don't [?] (2) S10: [1736.618] is it [?] [1743.050] i don't, so, if it's just more kind of the genetic cause, well S15's doing er other causes S15_9_2: [1747.222] [?] S14_9_2: [1749.318] i don't think the [? pregnant] might also have, a role in Spina Bifida S16_9_2: [1754.321] yeah there was an article on S15_9_2: [1755.223] yeah. i i had that in my, report : [1758.875] [laughter] S15_9_2: [1759.796] [?] you can go to [??]. (2) i don't know [??] S16_9_2: [1766.923] i came across the same article S14_9_2: [1767.284] i S15_9_2: [1769.347] also [??] S14_9_2: [1772.032] ok S12_9_2: [1772.989] ok S15_9_2: [1774.360] causes of Spina Bifida. first of all there are two causes the genetic and the environmental causes. in the genetic causes it includes the family history. so as S10 said like if er, in in today's lecture [? name] mentioned that if a parent has a child with a previous child with NTD, or, the parent is affected then the child has a high risk of carrying the gene, the future pregnancy. and ah the other risk factor is whether the Down Syndrome and, Spina Bifida related to each other. this was a very interesting article where, NTDs caused er because of er deficiency in folate as S10 mentioned. so, er there are, mutations in the folate genes and also, there's ah no [? proper] metabolism of folate. so, this factors featured are also interestingly seen in the [?NT] mothers. so because of the similar features like you know folate metabolism and this thing seen in both NTD and, Down Syndrome, these things these two diseases can be linked to each other, but because of the lack of studies this link is not fully established. so there are still research going on, in linking these two, studies so you can say that, if a mother had a NTD child, there are high chances that the future pregnancy will have er Down Syndrome a child with Down Syndrome. yeah? so it's the [?] and then folic acid. this er this thing inadequate dietary intake of folic acid can, folic acid can cause, Spina Bifida, because folic acid is important to cycles as mentioned by S10 by as nucleic acid synthesis and methylation reactions, and this, if no er, proper amount of folic acid is [?] is, what it says is taken in the body then these cycles are affected, and again [? without ?] they can also be causing, neural tube defects. another cause is maternal diabetes. it is er the reason for why maternal diabetes is still not established but there is one the, you cannot it's not is [? perfectly ?] whether, the increase in glucose levels, are direct teratogenic factors. the teratogenic factors are agents which affect the embryo then the foetus so it it's not still established whether, the increased glucose levels are direct teratogenic defects, but, or this increased amount of glucose levels act as factors for, for other factors which cause this teratogenic defect, it is still not sure what is the cause, is it like increased glucose levels or is it, but there was a study which was carried out on mice where they found that glucose, the increased amount of glucose has direct effect on NTD. and then drugs, er as S16 mentioned, S8_9_2: [1966.391] S16 S15_9_2: [1967.713] mentioned that er, (2 ) there are drugs which also caused, NTD er the drugs, in- involved are anticonvulsants. anticonvulsants are used for treatment of epilepsies and migraine chronic pain, ok and er, the, anticonvulsants er like valproic acid and arbamazepine alone, only alone can cause NTD. or these drugs in combination with other drugs can cause NTD. the reason for this is, there are two hypothesis based on this, one is that, free radicals formed due to the metabolism of these drugs, can affect, the embryonic tissue. the another hypothesis is that, these drugs affect folic metabolism. so as a – it's all related to folate again. that's [?]then there are other risk factors which also cause, er, NTD which are, obesity, gastric bypass surgery, hypothermia hypothermia in pregnant people, and maternal diarrhoea, during pregnancy. and one interesting thing was that, men who were exposed to herbicide agent orange.this was eh this was a thing which was, during the Vietnam war the US or something they put this in Vietname they, it was a chemical which was, er S16_9_2: [2053.033] used to burn down trees S15_9_2: [2055.113] yeah S16_9_2: [2055.584] but [?i don't know] : [2055.584] [S13 & S10 looking at S16 ; smile; S16 from that country] S10: [2056.160] yes sure S15_9_2: [2057.938] so during the Vietnam war so men who were exposed to this, they, they have a child they have chances of child having NTD. and women also who are exposed to electromagnetic fields, hazardous waste sites and pesticides are also at risk of developing NTD.that's it any questions? S13_9_2: [2077.972] ok just one questions. what do you mean by tera- tera S14_9_2: [2078.883] [?] S15_9_2: [2081.679] yeah, teratogenic are [?substantive] agents which, affect the embryo or foetus S13_9_2: [2087.860] right. (5) S12_9_2: [2092.729] there is also the maternal age i think, it's quite important factor S15_9_2: [2096.549] yeah S16_9_2: [2097.600] maternal age? S12_9_2: [2098.410] yeah S16_9_2: [2099.035] really? S12_9_2: [2099.755] yeah S15_9_2: [2100.405] no that's for Down Syndrome. that's i have not found, a link to NTD. i didn't find anything. S12_9_2: [2103.138] not [?] [2106.323] actually it's used as in screening test for NTD. the maternal age. it's taken in account S15_9_2: [2112.358] yeah? S16_9_2: [2113.118] is isn't that because of the amount of, er AFP [?] to different, age group? or does it have anything to do with S12_9_2: [2122.275] no that's, with the gestation. different level AFP. but they taking age maternal S15_9_2: [2130.029] [??][accent and then overlap obscures] S16_9_2: [2131.109] [?] yeah S12_9_2: [2131.744] i don't [?found] the reason but, it's important factor and they take it in account, when they screen for AFP, for NTD S8_9_2: [2139.439] maybe because NTDs are associated with Down Syndrome S12_9_2: [2142.420] probably yeah, maybe. (2) the [?] is, it's like one factor of these enough, to lead to NTD or, a combination of S15_9_2: [2154.709] no. they have said that, you know if you have maternal diabetes like isn't not, a hundred percent that you're going to have a child with NTD but it increases the risk, that the child will have NTD. so it's, each factor on its own, which can affect cause NTD in the child. it's not the comb- even combination but if you have combination, there's more higher risk of S12_9_2: [2173.103] ok [?]. (5) ok any more questions? S15_9_2: [2180.533] questions? S12_9_2: [2182.515] no? ok. (4) [2187.681] now screening tests. (11) ok er, prenatal screening is the identification at risk of particular disorder. (2) the measurement of alpha er feto protein in the maternal serum is used to screen, for er, NTD. alpha one protein is glycopreitn found in fetal serum, and produced by the fetal liver and the yolk sac. in in normal pregnancy it reaches the highest concentration in the fetal serum, in the late of the first trimester, with a value of three hundred miligram per decilitre. this protein is encoded by the AFP gene in chromosome four, and is considered to be ah the dominant, protein in the fetal serum. (2) it's used as a marker for NTD, but it's also used as a marker, for other abnormalities like a cancer so it's not specific for NTD. er it's been found that there's an increase er in the level of AFP in pregnancies with er open NTD, and this can detect, from er seventy five, to ninety percent of open NTD.(2) the optimal time to use ah, the level of of AFP as a screening test is from, er sixteen, to eighteen weeks gestation, however, you can use it from fifteen to twenty weeks. the result, from from this test actually the result from the all tests mentioned here is expressed as a, multiples of the median, and the reason is that allowed to take the variation between the marker concentration, with gestation, into the account, so, the concentration of AFP in fourteen weeks gestation, is different that the level in fifteen weeks gestation. (2) for a pregnancy to be considered at high risk, the level of AFP, must be equal or higher, than two er MoM [pronounced mum], and that's mean, the level of AFP in the tested pregnancy, is twice er the normal level of AFP in unaffected pregnancy. er there is study they showed that the maternal serum AFP, greater than two point five, two point five MoM, occurred in eighty eight per cent of cases of anencephaly, and in er seventy nine per cent of cases of open Spina Bifida, and in thir-three percent of unaffected er sin-, sorry, unaffected singleton pregnancies.(3) the test, has an overlap between ah the maternal serum AFP in affected and in unaffected, and, the level of AFP increased, because other abnormalities like a cancer, so it's not really good, test to use as a diagnostic, to use the level of maternal er, level of AFP. now screening tests. (11) ok er, prenatal screening is the identification at risk of particular disorder. (2) the measurement of alpha er feto protein in the maternal serum is used to screen, for er, NTD. alpha one protein is glycoprotein found in fetal serum, and produced by the fetal liver and the yolk sac. in in normal pregnancy it reaches the highest concentration in the fetal serum, in the late of the first trimester, with a value of three hundred miligram per decilitre. this protein is encoded by the AFP gene in chromosome four, and is considered to be ah the dominant, protein in the fetal serum.(2) it's used as a marker for NTD, but it's also used as a marker, for other abnormalities like a cancer so it's not specific for NTD. er it's been found that there's an increase er in the level of AFP in pregnancies with er open NTD, and this can detect, from er seventy five, to ninety percent of open NTD. (2)the optimal time to use ah, the level of of AFP as a screening test is from, er sixteen, to eighteen weeks gestation, however, you can use it from fifteen to twenty weeks. the result, from from this test actually the result from the all tests mentioned here is expressed as a, multiples of the median, and the reason is that allowed to take the variation between the marker concentration, with gestation, into the account, so, the concentration of AFP in fourteen weeks gestation, is different that the level in fifteen weeks gestation. (2) for a pregnancy to be considered at high risk, the level of AFP, must be equal or higher, than two er MoM [pronounced mum], and that's mean, the level of AFP in the tested pregnancy, is twice er the normal level of AFP in unaffected pregnancy. er there is study they showed that the maternal serum AFP, greater than two point five, two point five MoM, occurred in eighty eight per cent of cases of anencephaly, and in er seventy nine per cent of cases of open Spina Bifida, and in thir- three percent of unaffected er sin-, sorry, unaffected singleton pregnancies. (3) the test, has an overlap between ah the maternal serum AFP in affected and in unaffected, and, the level of AFP increased, because other abnormalities like a cancer, so it's not really good, test to use as a diagnostic, to use the level of maternal er, level of AFP. (39.37) (2) for a Down Syndrome you can screen for Down Syndrome in the first trimester, and you can scan for a second trimester. at the first trimester combined ultrasound and biochemical, which is known as CUB [pronounced cub], it's used screening for Down Syndrome, er during fourteen eleven and fourteen weeks, er the de-detection rate is eh ninety percent, and basically this this test is combination of, physical and biochemical test, the physical test is the measurement of er, nuchal translucency. er, which is term used to describe, er, the area of fluid that present between the fetal skin and spina. and, as you can see in the picture, the area where is the circle, it's it's the area of NTD. actually it's is present in the normal and the abnormal, er foetus, but it's get er bigger in in in foetus with Down Syndrome. this area can be detected by by ultrasound, as you can see in the down, of the picture, there is like er, a figure black hole which is the increase of NTD. so they measure, like this black hole, [all looking at picture here as is speaker] and they divide the result, the measure as er, milli milli centimetre i think or millimetre [S13 nods] i'm not sure. and they divide it er by the normal range and they get the MoM result of of this test. the second part of of CUB, screening is the bio-biochemical test, and is the measurement of, two biochemical markers, in maternal blood, the first one is based the human er, chronic gonadotrophin, er, it's found to be increased, er in case of Down Syndrome, and if the result higher than one point around six MoM, then, the pregnancy will be, at high risk. having Down. the second marker, is er pregnancy associated plasma protein A and is found to be decreased in in pregnancies with Down Syndrome. so what should happen is, the final result will be combination from the measurement of NTD, from NT, and from ah, (2) free beta and from pregnancy associated plasma protein, with maternal age. (2) the the result will be entered in a software, in in MoM format, the software will give final result as a risk for example the final result will be, risk of one in five hundred or risk one in three hundred. there been agreed to use eh one the risk of one to hundred as a cut off, so if the final, if the final result of of this screen was, one in two hundred, then the pregnancy will be at high risk, for having Down Syndrome. if the final result was like, one er in three hundred, then the risk will be at low risk for having a Syndrome. er for, for the second trimester, er in the beginning they used the level of AFP, as a screening test er, they [?be] found that there's increased there is decreased [emphasis] the level in the level of AFP, er, in pregnancy with Down Syndrome, but the issue is that, AFP test, was [?able][mispronounced?]] detect about thirty five percent of the cases, so there will be around sixty five percent of of pregnancy with Down Syndrome, undetected, so we start to research for another ah, markers, then they find out two markers HSG [HCG? On handout ] which is placenta product, and it's increased eh, in women with Down Syndrome, and the other markers UE three and it's been found to be decreased in maternal serum, with Down Syndrome, it is the same as i said before with the first trimester, eh, [?SA] HG HCG, result and UE three result, with the maternal age, all together will be account, the final result will be as a risk, if-if the final result is er is higher than one in two hundred and fifty, then it will be, in low risk, if it's lower than one in two hundred fifty, it will be in higher risk. (2)er, criteria for a good screening test the test should be safe and simple, er, the test should be acceptable by the population, the distribution of test value er in the target population should be known, and suitable cut off level defined and agreed upon, er for example i found a paper but, er, (2) the university don't have access for a journal so i wasn't able to read it. but was interested because they was AFP protein and screening test, in the population, i tried to find what's the population but i couldn't, but this test failed, as screening test. it was able [mis pronounced ] it was able to detect around thirty to twenty five percent. but for example in case of Scotland it was able to detect around sevnty five to, ninety percent. so it's also, by, have a variation of of of the popu-of the population, should be taken in account when we chose a screening test. (2)er, also there should be an agreed upon policy for the for the further investigation, and our scenario er, actually i missed the scenario. she was in fourteen weeks gestation right? S14_9_2: [2737.709] irty weeks i think S13_9_2: [2739.499] no S8_9_2: [2739.690] no i think she was eleven weeks S16_9_2: [2740.960] no eleven weeks S12_9_2: [2742.040] eleven weeks? S13_9_2: [2742.484] eleven weeks S14_9_2: [2742.992] oh you mean er so the mother's age? S12_9_2: [2743.882] yeah because i i missed my my – i lost my papers so S14_9_2: [2746.993] eleven weeks yeah. the pregnancy. S12_9_2: [2748.324] so for er for NTD, we cannot offer her, er AFP protein, (2) because AFP protein, er carry out between, fifteen to twenty weeks, so the best thing to do is to offer her ultrasound, eh it's possible to offer her, it's thirteen sorry. thirteen or fourteen? : [2748.454] [=concurrent s14 & s8 inaudible] [2759.771] [s12 seems to be addressing S10 a lot- who is ‘actively' listening/nodding ] [2768.239] [looking over to S8's paper] S8_9_2: [2770.376] eleven S13_9_2: [2770.755] thirteen S16_9_2: [2771.086] eleven S12_9_2: [2771.582] eleven so, maybe after three weeks or five weeks it is possible to offer her AFP. eh, for Down Syndrome, (3) i think, it's possible to offer her AFP immediately er screening test. (2) ok that's it S10: [2791.868] is it possible [??] let's say in general is it better to test, first trimester or second trimester for Down Syndrome. i suppose first [? one] S12_9_2: [2801.329] well it it will better, first, it will be better because, it will give you better management, eh for treatment, er for counselling eh, i don't know actually if, if you like if you get better chance, to cure a disease but it's not possible i think for, Down Syndrome. so i think S13_9_2: [2802.466] [nods] S15_9_2: [2802.466] [?] S10: [2808.181] [nods] S13_9_2: [2823.284] no you can't cure it S14_9_2: [2824.811] terminate less [?traumatic ] termination S12_9_2: [2826.396] maybe termination or management, of the case S10: [2829.616] and it's more accurate, as well you said it picked up S12_9_2: [2832.274] er S10: [2832.790] ninety S13_9_2: [2832.854] the third trimester's more accurate S10: [2835.024] is there a higher, miscarriage rate [?] S12_9_2: [2836.664] actually, ninety percent [referring to notes] S15_9_2: [2839.505] you're testing, maternal blood right? i don't think so [?] S16_9_2: [2839.505] no that's S12_9_2: [2843.509] no it's all maternal blood S15_9_2: [2844.709] yeah [?outside] S12_9_2: [2845.459] yeah amniotic fluid will be [??] as a diagnostic S8_9_2: [2846.634] diagnostic S10: [2848.791] ah ha ok S15_9_2: [2850.111] but the screening test, so you don't have CVS and [? other] screening tests S12_9_2: [2851.204] yes screening, [2853.427] no S10: [2856.475] right S16_9_2: [2857.445] but that's that's interesting cos like like i said there's three type of er, Spina Bifida, but the the last two are similar S8_9_2: [2866.178] yeah S16_9_2: [2866.649] because you can't have [?it] the nerves the nerves are actually getting in or out so i mean, but then you also have S12_9_2: [2872.388] maybe, maybe by ultrasound S8_9_2: [2874.519] and you can do that S16_9_2: [2874.865] but you won't see the nerves, with ultrasound S12_9_2: [2877.019] [??] ? i don't know. S8_9_2: [2877.729] yeah you can S16_9_2: [2878.745] so then again if you if you, S12_9_2: [2880.968] you can see the nerves. so S8_9_2: [2881.984] yes you can see the S16_9_2: [2883.140] can you? S8_9_2: [2883.995] yep S16_9_2: [2885.455] with ultrasound? S8_9_2: [2886.563] yeah. i'm going to talk about that just [?] now.[group laugh 48.04] : [2888.932] [group laugh ] S14_9_2: [2895.118] it's very hot : [2896.007] [other noises of agreement, S10 gets up to open window] S10: [2896.048] yeah S15_9_2: [2897.697] yeah S13_9_2: [2898.257] [?] S18_T2_9_2: [2899.147] do you want to? S10: [2899.360] are they closed? [talking about windows] S18_T2_9_2: [2901.019] [?] we're not used to this room being hot we're used to the whole department being freezing S13_9_2: [2905.590] it's boiling S18_T2_9_2: [2906.165] we've got, the heat affects everyone [?] the lecture theatre, and we can't believe people are saying to us, it's too warm, because we're used to people sitting in coats and scarves and hats and gloves. it's quite nice so, we turned it down yesterday or the day before we turned it down. it's so unusual having to do that. S16_9_2: [2923.248] it's sunny outside [? what ?] S18_T2_9_2: [2924.504] yeah but the wi—usual the wind is coming through these windows. S10: [2927.613] well you don't have to [?] [??] (6) S15_9_2: [2937.560] what are the [?] S14_9_2: [2939.580] i couldn't concentrate [gestures] can't concentrate, it's S13_9_2: [2944.661] it's a bit like that in the lecture theatre sometimes it's just too hot. S16_9_2: [2947.328] [?] [2951.615] ahh S13_9_2: [2952.850] oh S18_T2_9_2: [2953.616] not too happy if they fall out : [2954.819] [laughter] S16_9_2: [2956.534] no S13_9_2: [2956.978] if it makes you clean them S12_9_2: [2961.487] ok? so, S8_9_2: [2963.293] talking about diagnosis, i'll start off with ultrasound. firstly it's non invasive so it will be i mean all pregnant mothers will prefer to have ultrasound before anything else. em, till i mean from the eighties, up till two thousand seven or something, they had this two D ultra sound where, em you know the classic lemon and banana signs which you see in er Spina Bifida, could be seen but, these signs are also associated with the other neural tube defects, so you cannot say specifically that it is Spina Bifida. so er nowadays they have a three D ultra sound which is er you know which can scan through multiple planes. they have three basic planes which is axial you see from, like through the spinal chord. and saggital is like the sideways and, um the other is coronal, er, the three D ultrasound has accompaniment of volume to it so, you don't see it like just a plane of, thing you, (2) er in the figure, in the first figure you can see the two D scan and the three D scan, the three D scan has i mean a little stick image, which you can, em, kind of interpret better. so, and it also has two other modes which is called a skeletal mode and a surface mode, skeletal mode will give you you know the perfect image of the, vertebrae, and em the surface mode'll help you see, the er, i mean along with the skin intact, so you can literally see the defect as, with this on i mean [?alcephen/as we seen] like, so that's that's in the figure two in the bottom right, that's the surface mode image. where this is a a meningo- meningocele, S14_9_2: [3081.909] meninomengocele S8_9_2: [3083.339] no no it's a meningocele there, there is it's empty S14_9_2: [3086.221] mm S8_9_2: [3086.445] there is no spinal chord so, you can see an empty sac,[?oh yeah] and these are the vertebrae column, S14_9_2: [3092.929] oh S13_9_2: [3093.529] mm. (2) : [3093.529] [turn page ] S8_9_2: [3096.252] and generally they consider the B plane to be the most accurate because, you can examine each and every vertebra from the top. so, and er, along with, er just seeing the image they also measure the intracraneal translucency to now up to now they used to measure the nuchal translucency, they also measure the intracraneal transl- sorry they don't measure it. intracraneal translucency is like it's absent in, ah cases with Spina Bifida. (2) and er next is alpha feto protein test, the alpha feto protein test as he said, i mean he went over that the same thing as in maternal serum you do it for the amniotic fluid, and you measure the er, median values and the MoM. and then you put it into the data base and you check it, if it's the normal or not. and the next is, er but the thing about alpha feto protein test is that it's associated with the maternal age i mean the gestational age, but ah acetyl cholinesterase test is not associated with that. you normally see high levels of ah, acetyl cholinesterase through all the pregnancy. so, ahm, for the acetyl cholinesterase you do this you do gel electrophoresis, wherein erm, you, whatever differentiate er, acetyl cholinesterase from the normal cholinesterases. so this is just to differentiate this you also add an inhibitor which is specific, to this em, acetyl cholinesterase, so you have ah two gels wherein, you have an inhibitor and you don't have an inhibitor. so when you see actually the acetyl cholinesterase moves further down from, the the thing than, the normal cholinesterases, and when you add the inhibitor that-that band is absent. so, em that demonstrates that. and it's also like a secondary confirmation test with AFP so like if you have, a higher FP and a high [?acetyl] cholinesterases then you can kind of be sure. that er you have the, so if the foetus has a, a Spina Bifida or something like that. but the three D ultrasound kind of gives you almost a perfect diagnosis it it er can give you the real image of what's going on inside. so that should be, the most accurate thing. [?] S16_9_2: [3241.854] is it expensive? S8_9_2: [3244.348] er it should be expensive. (2)any questions? S12_9_2: [3252.337] what else? S8_9_2: [3253.698] oh sorry.[laughs](2) ok so for L erm if she screens positive for, er if she screens positive the AFP then er, you probably tell her, you can offer her a CVS or amniocentesis, but i think first you should offer her an ultra sound, and if the ultrasound er, i mean cannot detect it then probably you should offer her a CVS or amniocentesis, and then you could confirm and for, and she since she is also having a risk of Down Syndrome you could offer her a genetic test, in case you find any other structural abnormalities in the Down in the ultra sound, so er you could offer her a genetic test, but eh normally neural tube defects like the closed is, kind of non symptomatic and the open is like almost lethal. so er, then it make- doesn't make a difference to counselling or the, prognosis of the tests. (3) S14_9_2: [3319.221] excuse me? S8_9_2: [3319.988] mm S14_9_2: [3320.669] why er i mean regarding chorionic villus sampling. could we use chorionic villus sample to diagnose neural tube defect? we need alpha protein, so S8_9_2: [3330.666] oh yeah, yeah i don't think it can be [?] S14_9_2: [3333.865] yeah. (2) because acetyl cholinesterase and alph protein only [?on the] amniotic fluid S8_9_2: [3340.279] amniotic fluid S15_9_2: [3340.850] so regarding um S16_9_2: [3341.739] unless [?] S8_9_2: [3343.517] no you can you have to use amniocentesis S14_9_2: [3344.038] no well [3346.488] this is the only S15_9_2: [3346.878] only amniotic fluid S8_9_2: [3348.398] yeah S14_9_2: [3348.547] yeah [3350.960] because we don't need, we don't want to extract DNA. we just want to check for Down Syndrome. S8_9_2: [3355.152] yeah maybe you could ask her to do a CVS for the genetic test results S14_9_2: [3359.025] yeah S8_9_2: [3359.554] mm. (6) : [3359.736] [all writing] S15_9_2: [3365.923] i have a question i don't understand what this, different planes [?if they have a detect] a different type of ultrasounds, are there three, different types of S8_9_2: [3375.762] no it's you get all the three planes in one scan. you, you run a sc- you run one scan and you get, the image in three planes. so maybe it like it's automated and it does it in three planes and just gives you the image. S16_9_2: [3389.295] three different views S14_9_2: [3391.896] it's like three D cartoons or three D cinema, it's not ah just er S8_9_2: [3397.442] just kind of like one view from one way one view from the other like that. S13_9_2: [3397.882] [?] S14_9_2: [3400.224] yeah S16_9_2: [3400.954] that's quite [?] S15_9_2: [3402.475] is it? S16_9_2: [3403.595] it's like X Y Z S10: [3405.185] yeah S13_9_2: [3405.725] mm S10: [3406.746] so, axial is?, down [gestures] S14_9_2: [3407.187] like in the [?] S8_9_2: [3408.676] axial yeah it's, from top. S10: [3411.008] and saggital is sideways? S8_9_2: [3412.439] yeah it's like, sideways S10: [3414.081] so does that mean the other one goes through it S13_9_2: [3415.140] goes downward [gesturing] S10: [3416.502] [?] that way S16_9_2: [3417.725] that way S13_9_2: [3418.041] yeah S10: [3418.881] the corona S8_9_2: [3420.102] corona S10: [3421.202] ok. cool S13_9_2: [3424.145] do all hospitals have these now? or do they just S8_9_2: [3427.526] no it's, i think it's just [?] and place. this paper which i read was in two thousand and nine so, maybe not all hospitals have it S14_9_2: [3435.065] i understand that three D ultrasound is already ? S16_9_2: [3435.510] so S8_9_2: [3438.234] is already S14_9_2: [3438.685] yes since long time ago, it's long time ago and the ju- D yesterday say that, just they er believe that people are still not expert or not skilled in using ultrasound yeah. that's why otherwise, a lot of countries, use three D ultrasound, for any case they suspicious that she has neural tube defect child S8_9_2: [3439.701] yeah but maybe [?] S13_9_2: [3450.963] skilled at using it S8_9_2: [3461.286] uhum. right.(3) S12_9_2: [3465.350] yeah i have question er, S8_9_2: [3466.811] yes? S12_9_2: [3467.561] S H E, it's normally not present in the foetal, serum or present ? S8_9_2: [3468.785] yes? [3471.828] yes. it's normally not present. S12_9_2: [3473.796] not present. (4) S14_9_2: [3478.498] which one? S8_9_2: [3479.507] AC. acetyl cholinesterase S15_9_2: [3480.467] so [3481.268] so we don't measure it right? S8_9_2: [3483.219] no you don't measure [?] you just get a band S15_9_2: [3484.484] just, just see if it is, there or not then? S8_9_2: [3487.786] mm. (3) : [3490.073] [s18 goes to shut window..lull in proceedings] S18_T2_9_2: [3490.517] [??] S13_9_2: [3494.137] yes S14_9_2: [3494.963] ok good S16_9_2: [3495.693] just excited (2) S18_T2_9_2: [3499.344] aren't we all [??] S12_9_2: [3503.628] ok. any more questions? (3) S17 S14_9_2: [3509.950] thank you. S16_9_2: [3511.479] no it's s17 S12_9_2: [3512.166] no it's er S17_9_2: [3513.372] [?] (9) : [3514.839] [papers rustle ; getting h/o for next speaker] S14_9_2: [3523.660] i'm going to talk about, numbers, calculations and, the accuracy of screening test. actually i'd like to say first, that, em, screening test is a matter of, em we have to weigh between, er the cheap how much the screening test it is cheap and how much it is, non invasive, and also how much it is accurate. G er the cost, and being not invasive is much important, than the accuracy of the test itself which we want to use in screening. because we are going to er apply this screening test, for a whole number of population for a large number of population, maybe the whole population maybe sub groups like maybe now in our case, we're going to use this test, for all pregnant ladies. so we need this test to be non-invasive. (2)then, i'd like to say, what does it mean if it's, positive screening test or if the result was negative. positive screening test does not indicate that, this lady will have positive affected child. and most of those group, who have positive result, most of them will have normal children. and, negative screening result, doesn't exclude the risk of having affected child, so, it is probably that she will have affected child. we just try to exclude to select certain people, because we want to say oh yes, this group are at high risk, so we are going to, test them using the invasive techniques, instead of er doing this invasive techniques for the whole, er population or sub population group.(2) first, the first table, will show the accuracy of maternal serum from alpha protein screening, for neura-neural, neural tube defect in single and twin pregnancy. using alpha protein cut-off, of two point five, multiple of er of median, for the single pregnancy, and the double of that for, twin pregnancy which is five multiple of median.of course because we can, guess that, the presence of two er foetuses, that means production of, double of the amount of alpha feto protein and double of the profusion of alpha feto protein to the maternal circulation. so, the detection rate for an ancephaly would be very high, it's about, ninety eight per cent, for single pregnancy, i'd like to say that the detection rate means the sensitivity of the test. and for Spina Bifida, it's eighty two percent, and the positive predictive value, which means those people who are, we predict them they are positive, and they are not positive they are, they will have normal children, it's about five, point seven percent. regarding twin, the accuracy is much, less, for ah twin pregnancy. the detection rate would be about, will reduce to two eighty, three percent, and, for Spina Bifida would be just thirty nine percent. so it's not that much useful in twin pregnancy. and, false positive rate would be three point three percent. (2) regarding Down Syndrome, using alpha feto protein human chorionic gonadotropin and maternal age, the detection rate would be sixty five percent and the false negative, thirty five percent, the false positive would be three percent, and the specificity, of this test would be ninety seven percent. regarding using CUB screening which is higher, has higher accuracy than, eh the treble, marker screen, the accu- the accuracy reach to to, eighty to ninety percent. (2) going to, er diagnostic test of er neural tube defect. the detection rate for using alpha feto protein is about ninety eight point two percent, and with, acetyl cholinesterase, it's just less than one hundred percent. so we could imagine, if we use both of them for diagnosis, we nearly, one hundred percent.and detailed ultra sound, the high skilled hand also has very high, er detection rate. for Spina Bifida, it's nearly the same, the accuracy rate using, alpha feto protein is ninety seven point six, with a [?acetylcholine] itself one hundred percent, so both of them will be very high accuracy rate. and [?we heard] ultra sound also high, in skilled hands.false positive rate would be, four point five percent, with using alpha feto protein, and, just about point one percent, using acetyl cholinesterase, and using ultrasound, false positive rate is very low. i asked er, the lecturer today and he say, if just using acetyl cholinesterase is nearly one hundred percent detection rate, so why we need to use alpha feto protein, and she said that, there are some cases who has, acetyl cholinesterase, and they are not affected. so we, ten- we tend to use both of them, to be er, one hundred percent not just nearly one hundred percent. (2) ok. (2) then, i want to compare between the diagnostic and screening test. using alpha feto protein. so, if we see to this diagram, this will show, the er level of an alpha feto protein, by milligram per litre, er in different ges- eh in different weeks of gestation, er, and the amniotic fluid, and in the second column the maternal serum circulation. first, just we first er, think we we could em er we could spot, that the level of, alpha feto protein, and amniotic fluid, will goes down with with the er further with the end of pregnancy, while maternal serum concentration, ah alpha feto protein in the maternal serum concentration will be higher, wih- with the end of gestat- eh end of the pregnancy. ok? (2) we –ah we need to understand what's the multiple what's the, the median-multiple of median. in order to understand, what's the accuracy and how we calculate the accuracy. so, the multiple of median is the alpha feto protein, result of the patient at certain week of gestation, divided on the median of alpha feto protein at the same weeks of gestation. for example, we can see on the stars here, that the patient alpha feto protein, at fifteen weeks usually, it's about, we can see it's about, twenty milligram per litre. (3) ok, the upper, star. and because the median, alpha feto protein normally, it's about at fifteen weeks gestation it's about ten, milligram per litre so, it's easy to understand that, we can say yes this lady has, er alpha feto protein, double than normal people. so it's, em er she has two multiple of median. (3) after that, this curves show, the overlap between, eh the alpha feto protein level in affected, and in eh non-aff- pregnant lady who has, a feto child and those who have normal child. regarding, eh alpha feto protein level in the amniotic fluid, there is very small overlap. so we could guess that the diagnostic test, is very highly accurate, because there is no much overlap between the level of the affected and unaffected children. while, using the alpha feto protein in the maternal circulation, there is, a very large area where there is overlap between, the the alpha feto protein in affected and unaffected children. (2) and, we can see that the cut off, it has to be in certain place, the red line it has to be in certain place until we could say, yes, this lady at, er high risk or at low risk. (3) using modified or er this one maybe exactly the same as er D diagram, er i tried to modify the [? numbers] and make them easier, for us to understand easily, because you er you still remember that D say you have to memorise, er this diagram and this way of this calculation, so i think it's maybe impossible or at least it's difficult to memorise very complicated numbers, so if we imagine, that the whole population, is the green one ok, and then, the pregnant ladies are about one thousand and one hundred. let's imagine that there are one thousand and one hundred lady, pregnant now. and we want to screen them. using our screening test, we detect that, these one hundred ladies, as at high risk is at high risk. ok? the red group or the pink group, those one hundred high risk group. and the blue ones, are low risk group they are about one thousand. they are normal. and we say now they are at low risk. ok. and, those one hundred, who are at high- at high risk actually only, eight- only eight of them, are have the disease affected. and two, from the lowest group, are affected and we are going to miss them, so the affected people are only ten. eight of them from the high risk group and we are going to diagnose them, and two of them are from the low risk group and we are going to miss them. (2) ok? so, now we want to understand, what is sensitivity what is specificity and what's-, what's the predictive value, negative predictive value false positive rate false negative rate. if we concentrate, on the table, we can see, that the high risk group, are one hundred, we say they are one hundred ok? and the low risk group are the blue ones. all of them, one thousand ok? the one hundred high risk group, eight of them, are actually affected. and, ninety two of them, normal, yes? the low risk group, the one thousand, if only two of them, was affected and we are going to miss them, they are- they will diagnosed as false negative. we di- do diagnose them negative and it's false. so we can predict that, about ninety about nine hundred ninety eight, are the true normal. yes? (2) ok, let's now concentrate, on sensitivity. what's sensitivity ? sensitivity, it means how much i am sensitive when i say you are affected, sensitivity it's all the matter of affected people. (2) it's about it's sensitivity means, concentrate on the red curve ok ? you will see the red curve divided into, yellow, part and, red part. we need to divide the yellow part, which we are going to diagnose them, those ten people we are going to diagnose eight of them. the eight, over the whole affected people. they are ten. so eight over the ten, this is the sensitivity. how much i am accurate when i say you are, at high risk group. this is sensitivity. what about specificity? specificity, it's how am i accurate, how much i am accurate when i say you are at low risk group, you will not be affected. so how- how much how much i am specific when i say, you are, healthy. you are not being you are not having, risk of having er affected child. so it's all with nor- with normal, er people who are normal er population. so it's all work on the green curve. if we divide the green curve, into yellow part, those who we sai- we've told them you are negative and you are really negative, and, the green part which those, we told them, you are positive and they are negative so you are negative but, we misdiagnosed them we told them you are negative. we wasn't specific when we told them you are positive. ok ? so i just [phone rings] dia-dia- the part the true normal people over the whole normal people. so they are, they er, people who diagnosed them as normal, they the nine hundred and ninety eight, over the whole normal people including the ones, which we thought they are positive. which, about one thousand and ninety. ok ? that's gives ninety one percent. this is the specificity so it's all, with the normal people. how much you are specific when we say you are normal. ok. going to the positive predictive value, positive predictive value, it's the whole matter of, positive. positive predictive value. so let's concentrate on the diagram, forget all about eh low risk group, just concentrate on the, high risk group, the pink, circle. or oval. this oval shape, con- one hundred people are, we say that they are at as high-risk group. but eight of them only, are really affected. so, how much my prediction was right when i say, you are, affected. so, it's the true positive over the whole positive. so positive predictive value, all about the positive. the true positive over the whole positive. the true positive was eight, and the all positive which i thought they are positive, is one hundred. so eight, just eight was righ- really, positive, over one hundred which i thought they are positive. eight over one hundred it will be equal to one hundred percent. going to the negative predictive value, it's all about, it talks about negative people. those people how i thought they are, er have neg—negative screening result and they are at low risk. so forget about the red one, the high risk group just concentrate on the low risk group the low risk group, they are about one thousand people, but there are two of them, they are affected and we missed them. we thought they are at low risk ok? so the negative predictive value is, how much i am right in my prediction, that they are negative. so it's the true negative, over the whole negative. the true negative, is nine hundred ninety eight which is the one thousand minus that two which is affected which are affected, over the whole negative, which are, one thousand, and equal to ninety nine point eight percent. and thanks. : [3526.395] [laughter] S10: [4504.079] right. [laughter & smiles] S16_9_2: [4504.996] [??]. (4) i don't think the graph was relevant. i think if you use, like i i would think it would be better, use data like from real data from two different population then compare together, because right now you, you just making up like, the number of affected case and unaffected cases. which doesn't show how accuracy it is. [?] S14_9_2: [4535.364] we have already that, in our lecture. but the point that we are going to use that in calculation in the exam. so we need to know the, way of calculation, not the real, examples, which we got in the lecture. so that is why, if we put, the large numbers, one thousand one one hundred and er, forty seven and a thousand and er five S16_9_2: [4558.109] no no i say in two pop- different populations S14_9_2: [4561.241] excuse me? S16_9_2: [4562.362] the same method for two different populations because S8_9_2: [4565.793] oh he's saying the the use the same diagnostic test S12_9_2: [4566.047] there is [?] affect yeah yeah S16_9_2: [4568.075] see see i i what i meant is the research topic is accuracy of the testing right? S14_9_2: [4573.118] yeah S16_9_2: [4573.914] but you have two different populations, and if you apply the same exact method, on a calculation S14_9_2: [4576.015] yes S13_9_2: [4579.806] on two different populations S16_9_2: [4580.738] to the, and then you compare them, then you see, the same test would have different result S13_9_2: [4585.148] is it the same as accuracy S15_9_2: [4586.137] exactly S14_9_2: [4586.799] the accuracy the accuracy it doesn't mean that you use the same test on this population and this population and compare it, because it might- the results be different from here and here. the accuracy means, do the, screening test, and you want, to do diagnostic test, to see you are right or not. so you are assessing the accuracy of your screening test by using the diagnostic test, not by using the other population. the diagnostic test, will assess your screening test. [s15 nods](2) you make it like comparison between different populations and this is not the accuracy of the screening test. the accuracy of the screening test, how much you are right by using this method. S16_9_2: [4596.770] [?no] S18_T2_9_2: [4630.206] anybody else have anything to say about that ? S10: [4632.216] i think you've done it a very [?] S12_9_2: [4632.555] no it's it's correct but maybe it will it will help er to prove, like the effect of of the variation of S16_9_2: [4640.134] it seems that S14_9_2: [4640.896] yes S16_9_2: [4641.595] different populations S12_9_2: [4642.334] maybe it's a point S8_9_2: [4643.305] yeah but different population is S16_9_2: [4644.897] have different, yeah. you will have different numbers and values S8_9_2: [4648.559] yeah but, then the S16_9_2: [4650.256] but then it would be like S8_9_2: [4651.149] no there is a different incidence in different populations S14_9_2: [4653.263] yeah S16_9_2: [4653.753] yeah. so, (2) you will pick up, you will pick up a diff-, you will pick up different [?rates/bits] for different populations is what i meant, so by by seeing like, – it could be very [?effective/affected] in one populations but not the other. S12_9_2: [4671.859] exactly. S16_9_2: [4672.792] so, so you see, how accurate, that testing method is to that population. S14_9_2: [4679.622] mm S16_9_2: [4680.032] and not the other. because you actually using real data, like from different populations ? S12_9_2: [4685.657] but for this point you don't need, two population. S16_9_2: [4689.785] you could have, as many as you want S12_9_2: [4691.436] but yeah yeah but i think S14_9_2: [4692.770] but this is n– this is not the main idea of, testing the accuracy of the screening test i think S16_9_2: [4698.168] screening is mostly i think er to to check how accurate is the diagnosis. er because, you do it on a specific population a screening for a specific population S14_9_2: [4701.879] yeah S15_9_2: [4708.661] yeah S16_9_2: [4709.312] yeah. S14_9_2: [4709.943] because you you have good S15_9_2: [4710.213] so, then from that population [?you] make [different ] and do high risk and low risk. so we are using diagnostic test based on that on, that specific high risk population. in that population. i don't know why we are going to compare two populations, for accuracy S13_9_2: [4726.755] but S16_9_2: [4727.143] no, it's not for accuracy it's it's for, S12_9_2: [4730.509] the various populations. you know the various between populations, it's like [?improvement.] S16_9_2: [4734.792] no it's the same testing method yeah but it's on different populations S18_T2_9_2: [4738.948] was i being thick or did i just think that S14, had shown you, a a like she could have, instead of saying, eh ninety two she could have said twenty seven and and two hundred and thirty five, etcetera, which is quite difficult to remember when you're doing these things, i thought what she had done was actually make it very easy numbers so that when it came to the bit and you've to put in the numbers in the exam, if you get an exam and you get asked these questions you'd say right oh ok, so that was 100 S14 had for that this case, well we've got this and it's actually showing me how to do the calculation, i thought that was was i wrong in thinking that? S13_9_2: [4754.148] yeah [4767.845] yeah [4775.248] no that's what S10: [4776.308] very good S18_T2_9_2: [4776.768] that that's ok, that's fine it's just sometimes i wonder whether i'm right or wrong, because i don't do this much but, that's what i i thought she was, simplifying it so that it was easier S15_9_2: [4785.589] to understand S13_9_2: [4786.590] yeah S18_T2_9_2: [4787.100] uhuh, and then you could take it and you could put in the numbers that are in S10: [4791.330] i don't think there's any i mean i like your first diagram, cos you say the way of, the way the cost of the invasiveness and accuracy and you use weights tha- that was very clever [others laugh] you know i said it's very [?] S14_9_2: [4801.211] thank you. S18_T2_9_2: [4801.721] you so you'll remember that [?] S8_9_2: [4803.397] yeah : [4803.397] [group laughter] S13_9_2: [4803.586] yeah, we'll all be sat in the exam like going like this [gestures balancing weights] [group laughter] S10: [4807.333] very good and it's also very colourful and, very good. see i think that S15_9_2: [4809.604] sorry S8_9_2: [4810.055] [?] S15_9_2: [4811.270] yeah [?] S12_9_2: [4812.669] er who's next you or me? [looks to s15] S16_9_2: [4815.347] no you go S12_9_2: [4816.209] ok. is there a, a minimum, sensitivity or specificity, for a test to be considered as a good screening test? S14_9_2: [4826.014] no. i think they er, er in order to say which is suitable it's according to to the disease, like in our case, er Down Syndrome or or neur-neural tube defects, er they concentrate more they think that's it's better, to not, say this is a positive case, and terminate pregnancy, leading to unnecessary termination of pregnancy, it is better, to misdiagnose some cases. so they concentrate more, not on the sensitivity. sensitivity it means, that you are you say you are affected, yeah it's most probable you are affected, they don't worry a lot about the sensitivity. maybe specificity is much important. in cases like neural tube defect, specificity, you say it is-you are normal so, you are more like to be normal. it's much more important for them than, sensitivity. so according to that, they put the cut off, you you can see that the cut-off, is more [?award], if you look here, the cut off they didn't, if they put the cut-off at one instead of after two about two -two point five yes? if they put the cut-off, er at one, you will see that the sensitivity will be, very high. they, they will pick up all the cases, but also, they will er they= they will detect some er extra people, as as positive, er and they put them, at high risk, and they will, er exposed them to er non-to invasive techniques like amniocentesis, [nods] (2) and that would be unnecessary. so, it's better to lose some cases, er, than, to do, invasive techniques, for a large number of people. so, they deviate the cut –off, away from the even the middle, you can see that it's away [looks to S12] yeah. S12_9_2: [4889.984] yeah S8_9_2: [4909.762] [?report] S12_9_2: [4940.699] yeah right S8_9_2: [4941.430] yeah. (3) S15_9_2: [4943.951] i have a question about this er, the accuracy of the test, they [?] the current populations, is it like S14_9_2: [4952.397] the spe- specificity or S15_9_2: [4953.731] no accuracy of the test S14_9_2: [4954.556] the accuracy S15_9_2: [4955.382] the people between the different populations S14_9_2: [4957.625] mhum i think that accuracy, it's related to the test itself yes? S12_9_2: [4958.140] the [4962.174] the test itself. as i mentioned, they use the AFP, for population but it is failed it's completely failed. it was able to detect around thirty percent, it was able to detect around thirty percent, in some population. but here in Scotland for example it's detect i think, seventy five to ninety percent S16_9_2: [4963.799] yes S14_9_2: [4968.689] mm so [4971.801] so S16_9_2: [4976.166] is it due to the, factors that influence S12_9_2: [4978.657] maybe the environment the diet, that population in Scotland S16_9_2: [4982.496] yeah but, most of the accuracy is caused by, the same factors, like folic acid and, this is the common factors, so i don't know why the accuracy should shift from different populations S12_9_2: [4993.757] why the incidence is different, why the incidence is different between, between different population, if-if they have the same factor. for example S10 mentioned in Mexican : [4993.757] [aside inaudible S16] S14_9_2: [5005.307] the incidence is different S12_9_2: [5006.682] fifty percent, fifty America they are [? Mexico ]right? S16_9_2: [5007.142] okey doke S10: [5010.318] yep S12_9_2: [5012.448] ok it's the same, [laughter]no iiI mean to say the same factor around the world. why there is different in the accuracy. so i will say to you it's the same factor around the wor- around the world, why there is different, er- incidence, betwe- in different parts of the world, (2) you know my point? [? i ? it] S16_9_2: [5031.975] i think S15_9_2: [5033.457] but the, accuracy of the test is, how much you can detect, like S8_9_2: [5037.594] but he's saying, you mean [?the same ] the population where, AFP was not successful there was no AFP in the S15_9_2: [5038.064] so S12_9_2: [5045.499] no er S8_9_2: [5046.641] in the foetus or S14_9_2: [5047.622] so S10: [5047.727] you mean if regardless of the population, you want to pick up let's say ninety percent of every population whether they're Mexican Spanish or German or whatever like, there's still going to be this accuracy, it's just [?] the prevalence is higher S12_9_2: [5056.187] no [5058.015] no no there will be different [?of] accuracy S15_9_2: [5059.539] that's what i i don't understand why is it different S13_9_2: [5062.108] mhm S12_9_2: [5062.206] [gesture questioning look] S14_9_2: [5063.580] so mean, maybe there are factors cause the variation of the er among the er, the of the population, er in different population, also there is factors, makes it, em, the ability to detect this, er group of people in this population, would be er, we can do that in others we couldn't, i mean the risk factors for this and the risk factors also for that. (2)i don't know how it would work but S18_T2_9_2: [5089.778] it's got [?a peak] here, if, if, em what you're looking for in the screening test is a level, in comparison to the median. the [??], does it matter if, if, the incidence is higher? because it's the test that S13_9_2: [5090.222] yeah S14_9_2: [5094.540] yeah S15_9_2: [5107.578] yeah [?] [overlaps] S13_9_2: [5108.088] even this, it shouldn't matter if the incidence is high or low because they are all going to have, elevated AFP, so it shouldn't, in my head it shouldn't differ [laughter; S10 pats her head] S8_9_2: [5108.168] [?] S15_9_2: [5110.364] no S14_9_2: [5110.924] umm S18_T2_9_2: [5114.492] uhuh S15_9_2: [5115.063] so it's : [5117.794] [group laughter] S14_9_2: [5120.873] i thought exactly like that S18_T2_9_2: [5123.186] well well why not make that a wee thing for Monday, maybe over the weekend since you've got absolutely nothing else to do [laughter] i'm sure, maybe maybe that's something you could find out, i'm just going to ask DA actually [?] S12_9_2: [5135.377] maybe if if they have just, er the multiples of the median, so the accuracy would be the same. i mean for example the multiples of of the median here in Scotland is, is two. maybe the level of AFP in other population, is quite low. it [? doesn't ] the same concentration. so if they used one point five multiples of median, the accuracy of the result would be higher but but S15_9_2: [5154.335] but then you would S14_9_2: [5159.982] but S15_9_2: [5160.740] but then, even if you, if you wanted to test the difference you already detect, er NTD you see that there is NTD there even if it is low [?observed ?] but you say there is NTD in that population if that person has [? NTD]. so then the test is accurately detecting the NTD in that population and in this population also. so there's no [?]i don't understand why there is an accuracy difference. S12_9_2: [5172.365] yeah S14_9_2: [5184.323] maybe it's S15_9_2: [5184.323] because it's detecting NTD in both the populations whatever the changes [?] S12_9_2: [5190.799] but there're different in the detection rate, the detection rate here will be seventy percent, there will be twenty percent. S15_9_2: [5198.352] why? S16_9_2: [5198.763] because of maybe a genetic factors like S12_9_2: [5200.451] just a question S16_9_2: [5201.875] [?popular question]. [laugher] S15_9_2: [5203.500] [?] questions. [laughter] S14_9_2: [5204.262] it might be [?lab]. it might be techniques, the technique itself S16_9_2: [5208.051] ethic approach, maybe? S14_9_2: [5209.469] it's possible. i mean the technique which they use it might be different, [s13 nods] the material, the company which they deal with, so all these factors might affect S12_9_2: [5219.936] also the cut-offs some centre use, two as the cut off, some centres use two point five. S8_9_2: [5225.560] yeah that S12_9_2: [5225.842] and that will will change the S16_9_2: [5227.755] rates of the [?] S12_9_2: [5228.382] yeah. exactly S15_9_2: [5230.430] but if you use screening test for a specific population (2) S12_9_2: [5235.712] yeah S15_9_2: [5236.149] do you use a particular screening test for a particular population ? S14_9_2: [5239.261] yes S12_9_2: [5239.730] yeah S15_9_2: [5240.192] so that, different S12_9_2: [5241.801] diff- difference centres in the S15_9_2: [5243.389] you get a particular accuracy. so if you use another test, yeah, [? even for a particular ] accuracy for that population. S16_9_2: [5246.550] that's [5250.438] right S15_9_2: [5250.788] so if you use another test for another population, you get a particular accuracy for that population. S16_9_2: [5255.830] right S15_9_2: [5256.260] yeah? S12_9_2: [5256.700] ok S15_9_2: [5257.081] but i why should they be [ ?] i don't understand (4) S12_9_2: [5263.246] i don't know if it's S16_9_2: [5263.754] but that's based on different testing methods no? [?] S12_9_2: [5267.995] it's quite the same to an extent it. some you know it's the chemistry also, they use the [?] chemistry they measure they measure [?] the level by antibodies and, a spectrophotometer. (3) so (2) S17_9_2: [5270.648] [?] S15_9_2: [5284.191] if it's, the different testing methods then [? reliability] will be different. the accuracy. if they are using a different testing methods then the accuracy can [?well] vary, but otherwise there's no [?] S12_9_2: [5285.461] [?] [5295.576] [?once] there is other factor involved, but what the factors, do not say if it's the environment if it's AFP, i don't know really. (2) ok let's move on. (12) : [5305.894] [ all finding right paper ] S14_9_2: [5317.134] this one? S13_9_2: [5317.642] yeah S17_9_2: [5331.364] and the counselling usually first, er in the patient information about the, disease or some [?] the [?] so the [?] about, something like that. so er, it's important for the patient or, the mother of the foetus, who will be the patient for, this one, er to have, an information for this one, er about spina (2) bifida which is, er involving incomplete form of er, of the spine. er usually it happens in the first month, of the pregnant. even before the mother or the women knows if she could be pregnant or not. er the causes as er, many of you mentioned, exactly the cause is not, known yet, but they believe there is, er genetic cause, or there are genetic causes and environmental, er causes. er, some causes, may involve like er the high fever during, pregnancy er, having some drugs, (2) or even sometimes if the patient have, er family er history, well, about the family history actually it's er, ninety five, or, approximately ninety five of the patient who has, who has er, Spina Bifida, they don't have, or they don't have er a, family history with this disease. (2) er, there are many types of Spina, Bifida, the mildest one is Spina Bifida Occulta, and the most severe one is Spina Bifida, mylomenim-menigoc S13_9_2: [5459.274] that one : [5459.972] [all laugh- nice/joining in ] S18_T2_9_2: [5461.397] that one S17_9_2: [5462.318] yeah, that one. er, the incidence of, er of babies with, Spina Bifida in around the world average, in the average is one, per one thousand births. (3) er people who is, who are in high risk, or at high risk, of having er baby with, Spina Bifida who are the siblings, of one, of patient, er (3) these are have, a high rate even [??] some sometime, (2) many patient of Spina Bifida have no family history, so maybe sometimes they (2) there is er [?] er, there are many tests, to find out if the mother if foetus, has Spina Bifida so mother, the mother may offer many tests like AFP test, er and that can be used between the sixteenth and the eighteenth weeks of her pregnancy, er other tests may also used, er, er (2) ultrasound (2) er, also amnioce- (3) S18_T2_9_2: [5555.089] amniocentesis [pronunciation] S17_9_2: [5556.683] amniocentesis. also may help to detect if there is a, a Spina Bifida,of the foetus or not. eractually they found er a link between er, folic acid for the mother, and having, this er, this disease, er, they recommend er, they recommend it is important to have er, doses of folic acid before the pregnancy. to get more more protection. [turning pages] (6) [5598.647] er, (2) actually we we cannot, tell any mother, or any er (2) pregnant lady if she will has, or if she will have a baby with Spina Bifida, er, because, as what i said ninety five percent of the patient, have no er, family history with this er, disease. (2) er the treatment actually there is no accurate, treatment for this one if it's happened, er when er especially the nerve system, is damaged, there is not treatment to or, to replace or, fix or, something like that, er sometimes the surgery is, important, to, to er to give the foetus or to help the foetus, if the, nerve system, did not damage. er, that surgery is often, used or the foetus have the, surgery in the first two days after birth. (3) er and if the foetus have, the Spina Bifida and if the treatment by medicine surgery, or anything like that, er there are many, percentage based on survey in the UK between nineteen sixty three and nineteen seventy one, (2) and, twenty years later, er the survey showed us fifty one percent of the patient have died, while thirty nine percent droven a car so they got perfectly healthy, they don't have any problems or health problems, er thirty percent walk more than fifty, metres, so may have a less, er healthier than, normal people. so, having, Spina Bifida is not, that, problem if it has accurate treatment or surgery at the first time or, er after the, so it maybe er, patient with the Spina Bifida, they might be, er completely healthy. if we have the treatment, (3) [??] (5) so that's that's, all any questions ? (6) : [5780.552] [all look down at notes] S18_T2_9_2: [5786.692] when when we, when we talk about the PBL, what we really should be doing is everybody should bring, the scenario, back to bring their report back to the scenario. so like say for example, S10's doing it for all the world, you can say well if because of this ethnic background, her the chances of, Spina Bifida etcetera would be [?] for that. i haven't got your [?] check you know, umm i think you could mention well she would get these tests done, and she could say, well this if your tests were high enough she would be offered? this kind of thing, and go right the way round, you S17 would be saying, that the the sort of, percentage risks that she would have is higher because she has Spina Bifida, you would be telling her that, in counselling. and that every one of you should be trying to bring it back, to the actual scenario, and eventually what you should really be doing is, you should have a page at the end, where, because this is a patient. the patient i've [?], the patient should sit you know she wants information, so there should be a sheet with right, this is what the patient, information that would be available, or this is what we'd do or, like last week there was a cytogeneticist, wanted to know how you did this, that kind of thing. always trying to bring back to the scenario, i know the [?] sorry S13_9_2: [5873.429] well they're kind of self explanatory, i don't really know what else you want me to say. em : [5875.906] [some laughter] S18_T2_9_2: [5878.259] well, you should ask the rest of your group the group what they think of it S13_9_2: [5881.922] i tried to choose, nice kind of warm colours rather than, [other laugh] cold colours that would like put them off so something that would like, didn't want to use red cos i associated that with danger, em and like yellow [?] associated with like toxic waste, [lots of laughs] S18_T2_9_2: [5899.761] oh well S13_9_2: [5900.641] i know especially the Spina Bifida one, i wanted to, include like a nice photo with like happy child not like say if you have a child with Spina Bifida everything's going to be all, horribly and doom and gloom. so i wanted a nice, kind of happy colours so that's why it's pink. [she laughs/giggles; others join] and, i tried to keep the language, em as plain English as possible but still be informative at the same time, and em, especially in the Spina Bifida one, i wanted to end on a happy note, so i was like the last sentence was more like to just er see if you've been given the outcome that your child's going to have Spina Bifida, ther- there's still a lot of people that have it and lead a, normal, life like you were saying [gesture to S18] S18_T2_9_2: [5948.087] is that M? [?] the medic here S13_9_2: [5951.199] and then, also, the information is pretty much what everybody else has already said. but on the back also, just to find some web sites and, stuff that, if they wanted extra information they could, ring people, or have a look. and in the testing one, i included the names of the, protein of the hormones that you are testing for just in case, if they wanted to go and, look it up and, (2) see if they, find any extra information, i don't know, what do you think? S10: [5989.614] fantastic S12_9_2: [5990.843] i think it should be an art course [laughter] S13_9_2: [5993.417] no i used to do art S16_9_2: [5993.955] [?] S10: [5995.542] go into publishing [?] S15_9_2: [5996.934] how did you do this? S12_9_2: [5998.334] ah em, Windows em Windows has templates, so i just used a template but i modified all the colours and, moved S15_9_2: [6004.890] [??] S12_9_2: [6006.859] Word and Publisher does it as well, Publisher has templates for them S15_9_2: [6011.165] what's that? S12_9_2: [6012.085] Microsoft Publisher, it's just another programme that some computers have S15_9_2: [6015.049] uhuh S18_T2_9_2: [6017.144] are there any any comments on the language, of the, or the photographs anything at all (2) S12_9_2: [6026.470] the language is quite simple, (2) and that's quite[?] S13_9_2: [6032.854] it's hard to start writing like, simple when i just wanted to start writing like nananna [laughter] (5) : [6038.183] [group laughter] S18_T2_9_2: [6046.674] well then [??] i think they are lovely, i think they would attract anybody [?] that without a doubt, very good, and they would, the only thing i would say is you would [?] but you would definitely want to leave the diagram out S13_9_2: [6056.517] that [6061.288] i just had a empty box, [?] S18_T2_9_2: [6063.449] yes uhuh, yes uhuh, but if you were pregnant and you saw that, that would because pregnant women, [??] [overlap] umm you would not have a diagram in like that because that would frighten, the life out of anyone, em, i think i love the idea [??] i think that's absolutely excellent to put that in, that is really giving hope, and that's what people under these circumstances, i would just have said there are S13_9_2: [6065.953] oh [6068.874] don't want to cause [?] stress [6091.525] lot's of [?] S18_T2_9_2: [6092.142] several different types, of Spina Bifida varying in, severity and, actually you wouldn't say in a leaflet [?] i would say, that you can't tell, because nobody's actually said that, here today S13_9_2: [6105.787] you can only detect the opening S18_T2_9_2: [6106.761] you can only detect it's open, you can't detect the severity of it, and that was something you should have brought up, but you wouldn't, i think you wouldn't want to say that in a leaflet, because you'd want a doctor to explain that. S16_9_2: [6120.128] i wrote it down but S18_T2_9_2: [6121.948] yeah. yeah you wrote it down but you didn't S16_9_2: [6124.358] i forgot about it S18_T2_9_2: [6125.859] i'm going to beat him up : [6127.099] [laughter] S18_T2_9_2: [6128.366] i'm going to beat this boy up [laughter] [??] i can tell, no, ahm, i i think ah, it's, [door opens] (3).. i know you really sorry we're not finished, [to people outside] ahm, i would say that, you have to fit everything in a certain amount, em, it's a very difficult thing to do, it really and truly is, to to say well, this is just going to have nothing about the disease which is [?about the condition ] which is a bit of a waste of time, but just how, how much do you leave out, i mean i mean i think it's [?] S13_9_2: [6161.232] how much do you leave out [6164.280] cos you still want to be fully informed but you don't want to terrify them S18_T2_9_2: [6166.661] informed uhuh. see what would folks say [?] um, your, if somebody, if somebody's read up on it before hand or somebody, there are people who will be so terrified, it's a bit like rabbits in the headlights, waiting, hearing this and nothing will be going in, so we maybe want a leaflet that they can take home and can read a certain amount. so that they can then, at the next visit. asking at, i think a leaflet has to give them enough information, that they can then ask, at the next visit. i usually find it, you know that that, but the screening one, eh i wouldn't, you wouldn't really mention, alpha feto protein. because the person in the street doesn't know what alpha feto protein is. a lot of people don't know what alpha feto protein is but what i'm saying is, em, (2) it's a (3) i don't know how i would (2) i don't know what the ones across the road look like, i haven't read the ones across the road that we've actually got S13_9_2: [6184.168] [nods] [6190.822] [nods] [6226.729] i've got a new born screening one but i haven't because i had it to see what kind of S18_T2_9_2: [6231.068] uhuh so do you see how they do it you know, it would be interesting to see what they S13_9_2: [6236.366] [shows another brochure)that probably more like the one for like next week but : [6238.422] [laughter] S18_T2_9_2: [6240.581] that's it [?] uhuh, erm, S10: [6242.962] she's M, i've [?] S18_T2_9_2: [6244.773] MT she was [?], S10: [6245.793] [?] S18_T2_9_2: [6246.753] yeah uhuh S10: [6247.454] [?] [very quietly spoken] (3) S18_T2_9_2: [6251.271] you know em, there's a lot of hope, in these ones and i think hope, not false hope, you can't give them false hope, but the leaflet's, a general thing. it's it's very much a general thing, not specific. [6254.791] but you're telling them, the tests are available. i went for a a job of doing these pieces you've made a very nice job of them, i think, they're very colourful very attractive, i like the idea of the wee boy's picture that's a chi- a happy child, [agreement nods and sounds]and that's, what you're looking for, i think that's excellent, i really do like that but i'd definitely not put any other pictures.[s13 laughter] S13_9_2: [6283.785] [laughs] S18_T2_9_2: [6284.403] you usually don't want that. as i say the pregnant women don't, they don't hear the same as, other women and they don't say, and words don't mean the same, and i can say that from total experience, this happened to me. i was expecting my son, took me in and in those days it was x-rays you got and the, a young doctor said, i think it's twins he. i thought oh my god [soft voice] i don't know if i've only another spare room, i was thinking you know, i've got my pram i don't need this, and this panic [?], and then, this consultant said, would you look at the size of that head (2) and i immediately thought oh my. [laughter] anyway i go, and i get the X-ray, and i come back. now bear in mind, i had worked in genetics at that point for several years. so the doctor says to me, you're not having twins. and i though oh. for [?] panic that i was having first to disappointed that i wasn't going to have [?] in that half an hour, and then i said i would like you to tell me the truth, am i having a baby with a big head. not [laughter] : [6345.430] [laughter] S18_T2_9_2: [6348.141] and he said to me, where did you get that idea from? and i said, you said it S10: [6352.819] yeah S18_T2_9_2: [6353.615] and he said, mothers.[she exclaims] and then he, i said you won't have two babies in there if one of them's that size. S10: [6355.676] yeah : [6360.841] [laughter] S18_T2_9_2: [6363.032] but that's not the that's not the [??] [laughter] [s13 that's not what you heard.] so mothers when you read these things, don't, they don't read the same as other people, i'm sorry, i've never [?] ? actually [laughs [??] week thirty nine S13_9_2: [6364.238] that's not what you heard. S16_9_2: [6376.500] so then it was a false positive S18_T2_9_2: [6378.870] no it was a young student, a young medical, a young medic who didn't know, his job very well, and, who had thought, i don't why he thought my one, son was a twin, and it was a S16_9_2: [6392.381] seeing double S18_T2_9_2: [6393.283] mm? see seeing double he might have been seeing double i don't know. anyway it was a, frightening experience and i must admit that i, so i'd say i'm very wary when i look at the leaflets but it is happened : [6393.283] [people packing up to go] S14_9_2: [6403.368] but it is happen S18_T2_9_2: [6404.809] umm? S14_9_2: [6405.319] it is happens sometime even, with the expert people. er, one day it is happen that a lady [?] tell her that she has twins, and in delivery she only has one child, the father outside shouting, i want the other one. : [6420.026] [laughter] S18_T2_9_2: [6422.603] [?] S14_9_2: [6424.317] yeah. it is just [? diagnosed where is take us to it ] S18_T2_9_2: [6427.015] well [??] down the stairs who works, she works in the screening, place and em, she had the baby and they said there's another one, she didn't know she was having twins, you know, the thought and in olden days when they didn't have all this high risk investigatory equipment, but anyway. ok. S12_9_2: [6447.452] ok S18_T2_9_2: [6448.283] right you are, em, we will have our meeting next week we're in the lecture theatre, and as i've said to you, that you'll be ahm, PowerPoint time next week, ok i'm looking forward to that tremendously, i like a wee film show, and i'll give you my em, i'll bring in a video camera, S13_9_2: [6469.422] oh no S18_T2_9_2: [6470.004] oh yes S16_9_2: [6470.684] so you S13_9_2: [6471.624] why? : [6472.297] [laughter] S18_T2_9_2: [6473.106] Youtube. Youtube, they're going on Youtube. : [6475.949] [group laughter] S18_T2_9_2: [6477.979] [??] and the annoying thing is, i let you S13_9_2: [6481.495] watch yourself back? S18_T2_9_2: [6482.320] yes S13_9_2: [6482.801] ah S18_T2_9_2: [6483.400] so that you can see, your S13_9_2: [6485.381] how terrible i am S18_T2_9_2: [6486.293] no no no so that you can look and say oh, that was good but, i'll do this better, or you can say, i don't need to improve i'm perfect.[laughter] that's it ok? right you are. yeah i'll i'll put it down again in a wee bit yeah. i don't know whose it is : [6486.293] [laughter] [6494.224] [laughter] S16_9_2: [6494.299] should it be S13_9_2: [6500.003] i don't know who that belongs to S18_T2_9_2: [6502.160] oh is it yours ? oh sorry. right ok. right was that all right for you today we were a bit late [to O/C] : [6508.637] [O/C thank you very much ] S18_T2_9_2: [6509.787] uhuh. right. very interesting talks i think uhuh. nice light reading for the weekend. i'll do my best again, this time i mean i tried to send out the report last Sunday, a six o'clock i sent them out, they all came back. at ten o'clock i sent them out and they all came back. and then on Monday morning, i sent them out and they all went. but i did do them on Sunday. you know. you're not supposed to work but [6536.566] at home S16_9_2: [6537.971] well maybe S18_T2_9_2: [6539.386] not [??] i sent them to myself because i'd already written them, and there's no way i was going to come in on a Monday and do it again. and it's not my own computer it's the university one. so i'd sent a n e-mail to me, and i got it, [?] cos i thought even if i send it and it comes back, it'll be in my sent folder i'll be able to use it [?] come back to me. oh S17 can i have a wee word with you S17ok? S24_T3_10_2: [5.707] ok S19_10_2: [6.373] [?? S6] S24_T3_10_2: [7.565] ok thank you [9.018] that's fine thanks S22_10_2: [12.485] S2 give me one for S6 S2_10_2: [14.344] here's one here S22_10_2: [15.774] ok [laughs] S20_10_2: [33.369] [?] order S24_T3_10_2: [35.637] did everybody get their feedback? S2_10_2: [38.071] uhuh S24_T3_10_2: [38.617] because i've sent it from home and sometimes i have [?] S2_10_2: [40.701] [?] [41.941] [?] S24_T3_10_2: [41.941] uhuh, (4) my husband [laughs] S4_10_2: [42.499] [laughs] NOTES: [43.889] [group laughs] S22_10_2: [48.840] are we doing presentation? S24_T3_10_2: [50.554] i don't know are you? S22_10_2: [51.264] uh huh, yeah S24_T3_10_2: [52.563] well all i know is i i said said, i, i need to get the staff to - in here to work this that's why i said if you let me know the day before because they S22_10_2: [60.906] oh sorry S24_T3_10_2: [61.780] well let's, i usually ask permission to use the equipment because it's no ours, i'll ask the secretary but, sometimes it's a faff but i mean i certainly can't help you to put it together i'll tell you that just now [laughs]. em, i'll ask would they mind ok? just cos it's not our department so it's em S22_10_2: [78.800] ok S24_T3_10_2: [80.141] are are there's only one of you presenting? S22_10_2: [82.582] i don't know S20_10_2: [83.411] yeah [nods head] S23_10_2: [84.254] yeah S4_10_2: [84.295] yeah you can get [?] NOTES: [85.558] [group laugh] S23_10_2: [86.328] [?] (25) NOTES: [87.088] [s24_t3_10_2 leaves room] S24_T3_10_2: [112.915] do you want them to kick off S22 since it's getting set up just now? S22_10_2: [116.425] ok S24_T3_10_2: [117.185] right [?] so. (3) does that mess up the plans? S23_10_2: [122.091] no she's second S19_10_2: [122.492] no S20_10_2: [123.002] she's second S24_T3_10_2: [123.833] oh well she ok well whatever ok but once it's set up though you can [??] S20_10_2: [127.732] [?] (4) S22_10_2: [132.948] you can start S4_10_2: [133.896] is it, oh does it go on there? [gestures to data projector] S23_10_2: [134.237] [? start] S24_T3_10_2: [136.386] uhuh S4_10_2: [136.917] oh right ok S2_10_2: [137.487] what things? S24_T3_10_2: [138.767] i don't know (5) S21_10_2: [144.528] ok you can start NOTES: [146.090] [some slight laughter] S20_10_2: [147.031] take it away S23 S23_10_2: [148.144] all right so, we'll start with the screening for, the screening for the [?] for CF, so the main, the main [?] i think for for the marker that is used for screening of the CF is immuno- immunoreactive trypsinogen or we say IRT for short. right so we can use IRT is an enzyme produced in the pancreas and is generally higher in, er the babies, with CF, yeah? than those without it. so this used as a neonatal marker for screening. so this used as a neonatal marker for screening. and basically how they –how they, measure this is lead to getting heel prick and get a blood blood spot onto the Guthrie card this a dry blood spot test using it. and you around five days of the first week you get this blood spot and, you're tested for the initial [?].and later, er although the tests is quite sensitive, but this have a low positive predictive value so that's why they will follow with the second –the second IRT test normally, and why they use the IRT test is because, er for the babies with CF the, the level of IRT will remain high. while the normal baby will go down. so it's a good indicator so that's why they use they have a second IRT test and [?]. so now we're going to, er the test actually. to er, neonatal CF screening [?involved]. so er, the first one i would say the IRT IRT screening protocol, which is a non DNA, non DNA one [?] no DNA is involved. so if you look at the first figure, er the first one is definitely to the initial IRT test and there's, looking at the, level of IRT. so if it's lower than six- sixty nanorams of of [?] other will be reported as low CF was suspected. but if there is you can say down to a, series of tests, so, if there more than sixty milligram per milligram per [?ml]], you you've first got to check recheck [?] duplicate the check the result is correct. so if it's, still high and, normally you would think above seventy milligrams per ml, then it will be followed by a second IRT test that just i want to tell you. IRT test the second IRT test performed by ah, between the seventh day or third or forth week you get a get a blood from the baby again. because the IRT will form so fast as the normal baby so that is why it's a good indicator. so they will be followed by a second IRT, if it still give –give a high -a high reading, then a sweat test is followed. a sweat test is followed, as a more more [?]. in here a sweat test although we know it's a bit of diagnostic because but it's still considered under screening for in this protocol. so if you got negative definitely the report will be no no CF suspected, but if it's, a positive result the first you got to, report as high risk and give genetic counselling. so if you got negative definitely the report will be no no CF suspected, but if it's, a positive result the first you got to, report as high risk and give genetic counselling. and, but first the report will be given to to [?] to the patient and, and there [? wife] so the CF physician and, child child health GP and the hospital which i think puts more in the [? UK side?], that's what they need to need to [? ] report to the reporting system here. so basically that's a non DNA test. so er this test, because it's followed by the sweat test that's the good the good thing about it is ninety per cent detection rate and zero point three per cent positive rate. so this is, and here then when you do this there is no worry of getting a carrier status. so that's maybe will arrest the problem of of the of the issue that the parents may have if they don't know any DNA results. so this is er as an alternative then. because this is not a for this test this is not a first test that you would do. normally they would do a second test which is DNA screening test, so ah we got to the point two which is screenings IRT slash DNA slash IRT test. right. so, basically this, this almost very similar similar to the IRT test. just ah we can look at figure two [referring to handout] it's easier i just read it out or you can [?]. so, the first thing [?] is the same thing then you had this initial IRT test. it's the same as the previous one. and this one [?] test high level of IRT, then they will retest duplicates. before they but before they get the second IRT test done, they will use the initial blood test er blood [?] spot for the DNA analysis, which is using the ARMS. and, the latest one that i i found is the DNA analysis is around fifty mutation they they have. but i i'm not even going into details of what the mutation is. so, basically once the DNA analysis is done for the common fifty ah mutations, it can be can be broken down into three categories. one is like the er if no mutation is detected, er one mutation is an indication of possible carrier or even a possible er CF patient if, if the mutation is not found in, in the, fifty fifty the mutation screening. another one is to have two mutation. two mutation is diagnosed so it's a [?]CF case. so for all of this if no mutation, is detected for normal one we say one Caucasian cos the fifty mutation is, er mostly the commonest mutation in white Caucasian population. so that's why if you have no mutation in one Caucasian population you'll most probably report as CF is not suspected. but because they're, we know that er mutation for CF there may be other types of mutations, in other ethnic group, so if this test is done on other ethnic group, further tests have to be done. and what's the further test it will be followed by the second IRT test. so er, that will be the same if you if one mutation is found it will also be followed by the second IRT test. all right? so with the second IRT test, this it will be similar it will be similar to the previous how the reporting goes. [10.11] if er the second IRT test, the level of the IRT is low, is low this you will be CF will not be suspected. er but genetic counselling will be need to be provided as we see, as we see for the carrier status in the carrier status may be found, because if you have one, one category's one mutation has been found, so this is what we need to discuss about. but if the second IRT test if the level is high, we [?] followed by a sweat test. this include in in the box that is ah i didn't write up. here it ah show that there's high risk of CF, and, it's doing, there's a genetic counselling also carrier status needs to be discussed. for the two mutation one this common CF so this need to be reported to see a physician child health GP in the hospital. so, so these are the two tests and ah the, the, the good thing for this DNA DNA screening test, er because this been confirmed by after you've done it and you've been confirmed by the sweat test and the second one, the detection rate is ninety five percent. and it can go up zero point five, zero point five per cent false positive reading. so this actually optimise the detection and the false positive rate, and minimises ah repeated sampling. and also, also minimises incidental identification of unaffected heterozygotes which is the carriers. so, this test has this benefits actually for [?alternative] but, we know that some people's concerns are not don't want to know their carrier status. so, so, i, the last one i put a statement that er patient case if a patient considered not to have DNA test on the baby, non DNA, screening for the IRT IRT test can be done can be offered, for those who don't want to have carrier status being test pick up. so this is the alternative test that er, we we may offer to the patient if they don't want the DNA testing to be done. so i think i'm done for [?] S19_10_2: [736.380] have, if that's true you with this protocol you don't test the DNA but, if we get to a diagnosis of Cystic Fibrosis we know that they are both carriers anyway. S23_10_2: [748.063] yes S19_10_2: [748.853] so what's the point? i don't get it [looks round the room, smiles; some laugh] S23_10_2: [751.774] well i think i think for the point that um, i agree with S19 really because once the sweat test everything's done. you know it's it's a CF carrier is definitely in the kid the parents. if S22_10_2: [764.642] but could it be like one par-parent is carrier and the second mutation is S21_10_2: [770.842] yeah, can be S19_10_2: [771.885] well could be, rarely but could be you are right. NOTES: [775.745] [some laughter] S22_10_2: [776.168] that's why they don't want to, i just have a question about why second IRT test is done on twenty seventh day, S23_10_2: [779.424] yeah [783.682] yeah [s23_10_2 nods] S22_10_2: [788.601] how something like IRT levels change after this day S23_10_2: [788.601] uhuh they [791.954] no bas- basically they they will say that a generic day is er three to four weeks. three to four weeks but ah, twenty seventh day is i think what a cut off date they put in. because this in the literature ah some people they don't give a definite day. a definite day ah this definite day i got it from the lecture, but it's a cut off. but, for some of the literature there i got this they mostly say four to three weeks i think this is so, give, as we know the [?] is very brief and er, it's not called midwife what is it call- the S4_10_2: [828.788] the health visitor S23_10_2: [830.208] the health visitor to to collaborate so and this, it's called [?wife] ah, ok, they go and collect it so, time must be given to them. and actually actually for the IRT rate er basically, it's produced in the pancreas and for CF patient there's also been reported that the pancreas i think er function, also decreases. so because er i think i my- my suspi-suspicion is that IRT when it's produced it's not being degraded it's not being going to be degraded by the pancreas or something, so that's why it's high. this is my assumption, this is my sus- suspicion, i'm not hundred percent sure, but according to some that this the pancreas this the function is not that well and this level, of IRT is still, high for the CF patient my suspicion is this can't be broke-breaking down by maybe the pancreas. so that's why it still remain high in the, in the baby and, and maybe around three to four weeks time so it's a good indicator. because maybe when the baby was born, when it's born, er in the first first week maybe it hasn't really broken down enough to make it low, so as times goes by the normal baby will have, lower IRT compared with the CF babies. S19_10_2: [831.794] so midwife S21_10_2: [868.490] ah so after [915.676] but after the twenty seventh day the [?range] yeah S23_10_2: [919.266] will go down S22_10_2: [920.342] ah it is reduce S21_10_2: [920.968] S23_10_2: [921.034] it will it will reduce S21_10_2: [922.264] so after the twenty seventh day you cannot do the test S23_10_2: [926.714] till the twenty seventh day S21_10_2: [928.184] yeah you can [?] S22_10_2: [928.615] [?][?] if it, it's reduce after twenty seventh day then it is not something, related to pancreas because S4_10_2: [935.924] maybe [?] trying to standardise it so that [?] protocol [?] to follow. you now they might want to just, does that make sense? S19_10_2: [936.827] yeah [942.534] ah um S22_10_2: [944.285] ah i think the, [?] S4_10_2: [945.286] i suppose you get guidelines, and follow the guidelines and take everything [?] and then compare it in a sort of [?] i suppose? S23_10_2: [951.881] yeah and nothing for normal blood testing, like for testing [?a guideline] to be done and especially if they, they know that the levels that, definitely the levels will go down. because like if you see the, [refers to handout] if you see what i have written here, the second [?] bit retest in duplicates is higher. but for the second for the second IRT it's still sixty. so actually they they i think they have condense it a bit for the dropping, of the the IRT level, but, er in a sense, this is still a high level for a a period of time. but first maybe if you the longer you go, the the level be lower but there's no [?] be a cut off but i think, er the the twenty seventh day or maybe the twenty forth is a good time, if you if you have confirmed the the [?child] then you can do with the treatment and management will more effective rather than waiting for it to be [?go] at a longer period of time. S22_10_2: [972.978] yeah [981.460] uhum [1015.303] just i want to er clinical features of CF S23_10_2: [1018.958] ah we S2_10_2: [1019.586] i did S20_10_2: [1020.008] you did it S22_10_2: [1021.038] ah ok. so then i will ask that question later NOTES: [1023.878] [group laughter] S2_10_2: [1025.159] oh no S21_10_2: [1025.957] come, come now prepared S24_T3_10_2: [1032.147] ok thank you. thank you S23. NOTES: [1032.147] [looking through papers for next speaker ] S20_10_2: [1034.577] ok (7) [1042.857] ok s22 its you S22_10_2: [1044.538] ok. do you have my PBL problem i forgot mine i just want to [?] numbers [to s21] ? S21_10_2: [1053.311] someone has got PBL problem S23_10_2: [1055.873] what's [?] S24_T3_10_2: [1056.333] [?] the problem? S21_10_2: [1057.069] yeah yeah [?] S19_10_2: [1059.699] ok? S23_10_2: [1060.981] this one? S22_10_2: [1061.551] yeah. [1076.594] ok? this is S6 and, my part. the i'm going to talk about ehm assessment of the CF screening, this case. em just briefly i want to mention what's ah important in choosing screening tests. um their requirements for the this programmes like choosing to screen for which disease, detection of the disease, ah which sensitivity and specificity of the test and interpreting diagnosis and screening test, and finally predictive values.[new slide 19.1] ok? population screening, why we do screening because we want to find out, er what the part, which part of the population are likely to develop disease or not likely. and, the main objective here is to reduce mortality and morbidity. [new slide] and requirements for a screening programme, first we should choose which disease to screen, then we should have suitable test for screening. then we could should have suitable programme like when they find affected people how we're going to [gonna] manage this er, for the diagnostic tests and treatment. and good use of resources like [new slide] screening tests shouldn't be so expensive, because it's like ah covers all population. and suitable disease, [referring to the new slide] like we should, should know the symptoms of the disease, or the environmental markers which with which we're going to test ahm find out the affected people in this population. [new slide] suitable test should be, safe accurate, acceptable with all members of this population and of course cost effective. [new slide] and suitable programme, as i said quality of control testing, follow up and efficiency of the test is important. [new slide] and good use of resources, cost of treatment, cost of screening tests and follow up diagnostic tests, and the most one of the most important points benefits versus alternatives. when we do the screening test em, we should have objective points how we're going to [gonna] benefit from this screening test.[new slide] ok. then, screening test we choose should be reliable and valid. like as we should get the same result each time, and er we should get like correct one of course. and the sensitivity and specificity of the test are the parameters er, which er management of the screening test will look at. sensitivity of the test is, the test that correctly classifies cases, which are affected with the disease. specific test er means, correctly classifies non disease cases. like em how er our detection test chose the affected people and not non affected people in this population.(4) [new slide ] and here is the, how we calculate the sensitivity and er specificity. as i will talk about then them i put numbers, in our case. (3)ok [moves though some slides] ok so this is screening test screening population, em [looks for something] this is not population. ok we have got em one population we [? have got to] screen and this in this population em people in our highest group and lowest group. people in our, highest group which are like, you show, er you see they're positive [refers to slide]. this group is consisted on true positives. and false positives. which equals A plus B. and er people in our lowest group, which are er negative in the result of this screening test, in that group we have false negatives, and true negative. ok when we calculate the sensitivity of the test, we just it's a ratio of true positives, to the all cases. em, just in layman terms i understand it this way, sensitivity, em means how, ah how successful was our test, to detect, the er cases, like er affected cases in this population. if you look in our, screening test it says like er number of, screened babies were, fifty two thousand four hundred and fifty six [referring to notes]. and from this, three hundred eighty two were in, had raised IRT and were in high risk group, so the number you can see three hundred [points to slide] er eight two is, the number of people in high risk group, and in low risk group we have, like total number minus, a high risk group which equals fifty two thousand and seventy four and in positive group it says, em DNA mutation analysis for CF of this group identified eighteen infants with two mutations, so in this group we have eighteen affected people in high risk group, and further twenty nine with one mutation. twenty nine with one mutation means they were carriers. and then there are sweat test performed in this group and just em (2) two of them gave positive results. so affected people in our eh high risk group will be twenty. eighteen plus two, the ones that gave positive after were positive after the sweat test. so as a positive em true positives we put number twenty, and of course three hundred eighty two minus twenty which equals result three hundred sixty two will be number of, non cases, like false positive cases in our highest group. is it clear? S21_10_2: [1489.382] yeah S22_10_2: [1489.743] [?]. ok. and one says like em (3), one we had negative, how did we get that? [looking at notes and slide, laughs ], em (4) false negative and ok in our negative group, em because em (5) em it says over the next few years one child in the study [?] is normal IRT in the screening who subsequently diagnosed with CF. so just only one person from our negative low risk group was diag- later have CF, so only one case em we had only one case that we could we put in low risk group but in fact this person was affected. so that will be false negative, we had one and true negative we had, fifty two thousand seventy three. and now we will calculate the sensitivity of the test, which equals to the ratio true positive to all cases. which equals positive ninety five per cent. and specificity of the test, er will be at ninety per cent. ninety five per cent means like er, in this screening population in fifty two thousand four hundred fifty six babies, our test could detect ninety percent of affected cases. that's sensitivity of the test. and we could detect ninety nine per cent of, non affected cases in this population because we miss just only one case, and so our specificity will be very high ninety nine per cent. [new slide] and when we have to interpreting test results, its about predictive values. positive and negative predictive values. in simple words positive predictive value means how successful was our test in erm high-high risk group, negative er predictive values means how successful was our test in low risk group. so that's why [changes slide back to first] to find that we divide true positives, we calculate the ratio true positives to all positives. so that will be and negative predictive value will be ratio true negatives to all negatives. so this is em like er positive predictive value and negative predictive value is our terms that defines low risk group and high risk group, but the previous sensitivity and specificity [?] is about the whole population in this screening. let's look at our numbers. so our- we have true positives twenty, and the number of all – total number of people in the high risk group was three hundred eighty two which equals uhm five point two per cent (2). so our test was five per cent er five point two per cent successful in high risk group, because we have many false positives and only five per cent of them were really positive. and negative predictive value was ninety nine, per cent because, em in our low risk group we really had, like ninety nine per cent erm real negatives but we had only one case which later was to be found er affected. so that's why our negative predictive values were about ninety nine point ninety nine per cent.. that's it any questions? S19_10_2: [1489.963] yes S24_T3_10_2: [1738.714] thank you S22_10_2: [1739.462] if someone didn't answer er didn't understand any of the numbers i put here, just ask (10) last of this um i forgot to mention because i had to calculate incidence of the C- of CF in this population, that would be number of the ratio of number of all affected people of in this population to the number of, total number of people in this group, which we had twenty one people affected people, uhm, (2) ratio to fifty two thousand four hundred fifty six will be one in two hundred er two thousand four hundred and ninety eight, so nearly one in [?ten] thousand is the same incidence in the screen population (2) [1794.456] ok S24_T3_10_2: [1795.357] thank you S21_10_2: [1796.338] thank you S4_10_2: [1799.593] [?] S22_10_2: [1800.453] is ev- everyone understand what's like sensitivity? S24_T3_10_2: [1804.263] you obviously did a very good job explaining it S22_10_2: [1807.043] yeah i, i tried to explain it in the way i understand it. then I don't know for me that's er easier S24_T3_10_2: [1814.652] this is the sort of thing that can come up, in an exam S22_10_2: [1818.271] yeah. it will come up in the exam yeah S21_10_2: [1822.530] yeah S24_T3_10_2: [1824.545] so it's it's good if you do understand what to do with the figures that you're given S22_10_2: [1830.824] no questions ? that's all? S20_10_2: [1833.500] yep S4_10_2: [1836.305] in my part i was going to talk about [?] what (15) [change over to next speaker; getting papers) [very quietly spoken] general principles in medical ethics are also applied to newborn screening. em the right to choose do good do no harm to be fair. em i think the guide the guidelines sort of [?] seem to come from em or are adapted from from a paper that's done nineteen sixty eight it's been issued by WHO, as in world health organisation. [laughs] and ehm, it's based em on em for chronic for screening for chronic disease. and it seems to have been adapted from that. em, so the right to choose, from what i read it seems to be a bit kind of different in different countries, and in America, eh i don't know if i've picked this up right it was mandatory to ehm the screening for PKUs so because of the benefit to the child who was ehm [?at risk]. but i don't know i think that's right anyway. but generally it's the [?] parental consent that ehm is em is needed. em the benefit is it obviously do -do good. so em [?? [speaks very softly and quickly] which is order there should be facilities available to diagnose and treat the disorder. ehm it might not mean that the lifespan person might be increased but they might have a better quality of life by [? having] diagnosis. em in america they seem they seem to do a lot more testing than we do. i think you only screen [?] or something like that but they screen for twenty nine disorders and with sort of twenty five additional secondary disorders. and em, i think for a lot of the secondary ones there there isn't er much actually treatment available so that there's kind of a question about the ethics front ethics - ethics there i suppose because, they can't do anything to help. but i think it is sort of argued or suggested that because they can find out the natural history of er rare disorders by identifying those affected earlier on they can find out more about it so it's a bit kind of, [?] [ 33.32] em (3) it might- it's often in some cases, (2) there's sort of like new technologies coming along like microarray and things like that and em the tandem mass spectrometry , which can identify a lot of the disorders. and there's some sort of em issues that although it might not, benefit the child, ehm and they might die anyway, it might be of benefit to the parents to find out if they're carriers, and if they can make reproductive choices kind of thing. em.(4) parental anxiety and things like that. the paper that S23 found it's a wee bit it's a bit old at nineteen nineties and i think it's before em the molecular em tests [?] and ehm but one of the issues that was raised there was from the initial screening to the final diagnosis em there was quite a delay in time and that caused a lot of parental anxiety and em in some instances i think the the mother sort of kind of almost rejected their child in that period [?] (5) [turning papers] and in terms of justice or fairness i think that it's all about the cost should be weighed up- weighed up the benefit to the cost and it shouldn't take resources away from other ares of the health service that could potentially em, more people could benefit from, other screening programme programmes. (3) that's really about it. any questions? S22_10_2: [2099.495] ahm yeah. do you [?say] like microarrays are also used in screening S4_10_2: [2103.335] they're not used but they're sort of questions about whether like S22_10_2: [2107.322] because they are expensive why [?] S4_10_2: [2108.981] uhuh but if in the future maybe in the future they might get used because you know as new technologies come along they start getting cheaper and cheaper S22_10_2: [2116.127] oh ok i see S4_10_2: [2117.418] you know that, ad- advances are made. and that kind of thing, but it was just questions, em there might be issues there as well because em, it could identify carriers, and that puts excess burden on sort of health services and resources because if they would need potential counselling because you've identified them as carriers. S22_10_2: [2135.343] uhuh S4_10_2: [2135.903] so you you're not treating somebody that's going to be ill but it's all about because you've identified them i suppose you've got a responsibility S22_10_2: [2141.685] ok yeah. thank you. S4_10_2: [2144.636] anything else? S20_10_2: [2145.486] i think i've a random question [laughs]. see how in America you have to pay for your health care, S4_10_2: [2150.984] yeah i S20_10_2: [2151.384] that [?would/wouldn't ] pay for screening? S4_10_2: [2153.035] i don't know because it said in that paper that i read it said when it, PKU screening was introduced it was mandatory so i kind i assumed that it was all children must have been automatically tested. the paper also said about i think [?] [looking through papers] where is it? sort of like there are bits later because eh, there wasn't a sort of uniform, sort of screening procedure like you saw it wasn't, or or because they can treat some of the diseases and they were screening for them anyway and and you know there was issues there, but yeah i i don't know if they can understand S20_10_2: [2163.138] yeah [2188.721] so if it's mandatory but if they're like, if they don't want to pay to get it done then surely they S4_10_2: [2194.497] uhuh [2195.935] but i'm assuming that there must be some sort of some some S20_10_2: [2198.121] yeah [2199.452] maybe it's yeah S4_10_2: [2201.204] some things are done [group laugh][? ?] just because it said it was mandatory S22_10_2: [2207.229] i don't, do people pay for screening tests? S24_T3_10_2: [2211.208] here? no S4_10_2: [2211.780] here no S22_10_2: [2213.670] oh S24_T3_10_2: [2215.182] however did you see what was in the the papers this week you can get your own DNA kit for doing, paternity [nods] S20_10_2: [2222.594] oh yeah S24_T3_10_2: [2223.214] so see that is the sort of thing you're starting off with paternity there but you can see if they produce kits people could be doing tests, like for things like like it might not be that accurate but they might be misleading to them and there you're opening up a whole can of worms really S22_10_2: [2228.526] oh S4_10_2: [2230.833] yeah [2234.274] [?] S19_10_2: [2236.731] might be NOTES: [2236.793] [aside starts not all audible] S4_10_2: [2239.926] [?] probably it's really for follow up what you've found in [?] kind of tests and they're [?] i don't know S24_T3_10_2: [2245.219] uhuh [2246.685] uhuh [2247.859] i mean a lot of pat- we used to do paternity tests in our department and the it all kind of became private because it was people were, em, you know they were just demanding paternity tests for other reasons and it was obviously a cost to us. so it's private but i notice just having read this that the company i think the kit that's being produced, you know the-when em ST gave the talk about Fragile X and i think Asuregen i think it's the same company that they're obviously produce now that's just to get your DNA tested for paternity but, they won't stop there, because where there's money to be made. [laughter] S4_10_2: [2261.255] yeah [2274.546] uhuh S21_10_2: [2287.360] yeah S24_T3_10_2: [2287.461] i'm sure S22_10_2: [2288.403] how- how it's possible how it works like S19_10_2: [2290.093] well S24_T3_10_2: [2290.799] well i don't think it gives just S19_10_2: [2291.598] just [?] samples that you need or what? [?] NOTES: [2291.905] [S?] that [?might]] S24_T3_10_2: [2294.703] i don't it's twenty nine ninety nine but [laughter] but but wait for it wait for it it's a hundred and twenty nine for the lab to process it. NOTES: [2297.797] [laughter] S19_10_2: [2304.323] ahh S4_10_2: [2304.323] right so they take a sample and then send it away S22_10_2: [2306.306] uhuh S24_T3_10_2: [2307.014] but i don't think it'll S19_10_2: [2307.104] hah S20_10_2: [2308.640] that's just [??] overlap inaudible] it S19_10_2: [2309.501] the three [?] S22_10_2: [2309.623] just [?] S23_10_2: [2311.674] you were saying, [?] S19_10_2: [2312.115] yeah well S4_10_2: [2312.761] [?] S24_T3_10_2: [2314.752] it's to listen to it says that the the sample collection should be left to the punter [reading from paper] that means the person. because this is just a tabloid S4_10_2: [2321.981] is it just a oh is it swab or something they take S24_T3_10_2: [2324.330] don't know it doesn't say i don't think S23_10_2: [2325.569] i i, i remember two years back there's one er test, they're saying that they're trying to produce a kit that a mother can pick up own blood so because we said-remember we said that [?] the maternal blood. so they are trying to get the foetus cell to detect [?] diagnosis to really find out the sex of the baby the foetus S22_10_2: [2348.407] like sometimes if, and special times if these cells get into water or when S23_10_2: [2353.225] no because like we [?] saying that we can in the maternal blood can get [?] cell S22_10_2: [2357.035] yeah S23_10_2: [2358.215] right so based on this theory they don't go for, er like mothers who don't want to go for er, to really know [ ?] ultrasound we need to wait until a certain term right, before we can see features also must be [?] the foetus able give you the right position and in order to find out, S22_10_2: [2376.422] yeah S23_10_2: [2377.044] so, some, there's there's a test that they're saying that you use this to get the maternal maternal's, blood and then then maybe some foetus cell and just using that, wee little bit of, of foetus cell will they just going to find out the chromosomes you know the X and Y for you and then you know the the sex of the baby. yeah because like i know like some people, i know it's not very ethical but some really, really would know want to know the sex of the baby S22_10_2: [2409.158] yeah it's a big issue in my country like S21_10_2: [2411.685] also in my country S22_10_2: [2412.791] yeah its really S20_10_2: [2413.160] really? S19_10_2: [2414.060] they all want boys? S22_10_2: [2415.301] i don't yeah i they all men they just want boys? [laughter] they want sons S23_10_2: [2415.301] yeah S24_T3_10_2: [2419.342] but is it a isn't that part of the, culture because sons obviously aut- i mean S22_10_2: [2423.357] yeah it's [?] S19_10_2: [2425.200] yeah yeah S20_10_2: [2426.020] ah yeah S23_10_2: [2426.020] yeah S24_T3_10_2: [2426.695] i mean you see well i suppose we should as well i you see [?] as sort of dominant [laughter] yes so they em i suppose they kind of want to it's almost like a hierarchy isn't it that they [directed at s22] S22_10_2: [2438.758] maybe S21_10_2: [2439.119] yeah S4_10_2: [2439.343] or is it a sign of their virility that they can come [laugher] S22_10_2: [2442.729] and, and the problem is that they always like, families for example [?] S24_T3_10_2: [2446.994] they carry on the family well i don't know if that's the same in your S22_10_2: [2448.791] they accuse women in it like if she just has daughters and daughters and they accuse women in it [laugh] S24_T3_10_2: [2457.109] but then if you have but then i suppose it's the same it's the same i suppose in some cases maybe years ago here because obviously well i don't know in your case but a son carries on the family name but a daughter doesn't really cos you're marring S19_10_2: [2458.429] that's just the sperm S4_10_2: [2459.849] yeah [?] [2469.827] i don't think over here it doesn't matter so much things like that. it isn't an issue S21_10_2: [2470.053] well for us no S20_10_2: [2471.964] no S21_10_2: [2472.676] no for us no S24_T3_10_2: [2474.228] no it's not S21_10_2: [2474.888] well the daughter carry nam-the father name S24_T3_10_2: [2477.160] ah right ok. so they carry the father's name right ok. S22_10_2: [2477.715] yeah all all kids carry the father's name S21_10_2: [2480.111] yeah all kids yeah S24_T3_10_2: [2480.985] but even when you get married S22_10_2: [2482.507] but when you get married you can you can change it or you can decide not to change S21_10_2: [2482.569] yeah. but i don't change my name S19_10_2: [2484.739] we don't either change. we don't change our our surname when you get married you don't change your name. S22_10_2: [2488.344] ifif [2491.225] ah but it's a choice like do you have a choice [to S19] S19_10_2: [2494.132] [nods]. we don't S24_T3_10_2: [2496.774] but that this this is the sort of thing that's the kind of thing even about this woman here obviously going to the clinic it might well be she's saying she doesn't want her DNA tested because S4_10_2: [2505.007] well and yeah some of the [?] issues were about DNA testing what would happen to the sample afterwards. i think there's a [?]. just that you know S24_T3_10_2: [2513.484] but also if it if it raises the issue of, we used to do huge pedigrees years ago when we did lots of marker analysis, and for the medics who got to know the families that was always a huge issue so there's non paternity, and, i mean that's the thing i suppose as well about counselling because the the the doctors get to know the the families and they can usually, for us in the lab doing the large pedigrees they used to be able to say i'm pretty sure that one's not, you know she -not the father but it will come out eventually you know S20_10_2: [2541.632] no S4_10_2: [2543.465] do they not em do that though, do they not is there not something that if something is getting tested it can also be, when they take a sample do they not say something about this girl's [?] tested for paternity or may [?] S24_T3_10_2: [2554.005] if i think the problem poss- i don't think they probably explain the clinic maybe if may-if the general public don't realise when the sample's being taken for so-[?] obviously for genetic disorders that that could be highlighted so it possibly is explained to them but i would imagine it would be which would then obviously if the mother's got any issues obviously it will trigger off and she might come back and say could i have an appointment on my own or, you know and that's, you know for these reasons it throws your pedigree right out of course but, [laughter] if daddy's not daddy so S4_10_2: [2556.507] [?] test [2578.749] yeah NOTES: [2587.675] [some laughter](7) S19_10_2: [2592.706] well yeah to realise he's not the father that's why you don't want to get, a DNA test. S22_10_2: [2598.543] that could be the reason, yeah S20_10_2: [2600.474] uhuh S24_T3_10_2: [2601.554] there's all sorts of reasons but yeah that could be something as simple as that S21_10_2: [2606.314] ok S20_10_2: [2608.215] ok. S21_10_2: [2608.789] ok S20_10_2: [2609.499] S21 S21_10_2: [2610.699] ah me? S20_10_2: [2611.221] yes S21_10_2: [2612.602] ok. ah i'm going to talk about the diagnosis of Cystic Fibrosis. first of all ah i'm going to talk different methods to detection ah, Cystic Fibrosis. ah actually, there are many different methods, er according to the mutation is known or unknown. er i put it in a table to make it simple. erm, for the detection of known mutations er ARMS reverse dot blot or RFLP, can be done. and erm, the advantage and disadvantage of each of them, er first of all ARMS um is it um is appropriate for large series and can detect up to twenty mutations by multiplex. but um, the main disadvantage of ARMS is uh, difficult to design the primer. er reverse dot blot, also it's uh useful for large series but eh, and also can detect up to twenty mutations, by multiplex. RFLP er useful for cascade carrier testing in case of rare mutations, but the disadvantage erm small number of the mutation can be detected, and sometimes not specific. er the others methods for detection unknown mutations um, QF MPCR em, that aiming to detect all deletions insertions and duplications in the em, in all coding region. and it is rapid and simple technique, and also the same thing for MLPA. [name of test] (2)er the, most er accurate test is sequencing. er, it can detect about, one hundred percent of and sensitivity, but it's er, cost, is expensive test. then i'm going to talk about er ARMS, ah the main principle of ARMS, em, you can see the other page er figure one. em, em the ARMS using em two er two type of er, tubes one, the first one is containing em, the mutant er primer and the second one normal primer. and er, the types of primers are used are three primers. er one is for the normal sequence, er the second one for the mutant sequence, and er also the common primer. (3) em after that the, the it it follow up to follow by [?] dual electrophoresis, to detect em, if there is a normal se- if there is a normal sequence or a mutant one. ah by the, by the dual electrophoresis we can determine if the patient is homologous or hetro homozygous or heterozygous, ah normal or mutant, but um the main the advantage of ARMS em is a rapid and er, reliable em, technique, er but the disadvantage em, cannot detect homozygo- homozygotes or heterozygotes er cannot differentiate between homozygous and heterozygous. em but this is em nowadays er there is some changes in the technique of the ARM of the ARMS, so can carry out this eh this ad- disadvantage. ah another test is the sweat test. sweat test em, this test em, depends on ah the measuring the amount of chloride in sweat. em children with the Cystic Fibrosis will have from two to five times more than the normal children. er and the sweat test this can simulated by er by adding specific chemical, to produce er enough sweat and collected the er, collected in um filter paper or a, capillary [says capilar] tube then analysed. the normal range for ah chloride (2) um, the normal range er is less than forty millilitre. but er when the result is more than em sixty so (1) that's indicate the the the patient have Cystic Fibrosis, ah when the result between forty to sixty, er it it's the borderline and it is better to repeat the test. and that's all. any question ? (5) S4_10_2: [2947.685] what kind of chemical is it they put on the skin? do you know? S21_10_2: [2950.549] no S4_10_2: [2953.180] do you know S19? S19_10_2: [2954.321] sorry? S4_10_2: [2954.711] do you know what they put on the skin to make it sweat? S19_10_2: [2957.270] no S24_T3_10_2: [2958.093] i'm trying just to remember about it, i can't remember S23_10_2: [2961.144] can can can't you just em make them exercise or [group laughter] NOTES: [2964.726] [group laughter ; overlaps; inaudible] S24_T3_10_2: [2965.995] [?] S4_10_2: [2966.056] [?] S19_10_2: [2967.900] no it's ah [?]. [??] exercise S21_10_2: [2974.853] yeah. usually the process er takes maybe a half hour, to collect them S20_10_2: [2981.804] [?] baby on like a treadmill [gesturing] [laughter] S22_10_2: [2986.847] ah s21 i have just a question like this primer. should it be like five in this way? [referring to handout] S21_10_2: [2994.038] which one? S22_10_2: [2994.879] because, in this case S21_10_2: [2997.820] no S22_10_2: [2998.005] [?] would extend this way. i think it's this one. (4?)like this is your. (4)[drawing]this is here right. S21_10_2: [3016.886] ok S22_10_2: [3017.306] and, this is your primer and this is your common. S21_10_2: [3021.268] ok S22_10_2: [3021.840] this will go this way this will go this way so you have this one, if you have from here then it would go this way S21_10_2: [3027.266] no like this. see. [referring to handout]from here (2) this is the specific primer. the common primer from here to here. the opposite side. to pick up the mutation. S22_10_2: [3040.821] yeah, they almost face each other that's why i said like, should be from here to here. S21_10_2: [3045.675] yeah S22_10_2: [3046.507] huh? S21_10_2: [3046.868] yeah S22_10_2: [3047.268] uhuh. because then five M is here. with the primer. three to five. S21_10_2: [3055.505] how how it's can be five, with five M? it cannot be. three to five three to five. S22_10_2: [3064.076] but i think when like [?term] extend this will go this way. no? S21_10_2: [3069.865] no the other way S22_10_2: [3072.247] from here? S21_10_2: [3072.928] yeah S22_10_2: [3074.619] if it goes from here S21_10_2: [3077.270] it would pick up this point mutation, from here this part S22_10_2: [3080.455] umm. we should check that i'm not sure about that S2_10_2: [3087.275] there's a tutorial on it on Monday [laughs] S22_10_2: [3088.905] ah yeah good [laughter]. that's Monday afternoon S2_10_2: [3093.873] it's Monday and Tuesday S22_10_2: [3095.016] ah ok. oh yeah Monday and Tuesday. S4_10_2: [3095.967] it's two [?] S21_10_2: [3098.783] yeah S20_10_2: [3100.135] S2 [?go] S24_T3_10_2: [3101.926] thank you S21 S2_10_2: [3105.419] ok, so [?] i was looking at the clinical signs and the management of CF.em, so i put in some basic figures at the start about, Cystic Fibrosis is an autosomal recessive disorder affecting one in two thousand five hundred individuals in northern Europe, which is approximately two million people em are carriers for CF in the UK which is one in twenty five. em, CF can usually be detected with infants at an early stage. em, it means the symptoms of Cystic Fibrosis is obviously thick sticky mucus, that is that blocks the lungs and it can affect other organs including the digestive system which also when blocked is a symptom, em, that or it's usually detected in children quite early. em so the main features that are listed were lung problems, em individually usually have a really strong cough like a really strong hacking kind of cough. em as they try to shift the mucus that is, em, obviously building up in the lung. em they also have recurring chest infections, because obviously the mucus would make it a ideal, breeding ground for bacteria so they develop a lot of bacterial infections which can be quite serious. em, mucus produced in CF can cause blocks in the pancreas and produce- that produce the digestive enzymes that are needed to break down food. em obviously when these foods are broke down that's how the body absorbs, eh the nutrients and you get energy and you put on weight, em so obviously, if if the mucus is blocking these em enzymes from being produced you can't you're going to develop a lot of malnutrition, that's obviously another clear sign in, em, obviously young children as they grow you can notice that they are not putting on any weight or gaining weight that can be a sign. em, i found something on older individuals can develop diabetes but the symptoms that they, of the of diabetes they develop is different from like, normal individuals who develop diabetes like they, normal individuals would usually, be really thirsty produce a lot of urine, em, might have things like [?cladema ]. em, people with CF, eh they just find it hard to put on, em, find it hard to gain or lose weight, and obviously just have a very severe deterioration in the lung condition. em, other symptoms include link blockage of the bile ducts em, which could led to the individual doing a liver transplant also some individuals are affected by infertility, and they can also develop like sinusitis osteoporosis and like arthritis. em, for the management i had that there is no cure for CF obviously em but the condition can be maintained well although the life expectancy is usually, mid to late twenties [?] there's been some reported cases of individuals [?] like thirties but a lot of the time, it's because they've had like a a lung transplant. em i had for medication, there's bronchi-bronchodilator drugs which help, em with breathing a lot of individuals with CF sometimes develop asthma, so these drugs it sort of inflates the lung, and the [?antibiotic] helps them to breath easier. em, lots of antibiotics em for CF obviously to fight different infections like the bacterial infections em, they can be taken in pill form with a nebuliser or an IV drip in very severe cases. em, all children diagnosed with CF this was something i found eh on the NHS website will be, on a course of antibiotics to fight bacterial infections but, and this will be continued until three years of age but i'm not sure if this is actually continued on after, because i i had a friend who had CF but she was continuously taking drugs, right in to her teens, em so that's just kind of a question mark but it's written on the NHS website. S4_10_2: [3334.871] i think D did mention it so. about and they generally em take antibiotics routinely S2_10_2: [3341.781] yeah it's what it says it's something like you just i don't think that they would stop at like three. it's a very young age. S22_10_2: [3346.270] so maybe antibiotic resistancy is another problem S20_10_2: [3346.299] it might just change S2_10_2: [3350.236] yeah definitely. as as you if you are continuously taking that drug for a long period of time definitely you could build up resistance. em, obviously you can also use steroids to reduce the swelling of the airways that would be a bit like bronchodilator. em, you can have like nasal drops and sprays, had DNase as an enzyme which is inhaled which break down the mucus, em that are, in the lungs so you could obviously bring it up easier instead of there's a lot of people coughing so much can make their throat raw and, em really hurting their chest. em, obviously because eh the pancreas em can be affected by blockage there's enzymes that can be taken and during before and during meals, that need to be taken with like quite big food. em, and that can help eh break down –help with the digestive system breaking down food so that em can get more absorption. and obviously vitamin supplements are really important, em, obviously if you're not going to be, obviously if your absorption levels would be lower than normal individuals so you should be taking the vitamins to help, eh build up immune system and give you more sort of strength etcetera. em physiotherapy is a really big part of Cystic Fibrosis em, there're different air weekly em different, air clearance techniques you've probably seen in D's lecture where they, sort of beat the child like you have the child lying down and they would beat their backs just to try and break the mucus up. em obviously a lot of young children vis-visit physiotherapists that can help them em and a lot of parents are trained, so that they can obviously do it for their children themselves and as they get older, there are techniques that are used em that they are taught they can do it themselves you don't have to deve- er depend, so much on another person to help you out. em, this is also these techniques should be done daily. it's not something that you know you should because obviously the mucus is obviously consistently building up. and obviously transplantation, em, is sort of like giving a new life basically to these individuals em, obviously as as time progresses your lungs are going to really deteriorate, so a lung transplant is something, that would be a big benefit to a lot of em older individuals with Cystic Fibrosis but obviously it's trying to find the right match and the waiting lists and things. (2) em (3) i think that's it [laughs]. S22_10_2: [3350.907] yeah yeah S24_T3_10_2: [3498.641] and isn't it a case they quite often do lung and heart transplant don't they at the one time S2_10_2: [3502.913] yeah S4_10_2: [3503.591] yeah S24_T3_10_2: [3503.918] uhuh. (6) thank you. S23_10_2: [3511.556] the nebuliser is ah S22_10_2: [3513.470] oh yeah i wanted to ask that NOTES: [3514.387] [? other inaudible start] S23_10_2: [3515.501] [?] S2_10_2: [3516.041] it's a it's a like a you know like an asthma inhaler it's sort of a bigger NOTES: [3516.410] [ lots of people gesturing to demonstrate how used/hand to mouth/mask] S23_10_2: [3520.035] ah. right. S2_10_2: [3520.895] it is a bit bigger isn't it? [looking to S4] S20_10_2: [3521.896] yeah it's like a S2_10_2: [3522.738] you just a sort of, inhale it like S23_10_2: [3525.485] yeah i think i saw it S20_10_2: [3526.315] [laughter] S2_10_2: [3526.725] i don't know how to explain S21_10_2: [3527.708] usually the patient with er asthma, they would use it S22_10_2: [3531.734] they put it like S23_10_2: [3532.132] [?] a small one right? S2_10_2: [3533.668] yeah only this one you put it over [?] S23_10_2: [3534.230] [?] NOTES: [3534.230] [multiple explanations; inaudible] S24_T3_10_2: [3534.916] you put it over S20_10_2: [3536.636] yeah S23_10_2: [3537.521] yeah ok that's solved [?] S19_10_2: [3540.645] er, i just S22_10_2: [3543.948] S2 here you say like S2_10_2: [3546.439] yeah that was [? someone coughs; inaudible] S22_10_2: [3548.184] er then em antibiotics, will be catching it after three years of age.what do they do later ? S2_10_2: [3557.095] that's what i was saying, i i don't think it's right, ehm because obviously if you stop antibiotics at three years it's a very young age so, i think it's consistently needing antibiotics that's why i, i just mentioned i'm not i don't think it's right it think it's something that continued all the way through but as you've said you could develop resistance so maybe they change the drugs, at different stages. S22_10_2: [3568.516] ah ok [3576.630] yeah that could be [?] S2_10_2: [3578.412] yeah. and obviously like depending on the infection as well S4_10_2: [3580.521] i think that is one of the issues antibiotic resistance like it's like a i suppose it's um to all [?] i don't know. S22_10_2: [3588.132] i mean antibiotic resistance i think there another issue in my country because like when you go to the paediatrician for two years three years all child they write prescribe such a strong antibiotic, and in later stage i mean, like it gets just difficult, they show resistance to this, antibiotics. S4_10_2: [3610.972] i think you try-i don't know so much about children but if they i think they try to stop giving, you know if someone's quite healthy they'll not give them an antibiotic unless they really need it they'll not just give it out [?] i think S22_10_2: [3617.543] yeah S20_10_2: [3618.063] yeah S4_10_2: [3620.495] yeah S20_10_2: [3621.139] go to your bed [ laughter] S24_T3_10_2: [3622.888] my my s- i've been off this week and it's because my son has flu. and obviously there's nothing really the doctors can give you for flu. but what he did he gave me a a prescription for an antibiotic and said just keep the prescription, and if he has secondary infection like coughing, you know then get the antibiotics for him so i've left the prescription in the house just to see how it goes rather than, get the antibiotic for him. S22_10_2: [3622.895] yeah cos S4_10_2: [3635.487] yeah [3647.007] yep S22_10_2: [3648.236] yeah. it's good they say. S24_T3_10_2: [3650.747] although some people i think just go along to the doctor S2_10_2: [3653.113] ahah S24_T3_10_2: [3653.505] they just assume, because again they don't realise whether it's a viral or a bacterial infection they've got [directed to s22] so they they almost think if they don't get an antibiotic then the doctor's bad here you know so. i've gone and they've given me nothing you know so [group laughing] S4_10_2: [3663.742] yeah S19_10_2: [3667.868] that's a big problem. sometimes when you don't prescribe something like an antibiotic they they are they can [?] you S24_T3_10_2: [3675.614] but it's because, again again it's dealing with you're dealing with the general population so they don't understand that they just assume that they must come away with something from the doctor. S22_10_2: [3677.999] we get people like this S20_10_2: [3681.808] yeah S19_10_2: [3682.813] you have to explain everything, but sometimes they want to kill you, with just one of their pills and that's [?] NOTES: [3686.259] [laughter] S24_T3_10_2: [3689.533] so i think for a well maybe not so much now because obviously it's all down to money now as well but i think years ago, for a quiet life the GP just gave them the prescription [laughing] S4_10_2: [3698.647] i think i suppose it was the wonder drug S19_10_2: [3700.490] [?] S24_T3_10_2: [3701.922] yeah it keeps them happy [to s2]you know just you know [shrugs shoulders] S19_10_2: [3705.713] em but that's worse S24_T3_10_2: [3707.452] yeah yeah [laughs] S2_10_2: [3711.359] anyone else? S24_T3_10_2: [3713.411] no S20_10_2: [3715.213] [?] S19 S19_10_2: [3716.979] ok so,i got to look into the mutation distribution according to the different populations. so we do know that eh it is different in different countries and in eh with eh people from different backgrounds. there's more than one thousand different eh mutations identified for Cystic Fibrosis.so we know eh, that the F five O eight del is the most common mutation worldwide. and it's responsible for about, two thirds of er what's three yeah just two thirds of all the Cystic Fibrosis not only eh affected people but carriers. but the problem is that they one er remaining with the one third remaining is really. variable and so. you can you can find the it is mainly, in about all the other one thousand mutations, there are so, for, there's a table. there was a big big big review, in two thousand two, which included almost every country in the world every country in the world that had data available. so, i tried to include Azerbaijan Singapore but i couldn't find anything [laugher- countries of group members] [3.53] so, em in the UK, there's i just included the five most common mutations for every country i could because there's a lot of information and it's not really that necessary, in the UK er there you have the five most common and in Scotland. it's always F five O eight del the first one. eh, that accounts for almost for seventy five percent of of every mutation. there you have er different countries er. in Saudi Arabia and East Asia they didn't really have much, em data like a specific things not percentages but it varies even in each region. [looking at Saudi student] so. still, in Asian in Asia, it's not it's a bit different because it's not actually five O eight del it's not the most common. the thing is that with this we we can see, that you absolutely have to to make the test, applied to the population you have a screening test, should always include the most common mutations for that population, and this may be an issue in in countries where you have a lot of immigration. so you you always will need em, to consider that if you are testing a person who came from, from such a different background like East Asia or something like that you will actually not pick up the kind of, of mutation, in in those child in those children. em and there is an increased risk, if a child does have eh a mutation and the screening test doesn't pick this up. eh the child is at the higher risk eh of not getting diagnosed, than if if he didn't take the test, in the first place. so that's something we need to consider. i don't know. [?] wasn't that long and we talked about like the classes of mutations so i included that too. em, we have five different types of mutation for Cystic Fibrosis. eh, the class one is mutations affecting the biosynthesis of the protein oh all these kind of mutations affect the different eh stage in the, of the protein, mm, of of the CF protein so, the first one affects the biosynthesis you can either er defective protein or no protein at all. that is is, the most serious phenotype you can get, and there's the examples of the mutations in this class. you can look at the figure. (2) in class two the mutations affect the protein maturation so you don't have a a, you produce a normal protein but, it it doesn't reach the cell membrane. it gets degraded first so you don't have the effect anyway that's the five O eight, the most common one. then you have in class three the mutations affect the chloride channel regulations and gating. so, it even gets to the to the membrane but you it doesn't bind to ATP, so it doesn't work anyway. in class four em, the mutation affect the C- the chloride conductance so it opens eh even, the, the ch-the gates and everything but the currents it generates are not eh-are not strong enough. so it doesn't work. and the fina-the final class are mutations affecting the levels of normal MRNA transcription. so it's eh the MRNA's unstable. because of defective defective splicing and it doesn't work. those are the five classes of mutations. S24_T3_10_2: [4055.253] do these show different severities then in S19_10_2: [4057.650] yes sometimes S24_T3_10_2: [4059.066] yeah S19_10_2: [4059.453] sometimes they do S24_T3_10_2: [4059.461] so it's sometimes different symptoms in the patients S19_10_2: [4061.806] yes the the most severe eh are the class one mutations. but I i don't know the the phenotyping the other ones might not be. because if you don't have any protein at all there, it will be more severe than the other ones. S21_10_2: [4080.128] yeah S24_T3_10_2: [4080.619] uhum S19_10_2: [4082.760] you always get the chance that some of the [?] protein is rich and do something S24_T3_10_2: [4087.444] mhum S19_10_2: [4091.055] [?] any questions? (9) [4100.086] ok? no questions? S4_10_2: [4102.095] ok NOTES: [4103.003] [laughter] S20_10_2: [4107.562] ok i was looking at whether er whole population screening for carriers status would be any use but i have there wasn't actually much, like in terms of papers on it and stuff it was kind of just logic. [laughs] but em, so yeah. i had, em, obviously you know um, these kind of like Cystic Fibrosis is not a particularly common disease but its quite common, in terms of recessive disorders and it, affects like for a third of paediatric deaths are recessive disorders. em, one of the main issues is that there's a lot of carriers of Cystic Fibrosis way more carriers than there's of frequency of like, em, actual occurrences of Cystic Fibrosis. so that's why you'd want to test you know try and limit the number, em. currently like you would just test, genetically the members of a family, if the screening came through on a new born, and that would be tested for diagnosis it wouldn't be for carrier. em, and in the UK obviously as mentioned before the carrier frequency about one in twenty five. so there's about two million, carriers of CF in the population and most of these people don't have any history of the disease so, if they get together they might get a little CF baby. [laughs/giggles ] em, one of the main issues with like if you were going to do screening, you have to pick up most of the population. but, in the UK about seventy five percent as you mentioned is the del five O eight mutation. which is fine and then there's about ten percent which is comprised of a couple of other more common mutations but the rest are kind of, really quite rare compared to everything else so, if you were doing like a screening, and if you got one of these mutations it would be like fine but, if you got one of the other ones then it would just they they think they don't have it, but then they will have it. but a lot of people are saying, like em. (3) it's not worthwhile because of the proportion of people that would be identified as being a carrier, em, and also the the issue of like if you had a couple say that, one of them, had the CF mutation the other one didn't have a CF mutation, so they thought right it will be fine. and then, they have a CF baby. and then they they, it'll just be, they'll get really angry with it you know. even with education and counselling and stuff it just doesn't seem to be worth it because, (2) they just the amount of people who pick up compared to people that em, (2) like the the risks would be increased. S4_10_2: [4282.547] but do you think it's also about imprac-impract- sort of impractical because you're going to put on such a huge because once like you've identified carriers you're going to have to out some, they've got to do something about that then and then it's a a burden on the NHS or something like that S20_10_2: [4291.359] yeah you'd have to test them as well [4294.982] yeah. yeah. i'll get to that. [laughs] it's fine. em. but yeah so for loads of couple the the risk would be increased when like there would be no reason to, for them to worry about it but em, it would create a lot of anxiety and [?] stuff so. it doesn't really seem to be worth it but, also, the actual screening protocol em, i had a look at like the ways in which you could implement it if it was to be done. em, but the actual process would be relatively inexpensive, apart from [?like] the quantity like because you're doing so many people there's just no way that it would work but. em, you could you could offer screening, em at birth. em of like if you have a baby i think you could screen it for carrier, but, there would be a lot of issues with it you could get non-paternities em, you'd have information on on a baby that doesn't, it obviously can't understand the information until it's much older and it's not relevant until it reaches like a reproductive age anyway so it's like, why would you just burden them with that but em, you could do it at high school. but, i think you could like combine it with like education but, for that, there's like issues with em, giving consent cos usually like when you're at school when you get like a jag or whatever, your parents give consent for it. S4_10_2: [4297.093] sorry. [laughs] sorry. S20_10_2: [4385.602] so, it wouldn't really be down to whether it was the teenager's wishes cos they're they're still too young to make that. ahm also peer pressure might be an issue if all their pals are getting it done and they want it done etcetera.[laughs] uhm, so for that you'd need a lot of counselling, to like so so they understand it. um you could offer it at marriage which i think was done in Greece for the,[?] where was it? S21_10_2: [4410.507] an oth- S4_10_2: [4410.507] was it Cyprus maybe ? S24_T3_10_2: [4412.105] Cyprus S4_10_2: [4413.392] [?] S21_10_2: [4413.517] another country also ? S20_10_2: [4415.073] yeah. but em, i think in those countries it's quite religious isn't it? whereas here. [laughs] they've probably already had sex by the time they're getting married so. [giggles in group] S24_T3_10_2: [4427.181] that's a very general comment isn't it? NOTES: [4427.181] [group laughter] S20_10_2: [4430.437] well. mostly [group laughter] S24_T3_10_2: [4431.298] [?] S19_10_2: [4434.287] yes you are right. S20_10_2: [4434.963] mostly. [4436.937] so, you know it's kind of pointless by the time they get to marriage age. [laughs] S21_10_2: [4440.450] yeah S20_10_2: [4441.554] em, eh you can offer it when they're pregnant but then if you're if you're if you give them it when they're pregnant and they're already pregnant, if they've got a Cystic Fibrosis baby they've only got one option if they don't want to have it and that's to terminate so it's kind of,it's not really giving them any options so it's kind of pointless there as well. em, (3) a- also it's there's there has been screening, for carrier status of like thalassemia and stuff, uhm but they don't use DNA based methods they use cellular protein [?analysis] which is much cheaper than using DNA. and DNA's a bit more complicated. so in order to carry it out, across the whole country it would be, very expensive and the the thing that would be the most expensive would be the amount of counselling you'd have to give to people because, like if you were go, for carrier status, you would need to really enforce all the sort of you know you don't have it but, S4_10_2: [4500.397] yeah. yeah yeah S19_10_2: [4500.643] you had a [?] S20_10_2: [4501.687] and it's all a lot of counselling that would have to be done so that would be the main sort of cost issue. so, in conclusion, eh S19_10_2: [4510.405] no S20_10_2: [4511.038] yeah no basically. em they could do it but it really wouldn't be worth the sort of, the anxiety of it and the the, the cost it just wouldn't be worth it so. there's none and they don't plan on having anymore, that's it. S24_T3_10_2: [4531.130] right thank you S23_10_2: [4532.912] the thing for this to work we must make it fashionable S2_10_2: [4536.261] yeah S20_10_2: [4536.538] yeah [laughs] S23_10_2: [4537.587] friends and the [?] S24_T3_10_2: [4540.471] well quite often because the the kind of conditions it's there isn't a lot of choice it's either they they people take the risk or that they just decide not to have children. S22_10_2: [4549.849] yeah [4552.452] ah S20 what was the test you said about non DNA test er for, finding the carrier S20_10_2: [4558.658] it's just like a like a bio chemical sort of test, like just like IR IRT, that sort of test. S22_10_2: [4565.103] ah like count the markers. so that's why they could have like false positive. false negatives S20_10_2: [4570.264] umm. they don't, detect like em you said [turning to S23] IRT doesn't detect carrier status, so you can't really use it so it would have to be DNA based. S19_10_2: [4580.393] there's no no way chemical marker [?] S20_10_2: [4583.425] no S22_10_2: [4584.531] for carriers? so it would be only DNA test in this screening. ok S20_10_2: [4588.279] yeah S2_10_2: [4591.289] em sorry i've just got a really just a random question but see, [laughs] you were talking about getting vaccinations in school and stuff, what was the BCG for? S20_10_2: [4594.062] [laughs] S24_T3_10_2: [4599.531] tuberculosis S20_10_2: [4600.500] yeah [4601.138] i didn't get it cos i got it when i was born because my gran had TB so S2_10_2: [4604.309] ahh S24_T3_10_2: [4604.675] stopped doing it just now [to s2] NOTES: [4604.675] S24 to S2 aside] S20_10_2: [4605.061] i was gutted there's that peer pressure thing i was really gutted i didn't get my BCG everyone one else was getting it [group laughing] S2_10_2: [4605.783] yeah S24_T3_10_2: [4609.173] [?] S2_10_2: [4611.641] [?] S20_10_2: [4612.084] [?] skin test i was like S2_10_2: [4613.579] [?] [4616.200] oh really? S20_10_2: [4616.857] yeah but i wanted a bit [?] [S2 laughs] S2_10_2: [4618.329] [laughs] S20_10_2: [4619.027] everyone else is getting it [?] [laughs] S24_T3_10_2: [4623.393] they don't do it at the moment, so. S21_10_2: [4625.757] they don't do they don't do it? S24_T3_10_2: [4627.203] well they no i think the the the levels of tuberculosis in this country dropped, but i don't understand why they're not doing it now cos it's actually on the increase now S20_10_2: [4635.885] is it higher [?] S19_10_2: [4636.699] yeah you need the vaccine anymore S24_T3_10_2: [4638.158] no. i don't know if it's a money issue again cos everything always comes down to money, eh [laugh]but i know cos my son would be of an age just now where he should be getting it, and they they don't S21_10_2: [4647.285] in our country at birth only S24_T3_10_2: [4649.612] sorry? S21_10_2: [4650.479] at birth only. S24_T3_10_2: [4651.340] at birth? S21_10_2: [4651.893] yeah only S24_T3_10_2: [4652.385] oh right ok. no. usually here by the time it's first and second year at school thirteen fourteen in fact my son should have been getting vaccinated today for, a booster for polio diphtheria and tetanus because because he's got the flu, he can't, he's off school he won't be getting it so he was getting texts last night oh you're you're missing the vaccinations.[laughs] S21_10_2: [4653.510] and also [?] S4_10_2: [4655.240] [?] S21_10_2: [4657.177] yeah S20_10_2: [4665.243] oh that's what i remember [?] NOTES: [4665.243] [1 other inaudible] S4_10_2: [4668.317] no [4674.561] but you just take him to the doctor's [?to do] S24_T3_10_2: [4675.883] we'll have to find out then what S20_10_2: [4676.681] they we get it at school i think i think [?]. yeah. S2_10_2: [4677.715] yeah i think we do NOTES: [4678.995] [multiple overlaps; not all inaudible] S2_10_2: [4680.047] i missed mine as well S20_10_2: [4680.982] well you just get taken in the next lot S24_T3_10_2: [4681.289] so. [4683.037] go through on the next lot S2_10_2: [4683.937] did he [?] Meningitis S24_T3_10_2: [4685.769] no. em, S20_10_2: [4687.139] i got meningitis when i was in primary school i think S24_T3_10_2: [4688.957] no he's i don't think he's had it S2_10_2: [4690.185] the actual Meningitis or do you mean the vaccine ? [laughs] S20_10_2: [4691.906] no [?] the vaccine [laughs] [4693.758] that's like what? [?] S24_T3_10_2: [4695.754] er no i don't he's had that no S2_10_2: [4697.558] like cos we had [?] S21_10_2: [4699.279] i think at five years old. [?] S24_T3_10_2: [4702.021] they get lots they get lots of vaccinations when they're babies and then before they go to school. em, and then they get what they get just now's boosters for all of these things. S21_10_2: [4710.296] yeah yeah. S4_10_2: [4711.073] is meningitis not quite new? S24_T3_10_2: [4712.818] uhuh, it is uhuh NOTES: [4714.765] [laughter] S4_10_2: [4715.071] [?] S20_10_2: [4716.359] well you know [?] S24_T3_10_2: [4716.484] because we, well you're not as old as me but i'm too old for have it so. [laughter] NOTES: [4718.942] [laughter] S24_T3_10_2: [4723.304] ok S2_10_2: [4724.175] [?] time he's born though S22_10_2: [4726.376] it's [?]genic [?] S4_10_2: [4730.186] i think they're doing it [?] were they not like in unis or something like that they were starting to they were starting to do at one time but then they tried to S24_T3_10_2: [4735.588] uhum yeah yeah. [4736.463] because ah, quite often in the population uhuh S4_10_2: [4736.753] eh [?] set up [4738.789] yeah S2_10_2: [4739.403] [?] see i was going to go off thinking that it was something like lung drainage [?] S20_10_2: [4741.334] i don't even know what ones i've got i just went turned up and [?] NOTES: [4741.948] [concurrent s22 & s2_10_2/s20 & s4_10_2- not all audible ] S4_10_2: [4744.222] i know just [?] S2_10_2: [4745.389] sort of insert something to drain it but i'm not really sure if that's right [to S22] S24_T3_10_2: [4748.159] what is this ? share with us [to S2] S22_10_2: [4749.800] uhm i just, oh yeah. autogenic yeah. S2_10_2: [4749.997] so it was em, autogenic drainage [?] i'm not really sure the word autogenic S24_T3_10_2: [4755.920] oh right well maybe s19 will i heard [?] saying is that is it draining the mucus? S19_10_2: [4757.696] where? S2_10_2: [4760.215] yeah i was thinking it was [??] S19_10_2: [4761.997] where where? S22_10_2: [4761.997] like airway clearance [?] S2_10_2: [4764.639] physiotherapy, that there [to s19 refers to handout] S19_10_2: [4766.859] physiotherapy [?] S2_10_2: [4769.132] and down to autogenic drainage [to s19_10_2 refers to handout] S19_10_2: [4771.980] oh S24_T3_10_2: [4773.350] i presume it must be some sort of tube S2_10_2: [4775.058] yeah i don't think there like some sort of tube to with to drain the actual mucus from the lung but i'm not actually sure of the word autogenic S19_10_2: [4781.569] well it's just the it's just the eh, there's there's it's an ugly thing when you, the babies well that that is not only babies but, em you get some sort of exercises and massages and sometimes these looks like you're beating the child. S2_10_2: [4799.114] uhum S22_10_2: [4799.703] oh NOTES: [4799.859] [some asides] S19_10_2: [4800.298] but yeah like like [gestures ‘hitting'/patting] [some asides]and you make like eh to help them eliminate the mucus all the secretions, but it's not like you actual put something in you just, make the [?] S2_10_2: [4807.279] yeah S24_T3_10_2: [4810.720] make the [?] S2_10_2: [4811.273] yeah S19_10_2: [4812.270] take the that stuff out S22_10_2: [4813.894] i thought that's positive expiratory pressure. (3) S19_10_2: [4818.879] no S22_10_2: [4819.869] because when you like press on, no? then what's positive expiratory pressure? S19_10_2: [4821.183] no no no [4823.052] no you see it's we explain here. these techniques use a device. positive expiratory pressure use a device. to help the clearance of mucus. S22_10_2: [4833.025] em, device, (3) [party reading out and to self from handout] oh.so positive expiratory pressure is done with something. it's [?] S19_10_2: [4838.989] my [?] S24_T3_10_2: [4845.297] you can look it up. S2_10_2: [4846.154] yeah i could find out [?that one as well] [to s22] NOTES: [4846.154] [to s19_10_2= concurrent with s22-s2_10_2 above; and S24 and S19/group- concurrents; not all audible] S24_T3_10_2: [4846.749] see the see the different classifications then so is the life expectancy [?], for these people then? or is it just much the same ? S22_10_2: [4847.979] [to S2] also, also the [?] [concurrent ; inaudible] S2_10_2: [4850.067] [?] but i think that's sort of like a S19_10_2: [4853.262] what? S24_T3_10_2: [4854.278] see in the different classifications with the mutations you were saying classification one [s19_10_2?] is there life expectancy? S19_10_2: [4857.932] oh yeah [4860.639] yeah yeah well i've read that the actually it it is worse with eh the mutations where there is no protein at all. but there's not really much much the other types of mutations it's like the, same thing. yeah S24_T3_10_2: [4867.095] uhuh [4880.775] okay thank you for that. thank you eh S22 for doing the present- nobody else rose to the bait. S22_10_2: [4888.186] i thought that everybody give it a go S24_T3_10_2: [4889.022] your big opportunity this is a good room actually for presenting it's it's not bad at all. S22_10_2: [4893.685] yeah actually er i have to i have to prepare a presentation for PhD for [?] so it's a good practice for it S24_T3_10_2: [4900.637] that's why we encourage you to do it em if you need come in to the office with it and if you want us to listen to you. S22_10_2: [4905.675] yeah. when i prepare it. S24_T3_10_2: [4907.273] uhuh S4_10_2: [4907.997] so where are you applying to? are you applying for a PhD? S22_10_2: [4911.126] yeah S4_10_2: [4912.131] where have you where S22_10_2: [4913.803] um i have been invited for interview from Cambridge university. S4_10_2: [4917.828] oh[?] [intake of breath] S20_10_2: [4918.258] [?] S22_10_2: [4919.999] yeah but i have to put S24_T3_10_2: [4920.838] which department ? S22_10_2: [4921.887] genetics S24_T3_10_2: [4922.374] genetics S22_10_2: [4922.829] yeah. but first before the official application they asked me to do PhD twenty minutes presentation on research paper or dissertation. so we don't have dissertation topic, then it should be about something a research paper, em, i have a research [?] [overlap] S24_T3_10_2: [4938.199] or if you want us to listen to you just just ask us S22_10_2: [4940.595] yeah when, i wanted to ask you like if when it's ready can i S24_T3_10_2: [4946.190] uhuh i'll say to S18_T2 that you'll come in and, listen to you S22_10_2: [4949.508] thank you S24_T3_10_2: [4950.169] and S31 as well she'll give you points on you're stance and things as well. that's why we try and encourage you to present because in our experience whether it's for a PhD or, as a scientist it's very common now to be asked to do a presentation in your interview whether it be five minutes or twenty, and, you know in the past we we always say, we encourage you to do presentations for your PBLs if the room permits but also if you've got one and you want us to check it you know if you want us to listen to you just to give you a wee bit practice, or to time you because eh D always says that when there's lots of that's why you only get five minutes if there's lots of people being interviewed, em the panel get a bit fed up if there's you know if people run over their time so that's why it's quite good to be, concise and accurate in what you have to say and you get, you know you get just with practice really it becomes easier and i know some people are more comfortable than others at presenting so if you get the opportunity i would seize it with both hands. [laughs] but. S22_10_2: [4952.455] yeah. that will be very good. [4963.781] yeah [5010.315] it's just i think it's just practice, you do more and more so you can get S24_T3_10_2: [5013.596] uhuh. that is it's practice. uhuh S4_10_2: [5016.494] so do you know is it a specific project is it for a specific [?] S22_10_2: [5020.119] yeah it's like em, there's a [?] models of neurodegenerative disorders. specially Parkinson's disease. S4_10_2: [5026.141] [nods] S24_T3_10_2: [5028.791] good. S22_10_2: [5030.306] yeah i'm interesting in neurodegenerative disorders, like one a relative of my close relative have Parkinson's disease and i just saw how suffer then i couldn't help him with anything and he was in his mid, em forties. so after that i just become interested in that disease. they always like something happens in your life. S2_10_2: [5037.939] like a [?] [5048.696] uhum S24_T3_10_2: [5053.071] that's right something happens in your life, that makes you want to do things. oh well good luck with that when is it? S22_10_2: [5053.480] [?] [5058.813] actually they ask me to, that's up to me when i'm going to go there S24_T3_10_2: [5063.988] oh right good S22_10_2: [5064.683] but i have to research find a research paper and prepare presentation and then go S24_T3_10_2: [5068.840] [nods ] uhuh S22_10_2: [5070.166] i think it's probably mid March S24_T3_10_2: [5073.509] ok S22_10_2: [5074.122] because we have classes and reports so, i'm thinking that time. but it should be ready before that perhaps. S24_T3_10_2: [5081.084] good. oh well we'll look forward to hearing all about it then [laughter] S19_10_2: [5085.401] well let us know how it goes. [5087.395] good luck. S24_T3_10_2: [5087.395] yes [5088.961] thanks for that. have a good weekend. [1.25.50][is that you got everything C that you need yes] : [10.692] [handing out copies etc preparing for presentations- students using Powerpoint today] S7_11_2: [13.563] i hate paper cuts S25_7_2: [14.798] oh i know. especially when you [?bend] your finger S7_11_2: [17.254] oh [18.461] S30 S27_11_2: [22.716] [??; inaudible; to S25 & S5, getting H/O]] : [22.716] [S ? ; inaudible] S25_7_2: [23.587] of course [response to S27] : [24.469] [students handing out copies, checking they have all reports] S25_7_2: [24.475] [laughs] [27.153] S27 have you got one of mine? [referring to H/O] S27_11_2: [28.615] yeah S25_7_2: [30.226] S26 S30_11_2: [31.081] right S31_T4_11_2: [32.132] can you all e-mail me a copy of your presentations just S5_11_2: [34.764] eh hey [??] forever ah? [to S28 setting up Powerpoint] S27_11_2: [39.978] these are the [?] S26_11_2: [42.899] my presentation is in platform five S31_T4_11_2: [44.768] that's ok instead of just S7_11_2: [45.954] is this [?] S26_11_2: [46.716] [?] something there, there's [?], probably S7_11_2: [48.430] yeah : [49.506] [laughter] S31_T4_11_2: [49.827] [??] S27_11_2: [53.191] ah did i give you one? [to S5] S26_11_2: [55.795] i've got yours anyway S25_7_2: [57.729] i don't have hardly anyone's S5_11_2: [58.305] ah let me see i don't know, ahha S25, S29 S26_11_2: [61.201] have you got the third one? S25_7_2: [64.574] i've got one with no name. oh S29 S5_11_2: [65.451] S30 S29_11_2: [68.343] [??] S7_11_2: [69.643] yeah exactly S25_7_2: [70.378] it moves. S26_11_2: [71.397] yeah S25_7_2: [71.712] yeah i handed i did it at the end so that i put put it back it's really annoying S26_11_2: [75.295] S28 [??] yours S28_11_2: [76.311] yes S29_11_2: [76.934] oh S25_7_2: [77.682] eh you didn't give me no thank you S7_11_2: [77.682] S25 [?] [81.749] S28 can i have yours S25_7_2: [82.445] S7 S28_11_2: [83.875] ah you don't have it S7_11_2: [84.619] ah [?] no i print my, [??] S5_11_2: [87.520] but i haven't got [to S28] S25_7_2: [88.458] ok. so we don't for you S26_11_2: [89.826] em who's, sorting out the order is that that the chair or is that the scribe? S5_11_2: [90.289] [??] S25_7_2: [94.067] it's S28 S28_11_2: [95.224] ah S26_11_2: [95.986] [?] S25_7_2: [96.494] uhuh S26_11_2: [98.169] do you have a set of our questions S28? S28_11_2: [100.421] uhum? S26_11_2: [101.279] do you have a list of what everyone's doing so you know who S28_11_2: [103.045] yes S26_11_2: [103.566] oh ok S25_7_2: [104.112] er, sorry i was actually [?] with this S27_11_2: [107.414] why we are [??] S28_11_2: [107.732] we will st-, we will start with eh S5, for Amsterdam rules S5_11_2: [113.620] oh S28_11_2: [113.944] and then eh, er FAP you're doing FAP yeah S25_7_2: [118.072] yeah S28_11_2: [119.088] and then eh, er S26_11_2: [123.238] me S28_11_2: [123.978] you, doing HNPCC, then myself i will do MAP, after S26 then S30, S29 and last S7 S26_11_2: [127.090] ok S7_11_2: [135.960] oh S27_11_2: [136.555] i don't have yours S25_7_2: [137.738] i don't have yours [to S28] S28_11_2: [138.755] no ? [to S25] S7_11_2: [139.340] [??] [background chat; inaudible] S25_7_2: [144.877] i'm [?] thank you very much S31_T4_11_2: [146.712] have you got a copy for me? S28_11_2: [149.106] ah yeah S25_7_2: [152.182] are the lights out? S5_11_2: [154.087] ah? S25_7_2: [154.468] turn the lights out S5_11_2: [156.131] oh yeah [163.534] dark [167.274] ok S26_11_2: [169.253] maybe yeah i'll have that one [talking about a pen] S5_11_2: [170.981] anyway uhm, (3) good morning everyone so, you know i will talk about the Amsterdam criteria and, anyone has the questions or whatever, just stop me and ask . (2) ah, well just a, brief picture ah those criteria, in general in medicine there are many, and some diseases er er the criteria depend on the people er, (2) who joined er and usually, they put the main where they have this [?join] that named after or or there are like Glasgow criteria or other things, ah mainly erm they're [?basically ] in kind of in three [?main] things, first one family history and in this case er, it's [?worth ]to notice the early onset and also, if if the family is realised other associated diseases or cancer also, another issue is clinical features can be present in the disease and diagnosis test ah so, depends on the level can be bio- biochemical molecular or some kind of [?biologic] so this is a, a general over- overview of the criteria that you have. so, ehm just to get in the all four Amsterdam ah the first Amsterdam criteria was known nineteen ninety one, er with Vasen and colleagues [?] and the [?] ahm, and those erm, i can say that it's too restrictive er those criteria . er there were like em, pff when they have patients, erm er with colon cancer, ahm following this criteria (2) few patients have those criteria so it was, useless the the the the criteria few fulfil . so, this is the criteria [shows slide; reads from slides] (2) does that work? oh yeah ok (to self about PPT pointer]. ahm so most of them should be in that division eh, three relatives with colorectal cancer one of whom the first degree relative of the other two ahm, the colorectal cancer er should be, at at least two generations. and it should be before of, fifty years old so, all of them must be in the family, so they found that that was useless, so they had another meeting em, some years later, ahm, we have the Amsterdam two, ahm, which is a little bit er, not flexible but, they found other things that can be, eh [?important]. and here we have a five, five points so the first one er three or more relatives with pathologically verified colorectal cancer, or other associated cancers . here it's important because there are other cancers, [?making] the endometrium ovarian, pancreas, and glioblastoma which is a brain cancer . so any of them, are associated with, the hereditary non-polyposis colon cancer . and also, one affected individual should be a first degree relative of the others, ok. ahm again two, successive ah, generations should be affected er the year ahm they are at onset, but same before of fifty years old. and also familial aden- adenomatous polyposis should be excluded . so in this case, to be excluded you can perform that colonoscopy . because in this one the, polyps are in the colon so the test should be performed, and also i- i think it's very important that, pathologically it's means that, there was some histological, er test and analysis, verified, by the pathologist . so should be verified . (3) ah, and then we have another criteria i'd like to mention because it's important, in in our case we have two criterias Amsterdam as i say, and Bethesda which is a group in the the United States . ah, basically, i cannot say it's the same but er the, the target is different. and here it's important because some schools depends on the school but also the place for example in Europe i think they follow, the Amsterdam whereas in in the States, er or Canada or Mexico ehm, Bethesda should be the the criteria followed so Bethesda basically it's a alert for the physicians . and it's when you have a patient when you have when you have a suspicion of hereditary non polyposis colon cancer . and, since you are with suspicious, er patients with colon cancer, before the fifty years old or that uhm, patients have polyps, you can think if it's criteria ok? so, later on i will explain this [?] so in this criteria we have five points and, just, er with one it's enough to follow up with the other tests ok? so, oh the first one is er the cancer it should be diagnosed in a patient er less than fifty years old. er another cancer should be present, also again those cancers i mentioned, endometrium ovarian pancreas, and should be synchronous means have the same time, or metachronous that means er, can happen before [?even] if the patient is cured, the other cancer what happens ok? so [?] should be taken into account. er, and also colorectal cancer with histology phenotype in a patient which is, with [?fifty/sixty] years old or younger and, also should be that patient colorectal cancer and a first degree relative with Lynch syndrom which is the same [?hereditary carrying] of this colon cancer. with one of the cancers diagnosed under the age of fifty so, ah also a patient with the colorectal cancer with two or more first degree or second degree relatives, with a Lynch syndrom related tumour, regardless of age. so, if any of them just came in just with one it's enough the meet criteria . (4) so if a patient has er one of them then we should, er can perform the MSI analysis or the immunohistochemical analysis er, test later on . (2) [?][looking at PPT] er so then, ah which one is better? as i said, depends of the er of the place if people prefer the Bethesda, or prefer Amsterdam . or for a patient what should be better? you know which criteria, fits the the patient. so as i said those criteria have [?] er, and they have different targets. so the Amsterdam, er were designed to take into account er small families. and also, the extracolonic tumours. so if, if there is, er tumours or outside of the colon, and the family in, present those tumours and there is one or two with colon cancer you can be [?thinking] Amsterdam. ahm, (3) whereas Bethesda, is mainly er to those where, i think of er, we are think about, or we are suspicious about something is wrong with the patient. so in in practical way i think is more, useful Bethesda and in those cases as i explained, you can [?go] the follow up . but i found a an interesting paper whi- which analysed the ehm, both comparing, ah we have the sensitivity of Amsterdam two was, ah seventy eight percent and specificity sixty seven. whereas Bethesda criteria, show a sensitivity of ninety four [?so you see] is high. and the specificity of these criteria was twenty five . (2) and, use the first three criteria i mentioned just with any of them, any of them ah, the sensitivity was the same but the specificity was higher . so, in conclusion we can say that Bethesda guidelines are more sensitive, criteria especially if we have or if we are suspicious, in a patient. and if we perform eh MSH, two or MLH one test er, according to criteria it's, more likely we found something wrong here ok? and, Amsterdam two er still miss many family, which they carry the mutations. so that's it . and that's the papers if you want to check it [referring to references on slide] (2) any questions? S25_7_2: [176.508] [??] [aside to S26] S7_11_2: [824.670] do- does it mean that the Amsterdam rules just does not, er give us information whether we have to go for an MSI or not? S5_11_2: [832.038] ah, (2) i mean you can go, if if the criteria of Amsterdam erm, you can go but, maybe you don't have, the the mutations [??], it's it's what's your question? er, you you have ok you have the patient [853.139], and according to Amsterdam you say oh ok, it's can be, ah can be it's colorectal cancer ok? (2) S7_11_2: [861.493] [shakes head] S5_11_2: [863.796] ah S7_11_2: [864.074] no in case er the Amsterdam rules fits your patient, then does it suggest that, er the the test that must be followed after you're actually matching the criteria of your patient? S5_11_2: [876.274] yeah yeah i mean, it should be it should be, but, here the the information that we have is er, just having those criteria you don't find everything on the test . [888.984] of course if you have met the criteria, and you go like follow up as you say S7_11_2: [893.884] mhum S5_11_2: [894.607] ok ? with the findings you will have won't show you everything that's the point. in in the Amsterdam S7_11_2: [901.448] so what what do clinicians do they generally use [??] testing? S5_11_2: [904.827] no it's just that the people so they know the, to Bethesda, or, if you for example if you the criteria and you say ok this matches, it has all criteria Amsterdam criteria, ok? and you thinking the basic tests, and you [?will ] find the mutations, then you can again follow up looking for another mutations, performing another test, ok? be- because the first ones, you in the first one you didn't find anything, (2) and whereas with, Bethesda er just, one of those criteria, and you perform a test, the tests match with your findings . S7_11_2: [951.866] so, that way doesn't mean that Amsterdam rules will have, er higher percentage of false positives S5_11_2: [959.739] uhm yeah. yeah ok. (3) basically it depends of the, in medicine it's like that, depends on the hospital on the [?] you know the school that they follow, it depends, but also here for example if you go to Amsterdam you will perform more tests ok, and then you are spending more money . so that that's an important point . whereas the other, it just what criteria you are thinking can be this, and you perform those tests and you can find something, saving you money. S25_7_2: [1000.273] oh S5_11_2: [1000.794] so that's something that, they take into account . (3) erm, any other questions? (2) hope it's clear S25_7_2: [1024.805] [cough] excuse me. ehm so i'm going to talk a little bit about FAP . (5) S7_11_2: [1033.865] S25 S25_7_2: [1034.974] [??] [organising slides] (8) [1042.008] ok so we'll just talk a little bit about eh familial adenomous polyposis em, and yeah about i've went and stole this drawing from M's lecture i forgot to reference it so i will go back to do that when i send it to you er and it's the same as what we were talking about this morning what, [? name] went over, ehm so FAP a- an instance of one in five ten thousand, ehm so it's relatively common for inherited cancer which they are not very common anyway. ehm, dominant, at the inherited level but, recessive at the mutation level so it's exactly what we were talking about today so i just put it in to remind us because in case anyone had forgot so exactly what [?] said so you inherit, one mutant copy, and you get another, mutation in the other allele throughout your life you know, whereas if you had somatic, MAP you would be born with two normal copies and it would be really unlucky to get a mutation in each allele . ehm, so that's why i put in, the two [?] hypothesis just to remind us that's how it [?goes] but we should know that anyway [?from the lectures] . so ehm, (2) always caused by mutations i mean, i say always, but, you may get misdiagnosis of [?a] FAP with like the recessive em, MAP, until you do the kind of molecular tests so i would once you do the molecular tests it's always bound to be caused by mutations in the APC gene, ehm APC's a tumour suppressor gene, so it would make sense that mutations would, kind of alter the rate somehow on the [? cell [?]]. ehm and it does loads of things, never mind [?supressing it's polyp]. ehm function transcription [?migration ] differentiation of the polyp so it's quite important, ehm [?gene] and it kind of cell cycle is regulated properly. ehm so there's quite a few, different types of FAP and they're mostly classified according to the number of polyps that you see, ehm, so, that that's just done by colonoscopy so that's normally the first thing we would do anyway. ehm if it's suspected, and the, severity or like the classification of FAP it's ehm, it's got quite a lot to do with the prognosis and age of onset and things like that so the more polyps you've got the more severe the disease. ehm but they have found that you can get this attenuated, FAP which, is what you know it would run in families as something kind of a lot less of a severe phenotype it might not even be picked up until people are well under way of you know in their late fifties and things like that because there's so little polyps, it takes longer time for any other like extra colonic to develop, so sometimes that kind of goes undiagnosed until quite late on in life . even though you have been born with a mutant gene so effectively, you know . ehm and different mutations cause each type as well so, ehm not just mutations are pretty much responsible for all of the ehm, ehm in severe FAP it's just called and in mild FAP it's just called, FAP. so you might read about FAP which will enclose like both of those types and A, FAP which is attenuated so if you should come across it when you are reading. ehm, so, pretty much non [?] mutations they, end up with truncated protein product, so basically you just have no protein product at all so it kind of makes sense that you would lose function . ehm and there's so there are loads and loads of mutations [?we can ] identified in the APC gene it's not like, er there is a few you know like a few hot ones i think there's like over eight hundred or something so it's quite difficult to kind of classify. ehm and the reason why it's really important as well to, to like find the mutation, because the different, you know the different genes have got a series of [?] for how you treat it and how your life expectancy and things like this like this ehm, this mutation, it's obviously been really serious you know it just [??] life expectancy by ten years compared to, other mutations that cause you know FAP. ehm, and just a little summary like although we're saying that with the eh mild, you really do need to have a colonoscopy first and it 's suggested in the literature because, you might find a mutation, first of all and, a lot of them can overlap so, if you look to mutation of one two five oh and one four six four are kind of the majority that cause FAP the different ones, mostly kind of non [?] ones but then, the majority of the mutations called mild, are between one five seven and one five nine five so there's a bit of overlap you know so, ehm, and but attenuated FAP is quite different, the mutations are mostly in five prime and three prime end i think the five prime end of the gene's got a lot to do with ehm, like [?active?] em, got a lot to do with, [?active binding] so it's not so much, to do with the actual gene function itself, it just so happens that these two mutations happen in series? so it's quite easy to, to distinguish ehm, and as i was saying the attenuated FAP, it's quite different it's quite, it's a lot less severe. em, and it's quite [?bearable/variable]. so, if we're looking for FAP as well, ehm, i kind of like something to look for in mutations and like if the clinician is seeing family members and things, is this ehm CHRPE, so it's ehm one of these extra colonic like you know extra things that happen, but there's no consequence of it so it's like giving a marker, so it's like the iris thing you know there's Brushfield spots so you can always see it in Down Syndrome people, kind of thing like you know cases of Down Syndrome so here, clinicians can look for this first of all before they even go looking for mutations. ehm so it's something else that kind of helps, ehm, so is it a [?] you need to try identify carriers who [?] mutations [?] detected . [very fast] eh just a little bit about the APC gene . ehm, [cough] so the, the the black bit here this is the kind of hot spot, for mutations that cause severe FAP with a load of polyps, ehm and you can see again there's quite a lot of overlap between this and intermediate, mutations ehm, and what we're seeing here at five primer and three primer end are where you can get a lot of mutations that cause [?F]AP. so when they're looking for mutations you know, it's quite useful to scan a whole gene, rather than to look at hot spots, it's kind of the? [??], ehm, so yep . (2) that's pretty much what she said so, these [?] tumours as well is another one of these extra colonic features and that is quite serious but they may or may not be associated with FAP it's sometimes you get and sometimes you don't, ehm and that this is a quick graph from the same paper, just to say, how where the distribution of the mutations are along, the codon so you can see like quite a lot of mutations here and here, so they're kind of hot spots . [directing to visual on PPT] ehm, and when it's mutated this is what how it works, this is how it causes the kind of, eh FAP, and the thought that here, this is just a normal in a normal cell, APC [?] eh beta catenin, and, beta catenin is a it's a transciptional activator, so we need beta catenin to be free, for these genes to be on . so it it sequesters it, in the cells so theses genes cannot be switched on, eh whereas here [?] cancer cells, ehm if you lose the function of APC there's nothing to hold the beta catenin back, so this constitutive expression of these genes and these genes are- it's the Win pathway and it's associated with kind of cells [?that are out of ] control and things like that so, you don't want, you don't want this on all the time , otherwise you'd [?be uncontrolling] cell differentiation proliferation, em and that's just em explaining what i said, and i've just put in the, ehm, (2) the, what do you call it?, you know ? the definitions of what the thing is yeah [laughs] sorry, ehm so like this is just a transcription factor of what [?] do, ehm [?] protein at which we all know is like a is like a, transcription activating as well, em so yes that's what it does in normal cells and cancer cells, and just really quickly, to as i said because the mutations are all in a gene, they generally do mutation scanning first or like sometimes anyway, em, using, SSCP single stranded confirmation polymorphism i don't actually think i wrote it down, actually what it stands for ehm so basically you can see if the gene has a mutation you can see the wild type, ehm when you do [? elector?] so so far but if you have a mutation that alters confirmation in a single strand, and it's going to be like a bit folded a bit funny, then it's either it's not going to travel [?so far] most of the time, so this is how they first of all say oh there is a mutation in this gene, and they can kind of pin point from there, where it is. ehm, and i i read they did a bit about MLPA, they've got a MLPA kit that they do for APC gene but it wasn't, particularly well explained and that was on the MLPA web site where it told you about this particular kit, it's a commercial kit for APC and it's a big there's a big statement on it saying this does not affect the vast majority of these mutations, because the vast majority are too small to be detected by MLPA, er so it's kind of bit of like, a grey area i wasn't really sure what to do with that because, they've manufactured it to use for screening for mutations in APC, but yet it doesn't really do the job, you know? so but it's in all the literature so that's why i put it up anyway, em and also because most of the mutations em, result in a truncated [?] truncations it's quite easy and quick you know it's often quick to do first of all when you've not really got a clue, ehm, and that's just a quick diagram to show you how they do it . em, (2) so they, take off, em the hybridised APC gene and then they just see how far how far it's going to run and you can tell, again you know it's kind of similar to SSPC em, ehm i think it's how far it's running [?the gel], and they can tell that if it's shorter or longer . S31_T4_11_2: [1053.208] laughter form? [1509.696] [?definitions] S5_11_2: [1645.370] [?] bases S25_7_2: [1646.560] yeah and also that's it the obviously get the, the sample, [?] remember because this is where a lot of the, em this is just talking about colons obviously S5_11_2: [1655.797] yeah S25_7_2: [1656.560] ehm, and again if you do this [? sometimes] you only do, colonoscopy because they're just checking quickly, for something it's if you see, the tests can be done everywhere, ehm so yeah, but i did just nick this straight from the figure, eh [??] might not i don't know about that bit S7_11_2: [1670.668] [laughter] S25_7_2: [1671.980] and that's it i didn't actually put in my reference slide because it's the same as what's on the sheet so i can always if you need it, for the purposes S31 of whatever ehm it's all the same [??] S27_11_2: [1684.691] the [?] test and what are the bases? S7_11_2: [1687.038] em like [?term] : [1689.290] [laughter] S7_11_2: [1690.276] [?] you need to get like a [?term] a dictionary : [1692.360] [laughter] S5_11_2: [1702.494] [?] [aside to S27] S27_11_2: [1703.920] [?] [aside to S5] [1707.685] [??] S29_11_2: [1712.643] who's next? S28_11_2: [1713.891] S26? S26_11_2: [1714.723] is it me? S28_11_2: [1715.089] yeah S26_11_2: [1715.529] oh S27_11_2: [1715.529] no it's me S26_11_2: [1716.808] oh yeah S28_11_2: [1717.491] oh ok yeah S27_11_2: [1718.489] and then it's you S28_11_2: [1719.501] it's you S27_11_2: [1720.154] that's ok S28_11_2: [1720.698] sorry, it's ok S27_11_2: [1726.313] oh no. : [1727.512] [giving out handouts? preparing?] S27_11_2: [1734.885] i didn't er, write any references [1749.808] i'm now going to talk about hereditary non-polyposis colorectal cancer or for short, HNPCC : [1757.103] [some laughter] S27_11_2: [1759.180] so i term this disease autosomal dominant syndrome which predisposes er the carriers in early er onset malignancies. this [?] there are different types of ah malignancies, ah it's a CRC colorectal cancer endometrial stomach pancreas skin ovarian and brain cancer . er people carry the, carry the mutations have a sixty percent ah, (2) risk, to develop CRC, and the women carry the mutation have a fifty four er, percent risk to, have an endometrial cancer . although HNPCC is an autosomal dominant syndrome, there are families where, it's recessive . the, the parents who are both carriers, they may not have any cancer, and ah the child ah develops cancer . but in those cases, the basic er cancers are er hematological and brain cancers . (2) HNPCC is usually, (2) caused by mutations in ah, the genes of ah mismatch repair system . these genes are MLH one MSH two MSH six and PMS two, and those genes are responsible to correct mismatches that er, are caused during replication. (2) as you can see in the picture, (2) i don't know if [?] here some ah mismatches er are caused, and er they let the DNA those proteins come and just repair it but if those proteins are not are mutated one of those proteins is mutated, (2) sorry one of those genes is mutated, then the other gene is not functioning so there's no repair. (2) in most of the cases er MLH one ah is found mutated in fifty percent of the cases, of HNPCC. in forty percent, ah MSH two is mutated, in seven to ten percent is MSH six, and in less than five percent we find that PMS two is er mutated (3) it's not [?fully] saying there is eighty percent ah, for ah colon cancer, sixty percent for endometrial cancer and just twenty percent for the other types of cancer . (2) as you can see there are different types of mutations that can be caused by those genes. ah endometrial percentages . they are nonsense- other types of mutations nonsense frameshift missence, in-frame insertions or deletions and the other types, that are not in the same percentage. (2) you see all the mutations in those four genes cause loss of function in the protein. there is a paper, but just one paper, that ah says that if there are mutations in MSH, six gene there is low penetrance and higher onset of age, but there not a lot of people who carry this mutation and so there can't be a very big study [?finally] and also mutations in PMS two, gene eh cause early onset brain tumours. so to identify a family that is eh in risk of HNPCC, as S5 said we use the, we use the criteria, the Amsterdam Bethesda and i also found the Dutch criteria which are eh, revised Bethesda and er, there are more ah, concentrated on ah, the number of polyps that were found . (3) and i think that none of you will talk about this so i didn't write anything about the testing for [looks round] ok these are the types of [?testing] S26 will tell you. so for ah this family, eh, (2) for this family i think, that the Amsterdam the first Amsterdam criteria are not satisfied however as you saw in S5's presentation, the Amsterdam two are satisfied . the Bethesday criteria are totally satisfied, about the Dutch criteria i don't know because it's the number of polyps, and the molecular results show the mutation in MLH one, so the diagnosis is HNPCC. S5_11_2: [2031.528] wow S7_11_2: [2032.645] she finished my report too : [2032.645] laugh [2034.894] [group laugh] S30_11_2: [2036.274] mine too i guess : [2037.379] [group laugh] S30_11_2: [2038.508] i think S26 will do the other half and i won't have anything to say : [2041.232] [some laugh] [2042.832] laughter S27_11_2: [2042.977] sorry S7_11_2: [2046.328] anyway it's mine it's just such a big conclusion [?] S25_7_2: [2049.183] see did you draw that with [?] S27_11_2: [2051.151] no S25_7_2: [2051.985] ah right [??] S7_11_2: [2053.344] [laughs] S25_7_2: [2053.720] so it's not not because you didn't references but i just wondered because i thought you S27_11_2: [2056.957] but i reference there you can see S25_7_2: [2058.927] ah right ok all right. but yeah i was thinking that, how did you how did you work it out if you did do it yourself. S27_11_2: [2068.516] i could but i didn't want to S25_7_2: [2069.824] oh all right S28_11_2: [2071.729] [?]want to ask you anything ? [to S27] S27_11_2: [2072.935] i don't know S25_7_2: [2074.015] [laughs] S5_11_2: [2074.635] [?] S25_7_2: [2075.495] yeah i wanted to ask about [??] diagram S26_11_2: [2081.318] i've got this [??], but now we know it but this is to diagnose it [2086.517] S5_11_2: [2086.665] [?aside to S27; not all audible] autosomal recessive gene right? S27_11_2: [2091.229] yeah S7_11_2: [2091.873] [? aside, inaudible] : [2093.640] [also background aside, S26 & ?; not audible] S27_11_2: [2093.651] [?] sometimes both parents have the mutation, have the mutation for HNPCC but they don't have cancer. however they also have test S5_11_2: [2102.559] oh S27_11_2: [2102.959] because it's like, they [??] both the mutations, it's [?not] recessive S5_11_2: [2106.262] ok but those cancers that you mentioned the [?] the brain, which, kind of cancer is it? the ovarian [?] S27_11_2: [2115.562] yeah [2118.483] it's not, [?] it's colon cancer but [?] in those cases it's mostly [??] S28_11_2: [2125.087] except Leukaemia MYH [to S27] S27_11_2: [2127.754] umm? [to S28], MYH? S28_11_2: [2130.754] yeah the same gene? S27_11_2: [2132.204] not MYH. and they are not [?MMR] these genes MSH MSL one and, this [??] S28_11_2: [2141.462] oh ok S7_11_2: [2142.174] S27,the endometrial [??] S27_11_2: [2146.873] [shakes head no ] S28_11_2: [2148.143] ok, er i will talk about MYH associated polyposis, MAP, er what is it first of all, er it's a inherited syndrome, er and in this stage MAP is not er, cancerous . er and it's associated, with development of colon cancer after [? sixty] . er it's usually appear between the age of twenties, between twenties and fifties, er, the shape of how we can recognise MAP, it's remarkable er, combination of, like er circles, cluster, ah of and er overgrowing tissue in the endometrial bowel . here is some pictures [shows visuals] ah this is how it's look like, (3) and this is the real one S25_7_2: [2217.453] uhuh S5_11_2: [2218.201] oh lovely S31_T4_11_2: [2218.469] ok you win the award for the grossest picture this week : [2221.510] [laughter] S25_7_2: [2222.745] is each one of them, a polyp? S28_11_2: [2225.673] er oops [closes picture ] S25_7_2: [2226.853] or is each one of the circles thousands of polyps? S28_11_2: [2229.386] i think [??] there S5_11_2: [2230.620] yeah S7_11_2: [2231.596] ah S25_7_2: [2232.330] yeah so it's like one to two S5_11_2: [2233.125] the other one at the, the top is a [?lesion]. go yeah that one [directing S28/pointer]. so the typical characteristic of the, polyps like the [?] S25_7_2: [2247.044] oh right uhuh [?] S27_11_2: [2249.688] that's why [?] [aside to S7] S26_11_2: [2251.271] [??] S28_11_2: [2251.271] er, i think this how it's look like with the microscope S7_11_2: [2255.419] better S27_11_2: [2255.419] better : [2256.732] [laughs] S28_11_2: [2258.468] ah yeah [??] (2) and this the, OCT the optical, er coherence tomography, when the patients must drink the, four cups of very bad taste er liquid, er S25_7_2: [2283.986] [laughter] S26_11_2: [2284.919] [??] S28_11_2: [2286.343] because of er, it gives some fluorescence molecules . (4) ok er what causes MAP? er a mutation in this gene, and the oxidation, in the er proof reading er process, er which leads the change from GC to TA. and this diagram here will explain little bit the, (2) idea of this inheritance here in the middle, in the central pathway, you can see in general the change from GC, to TA, happen because the oxidation here change the G to O, and in the er repairing system using using the MU er YH, it's associated in the er repair, with er the DNA repair, also, this one . ah can take the O back, but er it's not [? then ]to TA, and er, (2) also this, compound is associated with er repairing as, this one, (6) and that's it . there [?isn't [?] environmental factors i think, but er i didn't find for a specific MAP. (2) any questions? yes? S27_11_2: [2389.850] er first slide you said you said, maybe it's, this one [S28 changing slide] it's not cancer but it is shaded colon cancer i don't understand S28_11_2: [2399.782] yeah i in in this stage of MAP it's not a a cancer ok, but er, it may develop to, it might become more aggressive, then it become a [?main risk]. S27_11_2: [2416.044] you mean to say that they have polyposis the polyps? S26_11_2: [2419.716] i think it's this this one is the weird recessive one where you need two they have two mutations, but the other one you only have one and then you get the other one and this causes cancer, in this you've already got two, i think this is why S28_11_2: [2419.801] yes. this polyposis not S27_11_2: [2423.552] yeah S28_11_2: [2431.314] yeah you inherit this, but, it may it may become cancer after S26_11_2: [2433.132] yeah [2434.412] it's not cancer [2437.362] [??] S27_11_2: [2437.362] so it's like a [?] S7_11_2: [2439.047] yeah a [?] S26_11_2: [2439.889] no it's slightly different because this is recessive, as in you need two mutations to be inherited to get it S27_11_2: [2442.303] yeah i mean but S5_11_2: [2446.036] i i think that er the well you mean [?] is not true S27_11_2: [2446.036] yeah S5_11_2: [2452.267] is that you referring this, like it's not a cancer, you have [ ?MI HSG] polyposis is not cancer S28_11_2: [2461.358] it's not cancer S7_11_2: [2462.338] but it can be S27_11_2: [2462.783] ah but then it can be S5_11_2: [2464.505] yeah but it's a factor depend on colon cancer S28_11_2: [2468.683] yes it's one of it's one of the reasons of S26_11_2: [2469.264] [??] S5_11_2: [2472.397] but it's not cancer S25_7_2: [2474.011] but is the is em, MYA what did you say sorry? ML? S5_11_2: [2479.469] [?MAL C] YH S27_11_2: [2479.469] MYH, no [? but it's] S25_7_2: [2480.485] [?] [2483.183] oh sorry but then if it's a polyposis, S5_11_2: [2486.676] poylposis S25_7_2: [2487.671] uhuh S5_11_2: [2487.967] yeah polyposis is just, that you have found polyps that's all S26_11_2: [2490.952] polyps S25_7_2: [2491.953] [?] S5_11_2: [2492.603] polyposis means that it's cancer S26_11_2: [2493.011] [concurrent?] [2495.548] it's not exactly benign S27_11_2: [2495.548] [?] aside to S25] yeah S5_11_2: [2497.239] that is a [?] S26_11_2: [2498.763] it's [? making] a term S5_11_2: [2501.016] ah and, just to compare it polyps have the most common tumour, tumour in the colon but tumour doesn't mean that it's bad, ok? S26_11_2: [2509.889] yeah [??] : [2509.889] [some concurrent?] S5_11_2: [2509.967] [??] in the the skin you have your, you have your skin, so in the colon you have polyps, you know what i mean? after the sixty years old is normal S30_11_2: [2509.999] no but, it's tumour S25_7_2: [2513.428] [??] [2519.016] oh right S28_11_2: [2522.374] [?do ] the same polyps appear, on the face as well skin here [gesturing to face] S25_7_2: [2526.191] i think i've got polyps on my head, i'm not sure S5_11_2: [2529.080] oh : [2529.080] laughter S26_11_2: [2532.151] let's have a look S25_7_2: [2532.608] i need to go and get them seen to S26_11_2: [2534.574] really? S25_7_2: [2534.945] yeah S26_11_2: [2535.313] are you sure it's not like a [?skin] attack ? no : [2536.949] laughter S26_11_2: [2539.941] it's not like a skin [?attack] or something S25_7_2: [2540.406] no it's a like a lump it's a growth S27_11_2: [2541.943] it's not like a S26_11_2: [2544.007] i think they're something that's [?/] : [2544.007] [many people speaking, not all audible] S5_11_2: [2546.949] yeah but S25_7_2: [2547.751] [??] head it's weird feel it feel it but that's the only one [??] see? S5_11_2: [2551.953] [??] S27_11_2: [2553.698] ah it's like a lump [feeling lump on S25 head] S26_11_2: [2555.237] yeah so polyps not [??] S25_7_2: [2557.007] that's why i need them checked [??] : [2558.578] [laughter] S5_11_2: [2559.674] i think it's S25_7_2: [2561.478] a polyp S5_11_2: [2563.039] no not polyp [?polyp] it's [??] : [2565.151] [laughter] S26_11_2: [2567.159] yeah S27_11_2: [2567.886] [??] S25_7_2: [2570.903] [??] when i'm thinking about something or i'm writing and i'm always like rubbing it S27_11_2: [2572.116] [?] S25_7_2: [2580.735] it's weird, sometimes it gets bigger as well S26_11_2: [2584.144] my mum has like a lump on her head that gets bigger some [?how], she went and got it seen to and they were just like [?] no idea what it is S25_7_2: [2590.577] sorry sorry S26_11_2: [2592.187] moving on : [2592.187] laughter S27_11_2: [2594.199] i have one more question sorry. i didn't understand what is the [?toll/TO?] S28_11_2: [2599.134] what is it called? what's that? [goes over to look at H/O] S27_11_2: [2600.088] the O letter . it goes the place of er [? Y] S28_11_2: [2604.009] oh it's er it come from this compound. where [??] S25_7_2: [2610.097] so it's like a [??] it's like a funny G S28_11_2: [2614.171] eh no it's oxy[?] S25_7_2: [2617.163] uhuh S28_11_2: [2617.794] it come from a er, a compound structure very similar to the normal ah, [A and G and C?] S25_7_2: [2624.727] uhuh S28_11_2: [2625.208] but it [?carry] oxygen [?] one of the S27_11_2: [2627.409] is the oxygen [?] S7_11_2: [2630.702] yeah S28_11_2: [2631.377] yes S27_11_2: [2632.229] ah really? ok thank you [2634.175] ok thank you S28_11_2: [2637.358] but this compound is taking out, this one [pointing to H/O/ visual] S27_11_2: [2641.588] yes yes S25_7_2: [2643.755] [??] S26_11_2: [2646.015] [??] [to S25/aside; not audible] S28_11_2: [2649.945] anymore questions? S25_7_2: [2651.603] no S28_11_2: [2652.746] have we find the environmental factors in your FAP or your S25_7_2: [2656.449] well i'm sorry i forgot to actually say because i didn't include it in my actual report but in general it just says if you have a predisposition, then obviously you your diet, and things like that you shouldn't eat processed food and things so [??] small, and then they have a, any major, it didn't say on the effects but i didn't give you like the effects of, [?environment] for example it just said recommended, you know that you don't like carbohydrates that you have, aren't in the form of anything, processed or potatoes actually it did say that they said you should get carbohydrates from, ehm pulses, like beans and stuff yeah. it did say, like if it's not relevant to S7_11_2: [2669.298] [?] S26_11_2: [2698.275] yeah S27_11_2: [2698.941] ah not to eat S25_7_2: [2700.286] so to get you carbohydrates somewhere else . and not to eat [?red meat] S5_11_2: [2703.238] and [? chips] [2704.624] : [2705.371] [laughter] S25_7_2: [2710.326] ok S26_11_2: [2726.525] yeah my, my slideshow isn't great it's literally about four or five slides but i have details in the report. it's just so there's something there to, look at [? mumbles as sets up PPT] ok? so i'm doing, how we're going to diagnose HNPCC and MAP which i think a few people have kind of looked at but didn't really want to go into detail because then i wouldn't really have anything to say, so what's left, the first on is familial adenomatous polyposis, and erm, yeah that's this type of protein cancer is, polyposis it means there's loads of polyps formed in like the bowel. and it's caused by APC gene as we've heard and, the way that they use to detect it, is for a lot of these it's actually just sequencing because, i think as S25 said there's so many different mutations that can cause it there's not like a specific kind of technique you can do that can just narrow [?this bit] down, so, i think, they get like the coding region of the gene and it if they suspect this is it they, sequencing is the only way to actually find the actual mutation that's fine for most of them, but not all of them i think some of them they don't really know, what mutation causes it yet so some of them they know, [?] this will cause it and others times, they don't know. so, and that's why i've got eighty to ninety per cent of FAP cases. ehm, and also for people [?at] MLPA and stuff there's a tiny bit about it but, from the papers i was reading there are only two ways they really use, it's sequencing and protein truncation, cos like that, it says here that protein truncation testing, ehm finds like nearly ninety four per cent that's quite a lot and i think that's because, a lot of mutations cause a stop codon, so protein, might not be there or truncated so like you know run it on the [?gel] and then you'll see that, there's [? an abnormal] protein there so they're the kind of two tests you do, to analyse this and this would be on like a tumour sample so, if you like colonoscopy find a tumour, these are the tests you can do, to check this type of mutation, ok? ehm the next one hereditary non-polyposis colorectal cancer HNPCC, ehm this is the most common type of bowel cancer, and there's it's [?due] DNA mismatch pairs so there's like four genes here that are MLH one MSH two, etcetera, etcetera and this mutation in, one of these genes so, that's what going to cause this disease, and, erm as S27 was saying there's a lot of other, cancers that are caused by this as well, but the other main one apart from colon cancer is endometrial cancer which i think it's like fifty four per cent of women, who have this also, go on to have endometrial cancer which is quite high. erm, and the way to test it so, [?unlike/and like?] sequencing with this type cancer there's other ways you can actually narrow it down first which is quite useful, ehm the first one would be to microsatellite instability testing i think that's the one that we requested when we did the sample, ehm, that's because something like ninety per cent of tumours will have this instability because of the DN mistmatch repair's not working properly, the actual test itself it's, it's just it's the size of the micro satellites they test which is the size of the [?allele] so they get it it would be like running it on the [?gel ] and seeing that they're abnormal sizes to what you'd expect, ehm, and what they usually do is they test for like five microsatellites, in a sample and it kind of, they count it as it varies a little bit but they would say it counts positive, instability in two of them, er kind of mutated then it would be you know it's instable. ehm occasionally they only find one, and in that case they recommend that the testing more microsatellites, so maybe ten, just in case, you know, so that's what they would do for microsatellite instability . ehm [?when ] immunohistochemistry i've just kind of stole this from the lecture sorry i didn't reference it, ehm, it can be kind of a secondary thing till the microsatellite's due back as well as help narrow it down, or you can do it as a first step it kind of varies which lab you go to, at which hospi- you know, but ehm with immunohistochemistry you would get antibodies against, the DNA mismatch repair proteins, so if you've got a mutation that, er like the protein's truncated or it's like not there are all when you do the immunohistochemistry you can see it's not there. so that's the kind of two tests that you'd start off with, to diagnose this. erm after you've done that if you've done, like microsatellite instability testing and it's positive, you'd analyse the MLH one and MSH so yeah if we use MLPA and, if MLPA doesn't work, and again it's sequencing the gene i mean, the reason they do [?the] steps before that is cos there's four genes, you can't just say at the beginning i'm going to sequence all four genes, so by doing things like immunohistochemistry that kind of narrows it down, it's not [?about the] sequence so much. and er the last one is the MYH associated polyposis, so with this one it's it's i think it's similar to the FAP one so, if you're having like a colon exam and they find polyps and it's not FAP, quite often it would be this one, this is like, the next one they would kind of consider after this, erm, and how they screen it, again it's, analysing the gene by sequencing, but what they found is in certain populations, mutations are more common, like, which was an interesting paper so, they said that you can certain labs will say you know you're from this population we're going to look for these specific mutations first, other labs will just you know the best way to do it is just to sequence the whole gene, so other labs will just go straight into doing that, (2) erhm that's kind of it really that's the end oh the last bit i was going to say is erm, the reason they i don't actually go into this it's to do with counselling but, if they find the mutation which is what it means they can check with other family members, and so if you know someone has a susceptibility to cancer it means that, the diagnosis they can go and have like, colonoscopy exams like every year to check up on it and, you know if you've got the HNPCC one as a girl you'd have, like uterus examinations and stuff so that's kind of the importance of diagnosing these specific types of cancer separately. ok ? two genes first because, these are the majority of mutations found in these genes i think it's up to like ninety per cent possibly of these two genes, so those are the two that you would want to analyse, ehm but if you've done immunohistochemistry and obviously you'd found this missing protein it's not one of these two genes, you'd then do a sequence of that gene you wouldn't sequence these two . so that's all about that, and the way you analyse it i've got, is MLPA [they say malpa for MLPA] or gene sequencing, so, there's quite- there's not a large amount but it's something like thirty per cent or something of MLH one, mutations they're like like large deletions, so obviously you can use MLPA to test that and, i've got a picture, of MLPA which i [? picked ] from PBL four so i thought i've already got this so i'll just put it in, and you can have it as a reference and i've got an explanation but, but i will know what MLPA is kind of thing it's you know, if if there's a deletion there, the probes won't be able to find the right gap [?to ] check it, : [3012.210] [laughter] [3116.130] to start 9/1/2012] S25_7_2: [3116.936] yeah S26_11_2: [3117.257] questions yeah [?] questions : [3118.099] [?someone?]]can i ask a question? S30_11_2: [3120.267] did you say there was micro satellite analysis S26_11_2: [3122.020] yeah S30_11_2: [3122.764] so if you have, you know if you have the risk of getting the cancer can you still diagnose it? with micorsatellite analysis? S26_11_2: [3129.565] what do you mean? [hesitant] : [3132.922] [laughter] S30_11_2: [3135.014] like if a person is [?] can you use it as a screening method? S26_11_2: [3138.641] i don't think so S27_11_2: [3139.733] no S25_7_2: [3140.559] oh you mean the tumour S27_11_2: [3141.067] when you see the tumour [??] S30_11_2: [3141.179] [?] S26_11_2: [3144.750] yeah. you see if they find a tumour they might analyse the tumour the tumour they'll find that has instability but it wouldn't be something that's just in, the blood anyway S25_7_2: [3145.373] yeah [3151.737] uhuh [3153.386] so you couldn't screen because it wouldn't be there S30_11_2: [3156.075] yeah S25_7_2: [3156.940] it's [?] S27_11_2: [3157.131] it's depends on [?] the cancer is developed so [?] S26_11_2: [3159.856] because the DNA mismatch stops working which is like the tumour goes [? S27_11_2: [3164.180] [?][very quiet to self] S25_7_2: [3164.370] it's not that relevant but i was just wondering and i can't remember if you even said anything about it but, how big is the is the em, like the MY MYH and the like the DNA repair genes i mean like are they big in terms of if you do sequencing is it kind of relatively routine?, S27_11_2: [3180.537] it's not [?] S26_11_2: [3182.045] yeah S25_7_2: [3182.243] it's what ? [to S27] S27_11_2: [3183.450] [?] S25_7_2: [3184.365] yeah S28_11_2: [3184.592] sorry what do you mean by big? S25_7_2: [3186.195] like in terms of like big like really large genes so you [?] the relatively small like, you know i just wondered S26_11_2: [3186.980] like [?] S28_11_2: [3190.222] oh S27_11_2: [3191.489] for example one group sent to S38_T5 a request for ah sequencing of both the [ MY ] genes and she said no you cannot do that S25_7_2: [3200.821] yeah S27_11_2: [3200.978] yeah so that's why S26_11_2: [3201.889] yeah with with the HNPCC there's other things first but the other two didn't really say much oh [?she] can do a [?partial] sequencing so i know what you mean, i don't know if that is the first thing [?] S25_7_2: [3209.609] is it the step thing to do S27_11_2: [3209.800] yeah but the other [concurrent] S26_11_2: [3211.451] yeah but i couldn't really find much else apart from that truncation in the first one S25_7_2: [3213.901] that's it [3215.148] because there's so, cos most of them are i think quite varied anyway with what happ- with what mutations cause it S26_11_2: [3220.442] i think that can be quite rare though so maybe it doesn't happen that much apart from the HNPCC is the most common S25_7_2: [3222.892] that's true S27_11_2: [3227.173] and in the other it's only one gene S25_7_2: [3229.678] yeah S26_11_2: [3230.451] yeah S25_7_2: [3230.694] and the oh and the APC gene is quite smallish S26_11_2: [3234.060] and it's just coding areas as well [mainly to S26] and occasionally i don't know if i mentioned, they have erm hot spo- for the APC one there are certain hots spots S25_7_2: [3235.629] uhuh [3240.792] mhuhm S26_11_2: [3241.712] so, they might decide oh i'm going to just sequence hot spots first S25_7_2: [3244.111] that's true yeah that's what they'd do S27_11_2: [3244.385] yeah S26_11_2: [3245.279] yeah, rather than the whole gene S27_11_2: [3247.545] ok S25_7_2: [3251.815] next? S28_11_2: [3253.974] S30 S26_11_2: [3256.107] you have [??] [ to S30 as she comes down to front] S25_7_2: [3257.580] [??][to S26 as she passes] : [3257.580] [some laughter] [3260.802] [change over speaker] S30_11_2: [3266.267] ok first of all i'm sorry i couldn't make it last time, i'm not feeling well these days so [small laugh] . (2) so my one is the pedigree, and the cascade of testing, and i think everyone has covered my topic basically, i don't have and there's nothing much i can find in the literature you know to test whether it's present or not . so, i'll you can, basically just you know as an introduction, i think, this is what i thought ok this family showed HNPCC. ok because of all these er criterias, which are included here. then where's the [?][ looking for pointer for PPT] (2) : [3279.813] [laugh] S5_11_2: [3280.416] [?] : [3300.558] laughter S30_11_2: [3302.286] ok so, that's because earlier average er the onset of age is early, like in all the population it will be around sixty three years, but in this we saw that it's forty five, i think it's better you go to the pedigree and read it. [ switches slide on PPT] (2) you know it's forty forty nine and then thirty four years, and then the other factor is that you know er there are, patterns of primary cancer segregation you know like er, there are two different types or three different types of cancer, like er S27 explained eh for in this family we saw we can see endometrial cancer and colon cancer . and then the generation each generation is affected, all three generations. so we can say it's hereditary and most probably can be be HN, PCC. and then, a path- the pathological features there's the [?germ] line mutation will play a you know, will play a part in er, saying that it's hereditary but we don't know the pathological features here. so if i directly go for the testing, oh finally there's one mistake in this [directing to slide], i forgot to put the er [?F] and the consultant, but in the report it's there ok. so, in fact HNPCC we know that er it's, to do with ah gene mismatch genes which create proteins for this mismatch repair, so that would be microsatellite problem you know microsatellite could be [?] but that's why i asked S26 whether we can just go for a blood test with microsatellites but we can't . so what we can do is for for testing, we can test F first, to see whether she has the same mutation because we found the mutation in P . er so we can i thought we can do ARMS. (2) what do you think? : [3409.205] [laughter] S25_7_2: [3410.955] [?] F S30_11_2: [3411.803] yeah because we already found the mis- the, we already found the, problem in P right? we need sequencing S25_7_2: [3413.241] yeah [3416.734] yeah S27_11_2: [3418.449] what's the [?] S26_11_2: [3418.746] you can always [??] to find the mutation S25_7_2: [3421.288] [??] [S25 & S27 concurrent aside inaudible] S27_11_2: [3421.288] [??] [S25 & S27 concurrent aside inaudible] S30_11_2: [3422.019] [?] it's a point mutation so, i know we can do ARMS with F and if it's the same you know we can erm, we know it's inherited, then oc- then after the second testing should be done on J and, F because they actually came, they wanted the test . so we can check whether they have it, [laughs] and then, er we can also check J, S26_11_2: [3422.322] [?] it's a blood mutation S30_11_2: [3444.174] if she because she's still fifty three, and S7_11_2: [3448.177] she's not going to give birth i think S30_11_2: [3449.505] hum? S7_11_2: [3450.418] i don't think it's very productive age [laughs] [3453.362]  S30_11_2: [3453.362] yeah but if she wants you know, or we can just go for the colonoscopy if she wants to be tested because early detection is good in cancer [laughs] and then, if K wants, we can test her. so basically that's my topic .[laughs] S27_11_2: [3468.598] it's better to test I because if he doesn't have it then J and F are fine S7_11_2: [3469.971] yeah S25_7_2: [3473.583] you don't have to test J and F S30_11_2: [3475.006] yeah but i thought because they came, you know they were ready to go ahead with the test they wanted the test S27_11_2: [3479.965] yeah but it's lots of money . because S30_11_2: [3482.625] yeah that's true. but if the patient if the patient requires you cannot, say S27_11_2: [3486.792] but you can say that if your father doesn't have it you cannot have it so S25_7_2: [3490.607] i think that's what they would do first is they would ask the children to bring their father in, probably i think S5_11_2: [3493.337] yeah S7_11_2: [3496.235] mhm S30_11_2: [3497.524] it depends on whether I wants to be tested or not S25_7_2: [3499.751] exactly S26_11_2: [3500.584] this is normal advice so J, has to have it S5_11_2: [3503.328] yeah S26_11_2: [3503.893] is that how it works? S27_11_2: [3504.655] yeah but I S30_11_2: [3505.466] no [?] generation [?] S26_11_2: [3505.657] but i mean like, [3506.990] yeah S25_7_2: [3507.684] and [??] until he's seventy to acquire the other mutation S26_11_2: [3511.670] she might [?get it] S27_11_2: [3512.782] or never because [?especially] for some never develop cancers S25_7_2: [3513.801] yes S30_11_2: [3516.401] mhum S27_11_2: [3516.978] maybe she's a lucky one [3519.069] [?let's make up a test] S30_11_2: [3520.276] [?do] the test : [3521.330] [laughter] S5_11_2: [3522.520] but, it is not fully penetrant S30_11_2: [3525.287] yeah S5_11_2: [3525.966] yeah S30_11_2: [3526.161] we cannot say, whether S5_11_2: [3528.965] i suggest, to test J or S7_11_2: [3532.641] yeah S30_11_2: [3533.223] yeah we have to because who S27 said we should test [?] yeah S7_11_2: [3535.967] [inaudible aside to S27] S5_11_2: [3537.600] yeah because if as you say you test I but it's not fully penetrant S30_11_2: [3544.127] yeah S25_7_2: [3545.189] but at least if you tested I you'd see the presence or absence of a mutation S26_11_2: [3547.792] [? S27 to ?S28] S30_11_2: [3550.197] but still it's S25_7_2: [3551.499] regardless if it's penetrant or not if he's not got the mutation, he can't have passed it on penetrant or not S26_11_2: [3555.932] but actually if he does have it then you've still got to go and test them anyway havn't you? S25_7_2: [3556.608] if he does have it S7_11_2: [3558.727] yeah S30_11_2: [3558.727] yeah then we have to test them both S27_11_2: [3560.100] yeah but if you don't if he doesn't have it S26_11_2: [3562.084] if he does you still have to [?test him anyway?] S30_11_2: [3563.426] if he doesn't have yeah, i thought if he doesn't have [?] : [3566.322] [some laughter] S30_11_2: [3567.653] i went through i saw that it's penetrant so i thought ok if you maybe have to check J and S, J and F sorry . because it's penetrant. S29_11_2: [3576.306] [?? ] to test I, i thought, to test I [?] : [3576.431] [concurrents; not all audible] S25_7_2: [3577.208] what about ? [3580.706] yeah S26_11_2: [3581.099] yeah S7_11_2: [3581.531] yeah S25_7_2: [3582.006] so P [?and I] [3583.188] ? [3583.733] what [??] S26_11_2: [3584.942] [aside?] [3587.090] er [??] S25_7_2: [3589.415] i think you should test J anyway definitely S30_11_2: [3591.876] yeah J should be tested because like i said, we don't S25_7_2: [3592.792] because [3594.241] if she doesn't have it, then you might test her husband for some other S26_11_2: [3598.599] that would be so, you know S30_11_2: [3600.464] no S27_11_2: [3601.020] i don't think [?] would have it [to S25] S30_11_2: [3602.633] i thought it was for J you know if she has it then she has, a risk of developing although she has passed the age of onset like these two, still it should you know [??] even if her son is affected and her sister is affected S27_11_2: [3613.237] yeah that's [?] S26_11_2: [3616.696] how's it going to work if she went to, the doctor [?] and oh can i get tested, would they say no? i thought S30_11_2: [3621.815] J? S26_11_2: [3622.642] the doctors i mean would they say no no [? because you] must have it do they do it [?] or S30_11_2: [3626.176] no they actually i saw i saw in some papers that they, you you know genetic counselling and all those stuff, before you go ahead with testing S25_7_2: [3633.630] that's a point [to S26] S29_11_2: [3633.720] yeah [?] S26_11_2: [3633.727] cos you know we always say oh [?] has to test this person first but what if, some other person wants to be tested? do they [?] S30_11_2: [3638.838] they do give it they do but after all counselling, like you know S26_11_2: [3642.424] to help [?] S30_11_2: [3643.429] yeah you know but, what sort of effect it will have on their life and their relations' life and other stuff S29_11_2: [3649.590] yeah S27_11_2: [3650.302] they and they explain you that if your mother doesn't have it you will not have it and just, you understand S26_11_2: [3657.486] [?] S29_11_2: [3658.897] [?] it said like to be er develop cancers one and three so S25_7_2: [3661.893] what's your point? [3665.734] it will [??] [to s26; concurrent; not audible] : [3665.734] S26 & S25; & S27 to S29 concurrents] S27_11_2: [3668.894] it's better to test S5_11_2: [3670.235] yeah [??] but this is carrier. S29_11_2: [3671.685] [?] but that's S30_11_2: [3674.355] this gene's carrier S27_11_2: [3675.672] [?? ] that if you take three people, when they are born and you put them in a room without any other environmental factors, until eighteen years old, one of them will develop cancer. S25_7_2: [3682.721] yeah S30_11_2: [3689.482] ok S5_11_2: [3690.267] no [?] [concurrent] S30_11_2: [3690.267] so the other slides are what i just explained [??] S25_7_2: [3695.918] oh no S29 [?] even more disgusting diagrams [looking at visuals on H/O] S29_11_2: [3699.792] [laughs] S25_7_2: [3700.357] pictures yeah S5_11_2: [3701.443] oh no S29_11_2: [3702.711] colons S26_11_2: [3703.029] [?] [3704.066] colons S25_7_2: [3706.521] oh man where's [?] S26_11_2: [3708.034] oh [3709.116] [laughs] S5_11_2: [3709.644] oh no S25_7_2: [3710.559] [laughs] S26_11_2: [3711.093] i'll try and find pictures to put on presentation and they're not colon cancer it's not a good idea : [3715.410] [laughter] S7_11_2: [3716.810] no S30_11_2: [3717.340] [S26 & S30 concurrent while S30 goes to front to start talk; not all audible [3725.253] you know, because possibly [??] S25_7_2: [3729.481] but at least then you've got what [?] rather than just say [??] S27_11_2: [3735.451] yeah [?] but S29_11_2: [3741.423] er my er my objective is about genetic counselling and follow up. ( S27_11_2: [3749.702] no it's the right one [about the pointer for screen] S29_11_2: [3751.099] oh right : [3752.338] [group laugh] S29_11_2: [3753.284] er before i'm going to talk about er the genetic counselling, what's genetic counselling actually it's the first step, when any patient go and er, he wants like to know more about the er, the disease or the test er what we have to carry er to carry the test, and er, the counsellor er get the main point the main points er is er family history, inheritance patterns type of colon cancer er results from the diagnosis tests. as S26 said like er if a patient er goes to the clinic and asks for a test as a, a er from the doctors say no and the [?] they say no to carry the test or not, er he fir- first he er he must study the er, the doctor must study the family history, so they know the er, the inheritance patterns, as a as a high risk or the low risk, er then er, they know the type of er colon cancer and er and the results from the diagnostic tests . so er for carrying er any test they should know like er information as much possible, er to know the er inheritance patterns. (3) er and this the pedigree er for our scenario, so er J and I went er to the doctor and asked for the test and er, how it's inherited er what er, in the family, (3) er so for I and J should be explained clearly about the inheritance patterns, and what is the possible er possible er type of er colon cancer is in the family, er, and the mutation er and they should know the mutation gene in the family, and the tests that are er preferred to carry out, and er what er what er what the meaning of the results. and and they should like to know explain as er, if they er, say that the test is er specificity is eighty per cent, so if the the tested the suspect the er mutation it doesn't er mean that, they won't develop the cancer, so they got twenty er per cent to do [?with] the cancer. so er, so in genetic counselling er it it's better to to explain very clearly for the patient er what's look like the result. is it positive or er, negative. then er move to the treatment er, there there are so er so many er different treatment er and each treatment is er depends on the er the type of the colon, cancer and the stage of colon cancer as a early stages or the end of stages. for the er, for the early stages is er, using er the er, colonoscopy . and er one of the er the the ways that can be colonoscopy is, by cold er forceps, where the er polyps is er very small it's like between two and, one ML, er millimetres sorry are removed er without any er taking any further er, healthy cells from the er abdomen wall. and the other one er is er snaring, er for the larger, polyps with the size is er one centimetre and larger, they they just use the metal ring and er, getting the top polyps, and remove, the other er the other type is er, er polypec-[should be polypectomy] with injection, and tattooing S27_11_2: [3985.390] [?] [aside to S7] S7_11_2: [3992.947] tatto S25_7_2: [3993.699] [laughter] S26_11_2: [3993.878] [? polyp testing] S5_11_2: [3994.576] oh no S29_11_2: [3996.164] getting rid of of er er it . S27_11_2: [3999.441] [nods] S26_11_2: [3999.520] [?] S29_11_2: [4000.228] yeah S5_11_2: [4001.484] laughs S29_11_2: [4002.908] and the other er way of treatment is surgery, er there are two different types of er surgery, this er depends on the stage of er, the colon cancer . is it er first er, similar to the previous er er, colonoscopy, er local incision, er resection, er and er resection and colostomy. er these er for er local incisions, and er resection, [has slide visuals of procedures] where the the er the cancer cell is very, er very small, and they just er remove er some of er, the cancer cells, with the healthy er healthy cell. (2) and for resection and er colostomy they they remove the er, the ent - the entire colon, or er where they want er part of the colon, and they just replace it with er with a bag, (3) to, to do the other [?ones]. S25_7_2: [4067.402] [laughs] S5_11_2: [4067.402] [laughs] S29_11_2: [4069.052] and er, there there is also er chemotherapy, whereas in the it's usually performed in er the late stages is the second and third stage, and er they can apply it with the drugs or injection, er the two main er, regimens [mispronounced] er used with for, chemotherapy is er five er FU, and er levamisole, and er the other one is, five er FU er leucovorin. (2) er sorry [moves a slide too quickly]. there is not much er difference between these two er chemicals, er it's just the er, er the principle for, er each hospital, and er the amount of er, these chemicals, and er for duration er, apply these chemicals. so er it's like er nearly for the treatment takes like er six to eight months, er after surgery. and this radiation therapy, [new slide] er radiation therapy is high performance energy of X ray, and there are two er two types of er radiation therapy, er external and internal and external radiation. er this picture is er, explain the er the external radiation, where is the machine er that [?attend] the X-ray, er outside the body. but in the intern -internal radiation is like inside the body is just, they get some i think er, i'm not sure it's like some er (2) liquid and some er, machines like they they just get inside the, the colon, and er, just attend the er the er X rays (2) and there are also er, er clinical trials, er there are so many clinical trials, er one er one of is er mono- monoclonal antibodies, as the antibodies recognise the cancer cell, and er they try to er to stop er, growing er develop the cancer cell, or destroy the cancer cells. as and er, it's much better than other treatments, and they er, less invasive or low er toxicity. for follow up . [short laugh] (2) er, there are like, two stages if it, er already inherited, er sorry if already affected, or with the high risk of getting the er the colon cancer . so er the follow up for the er patient er is a measurement of er CEA, and er this er perform after the surgery, er like er, after two to eight weeks, and er perform also for every three months colonoscopy so they er, they just er they diagnose it if they find eh found er, polps- polyps in the colon can- the colon. and for eh who in the high risk er the er, they go to screening for by ultrasound and er colonoscopy like every few months, or like, every year or, two years . (2) and these are references. [new slide] S27_11_2: [4282.433] thanks. (3) S25_7_2: [4285.693] see under references in my i've got this as well you know all these, it's just a really silly question it's not even a question but who are all these Lynch people do you think they're brothers, or : [4296.507] [group laughter] S5_11_2: [4298.167] oh S25_7_2: [4298.553] or what ? you know like the third one, there's three of them S28_11_2: [4298.566] brothers S5_11_2: [4300.381] it's the name of those, family [?] S27_11_2: [4303.210] yeah but the the [?] it's not S25_7_2: [4305.646] [?] no i know cos all these S27_11_2: [4309.197] i think it's the same S25_7_2: [4309.960] but it's [??] are they, are they you know members obviously members of the same family S27_11_2: [4314.368] yeah maybe they're brothers S25_7_2: [4315.495] or S26_11_2: [4316.849] [?] i don't [?] [concurrent not all audible] S25_7_2: [4317.337] for three brothers to be geneticists S26_11_2: [4319.522] i wonder [?] S25_7_2: [4321.320] [?] S26_11_2: [4322.613] i know one person who's a [?] not [?] S25_7_2: [4323.509] yeah : [4323.905] [concurrent ? inaudible parts] S30_11_2: [4324.495] in fact we get comments on him S25_7_2: [4326.285] uhuh [4327.588] yeah, but i don't think it's that common that [?] like Smith [inaudible concurrents] S30_11_2: [4328.178] maybe he [?] S5_11_2: [4328.949] but, in one paper : [4330.716] [laughter] S30_11_2: [4331.084] because they're not related they're just S31_T4_11_2: [4332.685] Smith i could understand S25_7_2: [4332.799] yeah [4334.212] and even if it's really common [?it would be] S27_11_2: [4337.647] yeah maybe that's the dad the [? others are brothers ] . no maybe one of them is the dad, and i think [?] his son to reference S25_7_2: [4338.592] [concurrent S26; not all audible] S26_11_2: [4346.923] you know i was thinking [??] because i had a lecturer at my old uni who lectured in genetics called Anne Ferguson Smith and she does a lot [?] is that, is that related to the Ferguson Smith text book S25_7_2: [4353.353] uhuh she does a lot i've seen her [4357.095] it must be S26_11_2: [4358.303] is it? S31_T4_11_2: [4359.104] i think it might be but i'm not S26_11_2: [4360.442] really? is she like is she an expert in genetics and stuff? S31_T4_11_2: [4362.749] yeah S25_7_2: [4363.832] that's what is was we were doing [?] S5_11_2: [4365.191] Cambridge right, yeah S26_11_2: [4365.860] yeah S25_7_2: [4366.461] she ehm uhuh she was in one of my papers an A, Ferguson Smith S26_11_2: [4370.598] yeah, Anne S25_7_2: [4371.318] ah but at first i thought it was someone see cos this building is a double barrelled name, so i thought it was someone who was called Ferguson surname Smith, do you know what i mean for a while S26_11_2: [4380.172] yeah yeah S25_7_2: [4380.392] and now i know that it's a double barrelled surname but, i just wondered you know is this all the S26_11_2: [4383.846] yeah you do you think, oh S27_11_2: [4385.938] we can send her an e-mail S25_7_2: [4388.156] sorry that wasn't really a question, but i did just think who are these people? : [4390.611] [group laughter] [4392.821] [laughter] S31_T4_11_2: [4394.719] what slides, that one with the the laser coming down, that looks like something in that, it looks like something out of a James Bond film : [4401.570] [group laughter] S25_7_2: [4404.432] i'm thinking is that what they do, anyway [?where/when] you don't see the laser do you think? S29_11_2: [4408.074] no S25_7_2: [4408.386] uhuh, so you're just lying there, not really knowing what's going on : [4408.449] [uhuh? ] S26_11_2: [4410.880] you can see there's a [?] [? here] S30_11_2: [4412.882] you just see that, big machine you're not going [??] S25_7_2: [4415.407] yeah : [4417.139] [some laughter] S29_11_2: [4418.687] it was too much for my objective : [4421.154] [some laughter] S28_11_2: [4423.758] S29 you know in, in Gulf countries it's very common that every day we, we receive e-mails we saw in the newspaper there is a mixture or secret, er compound which, the final a treatment of cancers every day, and i know some people they use, this, um i don't know what's ingredients maybe, some medicine or plants and, [4449.961] (2) some people they use it and it's really work, [4453.815] it's kill the tumour, do you have, any idea about this? S29_11_2: [4457.279] i came across like a medicine that, er they use it for treatment but it's like, uhm S31_T4_11_2: [4464.074] is that [? what they use for [??]] S25_7_2: [4465.372] do you mean treatment as in actually cures or something to prevent? S28_11_2: [4469.434] well, it's very common in, in Middle East there is, like everybody's producing a secret, mixture and they say they advertise this is, for cancer type this type of cancer, and some people they use it and they they discover the doctors they shock in the hospital, yes the cancer is not there anymore. S29_11_2: [4490.726] it's like the herbal [?], medicine, oh yeah S25_7_2: [4491.703] wow S28_11_2: [4492.039] uhuh S27_11_2: [4494.026] do they use it [?] S5_11_2: [4494.764] [laughs] S29_11_2: [4496.941] there are some [?] S28_11_2: [4496.941] [?smoke it] [??fun] at all S27_11_2: [4498.864] no it's like they used to it S25_7_2: [4500.574] yeah but like they use it together? aye [to S27] S28_11_2: [4502.479] yeah S25_7_2: [4502.882] ehm that's really strange eh? S28_11_2: [4504.274] yes yes S25_7_2: [4505.000] is that the case that there aren't any they don't have any other treatment, you know like radiotherapy or something that actually, you know kills cancer cells, that's really bizarre S28_11_2: [4513.493] the i wa-i was trained in a er carcinogenesis, lab, research centre [4519.621] we used to make some, i don't know what it's called in English, [arabic word to S29] S29_11_2: [4524.835] no i (2) it's kind of se- seeds S27_11_2: [4530.625] [nods] S28_11_2: [4530.625] uhuh and with eh [arabic word to S29] S27_11_2: [4531.300] S5_11_2: [4533.856] [repeats the arabic word] S29_11_2: [4533.856] [laughs] S28_11_2: [4533.856] laughter [arabic word again] S29_11_2: [4536.216] it's like the black seeds, you know the black seeds S28_11_2: [4539.455] use it on bread sometimes S25_7_2: [4540.696] oh like poppy seeds? S7_11_2: [4541.391] oh you mean [?tin/thin?], the [?tin] seeds? S29_11_2: [4543.965] i don't know [?but] it's S28_11_2: [4544.827] with garlic with honey and [?] or something that we use it on the, toxic culture [sounds unsure of self] er, tissues and, we discover there is a selective toxicity, it kills the, the affected cells but not the normal cells S7_11_2: [4545.379] it it's really, small S26_11_2: [4548.422] [?] S25_7_2: [4565.038] what? S27_11_2: [4565.038] oh right S28_11_2: [4565.820] uhuh [4566.406] [laughs] S5_11_2: [4567.737] i think it's like broccoli : [4569.586] [laughter from group] S28_11_2: [4570.298] broccoli? S5_11_2: [4570.693] yeah broccoli has a [? effect] S28_11_2: [4573.376] ah broccoli because there is ah antioxidant and antioxidant, they stop the [?dangerous] S25_7_2: [4576.044] yeah yeah S5_11_2: [4577.081] [??] that protects the DNA, and there is some trial where they are using like a rich diet [?broccoli] [?] protects against some kind of cancer[?] : [4587.519] [laughter] S31_T4_11_2: [4590.948] nobody thought about doing it : [4591.202] [some concurrent S31_T4 & S25 & S27] S25_7_2: [4592.151] yes that's [? to S31-T4] S5_11_2: [4594.811] oh yeah on a [?standard/salad] basis S25_7_2: [4595.668] [laughing] S5_11_2: [4598.570] [?other] thing [4599.637] [laughs] S25_7_2: [4600.593] the [? difference] to like, trying to have a preventative diet, [?] something that that makes the cancer disappear [?] S27_11_2: [4608.184] i [?] S26_11_2: [4609.212] i think it's [?] honey and seeds? S28_11_2: [4611.461] uhum S26_11_2: [4612.375] but then honey : [4612.945] [concurrents inaudible] [S25 & 6?] S25_7_2: [4613.086] [?]like and all these things, i think there's some value, in, like herbal medicine i do, but that's, unbelievable [??] S28_11_2: [4613.693] another one is called -and the other one is like spices they use it in Indian food we don't use it but it's very common in Indian food strong smell S7_11_2: [4623.577] mustard? [to S28] : [4623.814] [concurrent S25 & S29 inaudible] S25_7_2: [4624.417] ah you [??] S28_11_2: [4624.579] no [to S7] S7_11_2: [4624.630] you mean clove or something like that. it- it's black in colour? S28_11_2: [4629.081] no it's like er, the colour like this [points to table] S5_11_2: [4632.486] olives it's [?] S27_11_2: [4634.159] yeah that's eh [olives?] S5_11_2: [4635.886] [?]olives with olives everything cures cure everything S7_11_2: [4639.840] with olives? S27_11_2: [4641.737] [?] yeah with olives S25_7_2: [4642.449] olives yeah S29_11_2: [4643.511] any questions? : [4644.756] [group laughter] S29_11_2: [4648.074] no S25_7_2: [4650.129] [?S25 aside to S26? while S7 goes to front to start] [4653.050] that's bizarre, i really can't actually believe that, like i'm not saying i don't believe like you, but i just don't believe, i don't know i do believe S29_11_2: [4660.804] i'll find out more and i'll give you some some official thing from [?] S25_7_2: [4664.204] [?i'd like an] official statement please [joking?] and like i do i do believe in the power of like, ehm herbal medicines and things like that i do think they can have a serious affect but that just seems so, unbelievable do you know what i mean? S7_11_2: [4665.027] no because[?] S28_11_2: [4676.415] [laughs] yes S27_11_2: [4676.804] [aside to S25] S7_11_2: [4677.199] yeah i have shown you this slide because after coming over here i just realised that all that i've got on [?molecular] is so wrong. ok anyway i got the template right though, S25_7_2: [4683.048] oh no S7_11_2: [4687.943] [group laughter] [4688.702] so i'll show you the template, be happy with it. ok, so er [4693.285] [group laughter] [4694.471] i must show you guys [quite loud and emphatic][more group laughter] i'd rather make the corrections and take the handouts and in a few minutes. so like how we ask S38, for an MSI, she told us that MSI was positive like how S27 told MSI is done for, er the genes the four genes that she mentioned, and then the MSI turned out to be positive, what i was thinking is that probably i was going the wrong direction thinking about P, because, like how we discussed it in the last PBL, why would a person go i mean what is the reason for referral, that he would go, and why would he er, spot polyps in his colon in the first place? it's because we see blood in the faeces. so i thought that was the reason for the referral. that's where i went wrong . so, in [?faeces/case there's] blood in in the faeces we would go er, you know for an ultrasound, and that was that was the test i actually put up it was an ultrasound to find the polyps but later i got to know yes we are sending the tumour samples for a test, and the MSI came out to be positive, and er the MLPA was negative, because the er the mutation was not large, it was point mutation, after which S27 suggested that we would go for er sequencing, of MLH one gene, and MLH one gene showed up a point mutation, and that's how we conclude that this person has got HNPCC. but then i was hoping you know S29 would [?code/quote on this [?]] ok for this case this is the follow up. but then she [?- she [?]] follow up i thought i'd use her slides then ok this is all we found, but then er, yeah so that's my diagnostic report, and for the, the conclusion the information would be, that, er, the conclusion would be yes this person is diagnosed with HNPCC, and the recommendation would be that the rest of family members like how she told the cascade would be carried out, just for the same the mutation the rest of family members and i don't think, ehm, this has any kind er er a particular follow up because this cancer is so, er, well it's unpredictable, we don't know what to do next, so i think the follow up would be and the recommendation of the diagnostic report would be that, after we test all the family members after the cas- cascade is done, then probably you know we would go for genetic counselling and how to manage, the cancer instead of treating - you know follow er, doing something else because we still and the way to do gene therapy and drug therapy, and the chemo therapy, so i think that must be the recommendation [?for] diagnostic report, which i will change and [??hand the thing in] S25_7_2: [4852.089] [laughs] S7_11_2: [4855.360] are you ok with that? S27_11_2: [4856.664] the recommendation is screening S7_11_2: [4859.297] yeah but i was wondering what would we do as a screening test for cancer in general S27_11_2: [4863.673] you do like [colonoscopy] S25_7_2: [4865.363] yeah S7_11_2: [4865.363] do they? S5_11_2: [4866.394] surveillance S7_11_2: [4867.174] yeah that is, colonoscopy will, will be like after we've, er after the patient is referred with probably blood in the faeces S26_11_2: [4875.905] no S27_11_2: [4876.472] no no S26_11_2: [4877.211] if they found the mutation in the person, then they'll go [?angio?ambio ] or something or what[?ever??] keep checking S29_11_2: [4877.639] the screening test [?like/not] ultrasound S25_7_2: [4882.838] [?angio?] S7_11_2: [4883.695] yeah you- you mean after the mutation is found S26_11_2: [4886.699] yeah S27_11_2: [4887.227] yeah [?] S25_7_2: [4887.383] yeah S7_11_2: [4888.038] i thought it was, at first after the mutation is found yeah like like any other cancer like, er even in [?rafa] like how doctor D told we'll be doing an X-ray every, er one year [?according to D] S25_7_2: [4900.925] [??] remember D said [?we always] do lots of X-rays S7_11_2: [4905.404] yeah we we can't do it once in six months, because again that's going to add to your cancer S25_7_2: [4910.306] uhm yeah S7_11_2: [4911.176] so so that's how he suggested once in a year S27_11_2: [4912.741] but [?she] can do it herself S25_7_2: [4914.440] yeah S7_11_2: [4915.130] but colonoscopy i think is really invasive isn't it? S25_7_2: [4916.948] i've actually got [or S26/row 4?] S26_11_2: [4917.581] it is yeah S5_11_2: [4918.851] ah, i don't think they do it often because it's S26_11_2: [4922.127] it's not nice S7_11_2: [4923.271] not to mention, not to mention the [direction ?] S5_11_2: [4923.368] not nice [4924.895] [?] S26_11_2: [4925.606] [?] S25_7_2: [4926.792] if it-if it was me, and i was you know, yeah you wouldn't mind because, you know regardless of how many times you had to do it S27_11_2: [4929.402] yeah [4931.141] no but [?] S25_7_2: [4934.554] if it's S31_T4_11_2: [4934.554] but then is there a possibility of damage S25_7_2: [4937.151] oh all right S7_11_2: [4937.309] yeah i- is there S5_11_2: [4937.704] and also, yeah S25_7_2: [4940.472] yeah probably S5_11_2: [4940.472] it's not much, i don't think it's [ ?like that ]hard or something S25_7_2: [4945.664] yeah S5_11_2: [4946.297] but it's it's not nice S26_11_2: [4948.741] [?S26] yeah S5_11_2: [4949.095] so i, i think S25_7_2: [4950.488] [? i think ] i wouldn't mind : [4952.050] [laughter] S5_11_2: [4952.623] [?] S25_7_2: [4953.320] [?] S27_11_2: [4953.779] it's cancer S26_11_2: [4955.527] yeah S25_7_2: [4956.950] eh i have a quick question for you S31_T4 you know on, Monday see do you know what i think we should've done looking at your post about, the surveillance of the colon, [4965.097] if we'd asked you on Monday, had you know the question in the scenario if we'd said we asked [?] polyps [?]or whatever if we'd asked you then would you have been able to tell us? [?if there were polyps?] : [4969.684] S7 & S26 aside concurrent inaudible] S31_T4_11_2: [4977.009] no S25_7_2: [4978.037] because i think that should've been the very first thing we would've asked M, is it was a polyp but then if [?] S27_11_2: [4983.230] i think it were [gets up and moves] : [4983.230] various concurrent inaudible] S26_11_2: [4985.192] but then how many [??] S31_T4_11_2: [4986.953] what's that?[lots of concurrent talk] S25_7_2: [4987.932] exactly [4989.236] so then we would've looked at [?] the very beginning and narrowed it down [?] if they'd said yes it was polyps, you could immediately exclude or or include [?] or whatever but we never S26_11_2: [4997.211] i think [? because they/P ] already has tumours [?] like if it was the first one in the family then you'd be like oh we should [type this?] which is why[S25 & s26] S5_11_2: [5000.626] yeah S25_7_2: [5004.644] yeah that sounds right[?] then you'd [?] the polyp number first wouldn't you S26_11_2: [5007.886] cos i said that before [?] that they would expect us to assume it was going to be that one [?] but S25_7_2: [5011.602] yeah that's true [to S26] S5_11_2: [5013.421] yeah but the practical [?elements] first thing just because it's, you can perform it, quickly the results are in the same day, and it doesn't take a long time [?high] and you know S25_7_2: [5026.755] and it's quite routine, obviously S5_11_2: [5026.755] it's [5028.337] exactly, yeah exactly. S7_11_2: [5030.987] are we [?] sorry because i just went, in the wrong direction i just, i don't know S25_7_2: [5032.736] oh no [5036.555] i'll help you [?] S31_T4_11_2: [5037.332] [?] the only kind of information i've got in here is the family in the scenario meet the Amsterdam two criteria apart from the fact that we do know know whether there is polyposis, present or not, and, it just says well if there's no polyposis then carry out testing, P's tumour sample, [?] [inaudible; concurrents] S7_11_2: [5054.743] why does he need it there are so polyps found S27_11_2: [5057.532] what's the last [?one?] S31_T4_11_2: [5058.181] it's it's not very, clear S26_11_2: [5060.931] [??] HNPCC is, non polyposis S7_11_2: [5061.093] is the whole point of S5_11_2: [5061.093] no polyps is found S31_T4_11_2: [5064.179] if there's no polyposis then it's not [??] [inaudible- concurrent now with S27] S7_11_2: [5064.331] yeah [5064.602], then the whole point of testing is not there then S5_11_2: [5068.082] yes it's S25_7_2: [5068.401] polyp in my head S7_11_2: [5068.823] ? polyp [5069.851] if there are no polyps, from where does he get the tumour? S26_11_2: [5072.601] [??] S25_7_2: [5073.962] well HNPCC doesn't have polyps [to S7] S7_11_2: [5076.071] yeah then? S25_7_2: [5077.455] so, that doesn't mean there's a tumour [to S7] S5_11_2: [5078.944] there are no polyps S7_11_2: [5080.705] polyps in the tumour right? [to S25] S31_T4_11_2: [5082.023] [??] there's no polyps found there's no, there doesn't seem to be a definite answer here : [5086.205] more than one concurrent- S7 & S5 and initially S25; S31_T4 & ? S27? & ?] S25_7_2: [5086.353] yeah but S31_T4_11_2: [5087.805] [??] which is why i think the answer [?][concurrent with S27?] S7_11_2: [5089.121] er S5 polpys are the tumour right? [to S5] S5_11_2: [5093.066] yeah S27_11_2: [5093.453] yeah S7_11_2: [5093.707] yeah, so is it the HNPCC and it's not polyposis then [?] S27_11_2: [5093.920] yeah S5_11_2: [5100.083] no no no [?non] polyposis means that there are a lot S25_7_2: [5102.851] oh so they problem is there is some in the tumour which are polyps, but there's no polyposis [S7 & S25 & S5] S5_11_2: [5104.195] yeah [5106.251] polyposis means that [5108.544] if you have one it's not polyposis S7_11_2: [5111.247] ok ok. so it doesn't mean HNPCC has polyps [turns and talks to ?S31_T4] : [5112.275] [concurrent conversations: S25 & S28 on terms/referring to screen; and then term/related to food and earlier conversation S7 & S31_T4 & ? on topic; ?S26 & ? ] S28_11_2: [5113.446] is this the word? [checking on internet] S25_7_2: [5114.494] fenugreek -yeah yeah yeah but i don't know how you say it actually i don't think that's how you pronounce it[to S28] [5118.215] is [?] S7_11_2: [5118.480] [??if [?] have polyps [?]do any of the tests you know what i mean? because it's [??] S5_11_2: [5120.219] no [?to S7 or with S26?] S28_11_2: [5120.368] no it- it's like a powder it's [to S25] S26_11_2: [5122.512] what's that? S28_11_2: [5129.224] do you know ginger? S25_7_2: [5130.371] yeah but we put it in curries S28_11_2: [5131.606] you can yeah also for curries you can make powder as well, it's same idea, but it's better than cook -cooking [to S25] S7_11_2: [5131.680] why [?] S26_11_2: [5136.503] would you recommend eating this? [to S28] S25_7_2: [5139.790] [?] i don't know i mean do you know like garlic [?] what do you call it ? they're not herbs but isn't that?[?] S5_11_2: [5141.564] no no no ok [?] you can call tumour but it's [??][ with S7 & ?] [5153.177] ok, so the polyps, understand? is the same non polyposis can be one polyp, ok[?] it's not polyposis, but also, can be [?] there also S28_11_2: [5153.868] ? [response to S25] S25_7_2: [5154.896] yeah like but it's not a herb [turn & S26 joins in] but S26_11_2: [5157.001] [?] S25_7_2: [5159.136] what would you call it? it's not a herb it is a [?] but i wouldn't call it [?] it is a herb[?] S7_11_2: [5162.251] [?] so smart and everyone understands S26_11_2: [5164.117] it's a vegetable i think S28_11_2: [5164.117] yes [to s25] [5164.951] a vegetable S25_7_2: [5169.178] yeah but yeah like things like that and, cumin seeds and, you know like healing properties you know like they all do good for you but [to S28] S7_11_2: [5171.708] no i i S5_11_2: [5172.498] you understand? S7_11_2: [5173.678] yeah i got that but i was S28_11_2: [5178.121] because separately, separately don't have an effect but [you can /if you?] mix them you [?] S7_11_2: [5178.271] is there, apart from the polyps is there another [?], in another S5_11_2: [5183.568] oh yeah yeah yeah S7_11_2: [5184.755] [?] apart from the poylps S5_11_2: [5188.124] yes S25_7_2: [5189.299] [?] but i don't think you get [?] you put it in curries and [?] S7_11_2: [5195.142] yeah that is what [??] S26_11_2: [5196.475] something like a S5_11_2: [5198.761] there are many S7_11_2: [5199.589] so the whole point of, surgery to remove the polyps, it doesn't make any sense because you still have the tumour S29_11_2: [5207.861] [?] [to S7] S5_11_2: [5211.149] no no S29_11_2: [5214.029] and then you er [?]up you you measure the CAP, sample [from blood] er you er [?] colonoscopy [?] so there is no way there is no depends after that you you try S25_7_2: [5219.003] how many letters are there [?] S5_11_2: [5239.371] but -but surgery is done, in case of polyposis ok S27_11_2: [5244.345] [?] a lot of polyps, maybe now i have one polyp not yet [inaudible] S25 has one : [5248.141] [groups laughing] S5_11_2: [5248.882] [? ] [responds to S27 inaudible] S7_11_2: [5250.750] i love that S5_11_2: [5252.648] S25 has one in the head [to whole group] S27_11_2: [5254.122] S25 has one S25_7_2: [5255.152] what is it? what is it? S31_T4_11_2: [5256.652] [?] is it a blood vessel?] S5_11_2: [5257.192] a polyp S26_11_2: [5257.340] you know one like a, i don't know what to call it S25_7_2: [5258.708] do you know what it actually is? S26_11_2: [5260.289] [?] [to S25] S25_7_2: [5261.001] uhuh S26_11_2: [5261.837] it's not [?] it'll just be like a [?] S25_7_2: [5263.689] [?] [responds to S26] S26_11_2: [5267.485] is it skin? [to S25] or is it like [?] S25_7_2: [5274.096] it's ? [to S26] [S25 & S27 & S28 all look at S25's head and lump] : [5276.722] inaudible concurrent conversations; another student comes in room; PBL over] [groups chatting and laughing] S38T6_12_2: [0.372] [?if ] you can just stand behind the podium out of the way and the person who is presenting at that time, and then you just swop, ok? and then [?if ] you all stay there until the end of the presentation by your group and then you come and sit down ok. so we're not having people running up and down, during the presentations okay so, all the presenters of the group three go to the front, and then they all come back at the end and then all the presenters of group five all go to the front, and all come back at the end, ok. OTHER_COMMENTS: [0.429] [background noise, door squeaking, students moving around; some inaudible background chat] [28.860] some inaudible background chat [31.224] [unknown speaker 1] why did you do it [33.015] [laughter] S38T6_12_2: [34.350] so group, group three, (3) obviously lots of other people want to join group three OTHER_COMMENTS: [34.350] [background noise] [37.047] [laughter] [39.667] [background noise] [41.718] [laughter] [43.267] [background noise, chatter] S38T6_12_2: [43.340] right, ok so S31 is going to be ehm, doing the timing, (3) and you've all, have you got the, yep, ok, right so take it away group uh three OTHER_COMMENTS: [60.088] background noise] S7_12_2: [63.411] [clears throat] [75.956] we are the group three. uh these are our members.(2) i'll be presenting about the multifactorial causes and inheritance pattern, and S27 will be presenting about legal and ethical issues of termination of pregnancy. (2) that's me. [points to presentation] genetic causes, well the genes contribute in two ways, syndromic and non syndromic. (2) oral facial clefting is supposed to be one of the most common birth defects, and they have been ranged between one and ten, and i've listed them out over here oral fac- eh oral facial clefting one to ten and the genes that contribute to each of them. the ones that i've highlighted over here are the ones which cause [?facial] syndromic clefting. IRF6, this is very important because since we're dealing with uh Van de Woude syndrome, IRF6 gene is present on chromosome one, and it's not one mutation on this gene which causes V- VWS it is snips [?up rings?] round the gene or IRF6 see 6 uh gene in ass- association with the other genes, and uh the, same gene which ass- association with uh environmental factors. this L important locus ninety Q one three point one, uh, there are three important genes on this locus, uh which, are found to be cause uh, i'm sorry [?i'm freaking] out uh which are supposed to be causing clefting but not syndromic clefting that's really important. does not cause syndromic clefting they cause clefting. maternal smoking, of all the environmental factors maternal smoking is supposed to be one of the most important uh, environmental uh, factor that, adds to the deformities in the foetus. uh it increases the normal risk by one point three four percent, and the confidence interval of ninety-five percent. confidence interval is an estimation of risk given to a certain population which satisfies the parameter. earlier the parameter is uh, maternal smoking so we consider all mothers who smoke and ninety five percent of the entire population considered , have babies with clefts. other factors are alcohol, maternal nutrition, in some way multi vitamin supplementation is supposed to be causing clefting, the age which is a common risk factor, [?] lowering drugs statins have been proved to cause clefting, and folic acid like we all know folic acid is an important supplement which causes neural tube defects and so does clefting. (2) biochemical pathways, there are many biochemical pathways but the most important one is the Wnt pathway which is involving cell signalling, and there is this important uh co- co-receptor [?the] low density liver protein, uh the genetic inactivation of LRP, causes does proceed , the cycle but then does not lead to cell signalling in fact uh it leads to produce only degradation of beta catenine, which uh okay this is a very complex pathway this is the LRP and which leads to the [?] degradation if it is genetically inactivated. this is a simplified version of it, this is beta catanine and this is the [?] and degradation and there is no signal [?across the ] nucleus, here cell resumes normal function. and so the investigation continues. over to S27 OTHER_COMMENTS: [104.788] [cough] [118.383] [cough] [152.773] [cough] [195.625] [cough] [198.867] [cough] [215.931] [inaudible] [242.983] [cough] [255.841] [clears throat] [257.646] [cough] [277.525] [clears throat] S27_12_2: [284.072] [inaudible] OTHER_COMMENTS: [284.173] [inaudible] [288.246] [coughs] S27_12_2: [290.457] ehm hi, i'm S27 and i will talk about the lethal and -the legal and ethical issues of the termination of pregnancy. according to the abortion act of nineteen sixty seven, in UK the termination of pregnancy is legal if several criteria are met. these are the weeks of gestation, a risk for the woman's mental or physical health, a risk that the baby will be physically or mentally handicapped, and also, whatever the reason is, two doctors must agree in order to proceed with the termination. (2) although the law permits the termination of pregnancy there are some ethical issues. the main debate is when life begins. according to the Catholic church, life begins at conception. other people say that it begins at im- implantation or at the different states up to birth, and some others say that it begins at birth. (2) because of these ethical issues there are two groups, one is ag- one is against the termination of pregnancy, and one supports it. (3) the group that is against the termination say that the foetus is a human being and therefore it has rights, and if we terminate the pregnancy it's like not caring at all about the rights of the foetus. some people also say that uh if we terminate every pregnancy because the baby will be handicapped then it's uh, like a prejudice for the handicapped people. and also there are religious groups, support that life is sacred to God and therefore we cannot terminate any pregnancy. on the other hand there is the group that supports the termination. these people say that the foetus is not a human being but, even if it is a human being and has rights these rights are not as important as the rights of the pregnant woman because she is already born. also they say that uh handicapped people have a low quality of life, and therefore, they, they suffer all their all their life and uh it's not good to be born. (2) also some groups say that since there are available contraceptive methods, the termination of pregnancy should also be available because the result is exactly the same. however there are people arguing, because when we use contraceptive methods there is no fertilisation, no implantation nothing. whereas when we terminate a pregnancy there is a foetus that has already begun to develop. and the most important statement of this group, is that every woman has the right to control her own body and decide if she wants to continue or not with the pregnancy. another issue is is if we can terminate a pregnancy, because of aesthetic or eugenic reasons. for example , if you had a cleft lip you would you like your parents terminate the pregnancy. but on the other hand would you like to have a, baby with eh very severe cleft lip and all the children, making fun of him and maybe he will afterwards have psychological problems. (2) there was a case reported, in uh nineteen ninety-five i think, i'm pretty sure, [laughs] where there was an early termination of pregnancy because the baby was affected with Van de Woude syndrome. the mother of this baby was also affected. so the doctor supported that eh, they took into account her own feelings because she knew exactly how it was and she also had another baby with a cleft lip. and er the doctors proceeded to the termination of pregnancy. also in some countries and i think everywhere the child has to be [?said to be] normal in order not to be stigmatised. and also some people said that the abortion of act in nineteen si- nineteen sixty-seven, does not really define what is a handicapped person. on the other hand eh Van de Woude syndrome has a good prognosis especially when the cleft lip can be repaired by surgery. and also, generally speaking, there is a definition of a handicapped person, and it he is a person that cannot live individually after [?an age that he could do so?] after eighteen or so. (2) so as we all understand medical ethics cannot really be interpreted by the law, and the debate must be continued in order to have a final decision however, i'm not sure if there can be a final decision because ethics is what people believe and different people have different beliefs. and that's our references and the end for our group. OTHER_COMMENTS: [315.609] [cough] [337.800] [clears throat] [464.398] [coughs] [484.016] [coughs] [535.377] [cough] [559.787] [clapping] S38T6_12_2: [567.814] right any questions for the group three? OTHER_COMMENTS: [572.501] [laughter] SFLOOR: [573.573] [S39] i just want to know eh, you know you were saying about the ethical issues do you think it's, do you think it's right that somebody is gonna terminate a pregnacy just due to the cleft lip palate Van de Woude syndrome. yes. yes. S27_12_2: [585.535] for me S38T6_12_2: [586.398] so- sorry to interrupt um, when the question is asked from the front sometimes it's hard for us at the back to know what was asked, so could the um speaker actually just reiterate quickly what the question was, thank you S27_12_2: [598.219] she asked if i be- if i believe my own opinion i suppose. SFLOOR: [601.031] [SA] yes. S27_12_2: [601.821] that the termination can ever eh ter- er a pregnancy can be terminated because of a cleft lip or Van der Woulde S39_12_2: [608.066] [S39] for the purely aesthetic is that the reason why the woman decided on termination of preg- pregnancy is it purely aesthetic reasons. OTHER_COMMENTS: [614.714] [cough] S27_12_2: [614.735] [inaudible] yeah here[?] because they didn't have any other, they won, she was not mentally [inaudible]. OTHER_COMMENTS: [615.002] [?but] they're purely aesthetic [reasons] is that the reason why [the why] decide on termination of preg- pregnancy is it purely aesthetic reasons [cough] SFLOOR: [621.853] [S29]yeah but she's ah- affected herself so she [inaudible overlap] S27_12_2: [624.687] yeah but she had er cleft lip and her er first child had a bilateral cleft lip OTHER_COMMENTS: [630.438] [inaudible] S27_12_2: [632.766] but it was aesthetic [inaudible]the reason was [?]. S9_T1_12_2: [639.128] eh, i was just gonna ask S6 ehm, you mentioned that there was like ten different, loci or at least ten [?or so] involved in oral fla- facial [inaudible] S7_12_2: [648.687] clefting S9_T1_12_2: [649.660] ehm, are some of them like really small percentages or, ar- are they equally you know equally split or, uh have their been studies looking at which ones are most involved or S7_12_2: [661.509] they're unequal. the, sorry [laughs], (12) [long silence / navigates to appropriate slide] do you mean these? er, this er oral facial clefting tree is supposed to be uh a little more effective than the others, because eh it's chromosome nineteen which is involved and the locus is not very far from three- uh one three point one, and so oral facial clefting three is the one which is more effective than the other loci OTHER_COMMENTS: [678.947] [cough] [686.717] [coughs] [689.494] [coughs] S9_T1_12_2: [696.521] and see see, the oral facial clefting ten one with haploinsufficiency, S7_12_2: [703.810] uhum S9_T1_12_2: [704.138] so what kind of way what kind of ehm pattern of intheritance do you see in that one OTHER_COMMENTS: [708.481] [sneeze] S7_12_2: [710.045] of what i have understood if this gene uh, is present in a single copy, that's when it causes clefting S9_T1_12_2: [724.179] so so does one working copy S7_12_2: [726.209] yeah it still causes clefting. that's all i have understood i don't know whether i'm right S9_T1_12_2: [731.104] yeah so what what would haploinsufficiency normally, [?] what would that be or do you think another condition [?for?] haplo-, with haploinsufficiency S7_12_2: [742.295] i'm sorry [?can you repeat it please] SFLOOR: [744.250] [S] [?really hard questions] [laughs]? S27_12_2: [746.734] can you give her an example? S38T6_12_2: [748.165] do you know another, syndrome in which haploinsufficiency, occurs S7_12_2: [753.294] [shakes head] [laughs] OTHER_COMMENTS: [754.768] [inaudible] S38T6_12_2: [757.145] can, can i ask you ehm, you spoke about syndromic cleft versus nonsyndromic cleft what what's the difference? S7_12_2: [764.957] syndromic clefting is where um, it is it has a particular inheritance pattern, in the family. when in nonsyndromic occurs sporadic most of the times. S38T6_12_2: [777.981] but it wouldn't be, sporadic if there's a genetic cause S7_12_2: [785.866] uhm , a mu- a mutation in these loci could be sporadic which causes nonsyndromic clefts. but (2) [inaudible] um it's not inherited yeah S38T6_12_2: [798.902] ok ehm, (2) right. oh yes you mentioned folic acid i wasn't quite sure whether you were saying that, folic acid causes clefting. folic acid you mentioned folic acid OTHER_COMMENTS: [799.580] [cough] S7_12_2: [807.804] [shakes head] [811.029] uhuh folic acid yeah S38T6_12_2: [812.917] so how what's the connection between folic acid and clefting S7_12_2: [815.723] insufficiency of clo- of folic acid is found to have uh cause clefting. S38T6_12_2: [820.823] so insufficiency, right sorry [?]. okay erm thank you S7 questions for S27? S7_12_2: [821.764] insufficiency S27_12_2: [829.297] yes OTHER_COMMENTS: [829.808] [clears throat / laughter] S9_T1_12_2: [831.379] have there been any studies done looking at the quality of life for people with cleft lip and palate, what they perceive as their own quality of life later on. S27_12_2: [841.218] the handicapped people S9_T1_12_2: [842.102] [S9] but do people with clef- cleft lip and palate, have their been any studies looking at, maybe adults who had this repaired as a child, what they perceive as their own quality of life. S27_12_2: [855.136] i don't know if there are studies, but eh for example i read er, there was a guy with a cleft lip that just gave ehm, what do you call it when you talk to uh, S7_12_2: [864.949] hmm? S27_12_2: [865.391] interview? S7_12_2: [865.784] interview S27_12_2: [866.664] yeah an interview , and ehm, he just said that he doesn't have any problems because it's [?repaired] but i don't know if there is a study [?no] S38T6_12_2: [880.243] any more questions? to another? (3) if not thank you PBL group three OTHER_COMMENTS: [881.003] [background noise / laughter] [888.368] [clapping] S38T6_12_2: [893.871] and the next one is PBL group five OTHER_COMMENTS: [896.641] [background noise / inaudible talking / students moving around / coughing; groups changing over] S20_12_2: [941.411] ready? okay so i'm S20 and i'm from PBL group five and i'm going to present today along with S4 and eh S22. so i'm going to talk a bit about the multifactorial eh cleft lip and palate , and just give a brief overview of both the genetic and environmental factors. [clears throat] so, mul- eh multifactorial cleft lip and palate is ehm classified as that when it occurs purely on its own. there's no other features it just is the cleft lip and palate and ehm, yeah. eh the understanding of it's been quite difficult ehm its quite hard to understand at the molecular level, there's no sort of way yet to understand it ehm but it's been mainly done through associations so looking at what genes are associated with it and also environmental factors. uhm, it's been shown as i said that genetics environmental factors are the main cause of it ehm, if you look at twin studies ehm you have, say twins one of them has a cleft lip and palate there's about a twenty-five to forty percent chance that the other one will have the cleft lip and palate if it came from the same egg, whereas if it came from different eggs there's a three to six percent chance , which shows that there's a big ehm, stake in the the genetic side but also the environmental side cause it's not full penetrance. so ehm, it's all been looked at through linkage and association studies the most recent ones have been genome wide association studies but there's been, about three of these so far, um but these are the ones that i thought, were [clears throat] coming up most in the studies. some of the interesting ones were TGF alpha, eh that's came up quite a lot but ehm it's not been consistent so, it seems that that might be uhm a modifier gene rather than causative, ehm the MSX one gene has also come up in quite a lot of studies including the recent genome wide association studies. but uh the evidence isn't still that strong. the two at the bottom, [?BACs/Vax ] one and IRF six have been recently confirmed, to be causative genes, uh the most i- interesting one's IRF six cause that's been consistent throughout all kinds of studies linkage and association, so i'm just going to talk a little bit about how they came to the conclusion that that was, something to do with it. so obviously it was first studied due to it's role in Van de Woude syndrome. uhm, it also has been seen in mouse models uh where it's been shown to be fully expressed in the palate of , uhm the mice but it's not been shown how that actually uh plays a role in the development [clears throat] again, through linkage and genome wide association it's came up in all the recent genome wide association studies uh it has been strongly linked with it, it's been estimated that it is about twelve percent total of the genetic cause, uhm through statistical analysis so it it plays quite a large role in the genetic factor. so these are the main, environmental factors, it's maternal smoking, alcohol con- consumption and nutrition, ahm as i said before [?like] you can see from the twins studies that it does play quite a significant role. uh maternal smoking and alcohol consumption ehm in both cases eh an increased ehm intake of smoking or alcohol has been ehm, associated with development of nonsyndromic cleft lip and palate, one of the interesting things is that eh folic acid which obviously, uhm is given as supplementation but ehm, in order for it to decrease the prevalence of non syndromic cleft lip and palate it has to be given a very high dose so it's not something that, maybe is any good for the future. so i had a look at some of the studies which show the genetic and environmental interactions. uh again like i said before you can't really understand it on the molecular level quite yet so it's all done through association. so, if you had someone that smokes, looking for a particular variation of a gene that's linked with that and then seeing if non syndromic cleft lip and palate does occur in those cases, so, i did little diagram er, the IRF six gene has been linked quite strongly with nutrition and maternal smoking, uhm, [?vax ] one which is one of the other confirmed genes there's not been much studies into how that in- interacts environmentally yet, uhm so that's something that could be looked at in the future, MSX one has been linked with maternal smoking alcohol consumption and TGF alpha the one i said that could be er not causative has been linked with all three. so in conclusion it's clear that both genetics and the environment are involved. um future research could be placed more on finding more candidate genes and also looking at the interactions between the genes and the environmental causes, and that's my references, and i'm going to pass you over to S4 (3) OTHER_COMMENTS: [942.045] [laughter] S4_12_2: [1229.859] hi there so i'm just going to speak a little bit about ehm, databases including ehm the London Dysmorphology database and OMIN, [clears throat] and also a little bit about the IRF six gene , which ehm mutations in this gene can cause Van de Woude syndrome and also eh PPS, i'm just going to call this PPS cause i can't pronounce it. (3) so, eh J was born with em cleft lip and palate, she also had lip pits, ehm these lip pits were also seen in her father and other members of his family, and on the basis of that it was considered that it might there might be a genetic cause, (2) so we searched the lo- London Dysmorphology database, ehm using features that were observed in the family, and ehm eh pulled up a few syndromes [clears throat], eh i think i got three actually from the search, from that then ehm i went on to OMIN just to clarify ehm, a little bit more about each one, and using both of them we decided that Van de Woude syndrome was the most likeliest cause, ehm it's a dominant mode of inheritance there's pits and sinuses of the lower lip and you- you may or may not have eh cleft lip o- and or palate, ehm and it's all because of mutations in the IRF six gene, so, because we had a target to look at, ehm we did some specific analysis an- and we also got a karyotype analysis, ehm which was normal and we had FISH over the region , where the I- of- where the IRF six gene is, and also we s- ended up with sequence analysis and showed that J- what J's muta- mutation was, and we also confirmed this and ehm her father and ehm one of his sisters. [clears throat] so the IRF six gene, codes- encodes a transcription factor, ehm eh which has ehm a highly conserved DNA binding domain, which is [?encoding] for by exons three and four, it also has a less well conserved eh protein binding domain em which is encoded by [?exon] seven and eight and J's and the family mutation was found in [?exon/ X one] four. (3) so there's ehm, different mutations [clears throat] so, in Van de Woude syndrome uhm and PPS there's mutations, and P ehm Van de Woude syndromes the missense mutations tend to occur in the D- DNA binding D- for- DNA binding domain and also the protein binding domain. ehm, and it's though to [sighs], (2) it's it's thought to ehm, just the the protein will lack function, and be inactive. but in PPS it's ehm thought that, the ehm mutations are just in the DNA binding domain, and ehm, (2) and it's thought that, in some way that the the protein binding domain still functions, and it ehm causes ehm transcri- eh other transcription factors to ehm, associate but it forms an inactive complex. (2) so the people that identified RF- IRF six, as the gene responsible for Van de Woude syndrome and PPS, ehm also did some expression studies, ehm and they found that it was expressing the ambrio- eh the embryo and adult tissues, and ingi- in the embryo (2) the ehm, they found that the highest level of expression was in the, he- here? ehm which is the tissues that form the secondary palates which form the roof of the mouth, (2) ehm they don't know the exact function of of the protein, ehm but it's it's it's clearly expressed in regions where we see, defects, so just to conclude that the da- databases were very useful, ehm they helped us narrow down possible causes, in mice IRF six is highly expressed in tissues which form the palate , and the eh mu- mutation identified in J- J was also seen in other family members o-other families that had Van der Woude syndrome. and now i'm going to pass you on to S 22 (4) OTHER_COMMENTS: [1236.527] [coughs] S22_12_2: [1492.863] good morning everyone i'm S22 from PBL group five. and i want to draw your attention to one of the problems we saw in this case scenario, to role of healths professionals in early diagnosis and incidence of syndromic cleft lip and palette. and i'm going to talk about the problems er consequences and possible solutions in this case scenario. so what we saw in this case scenario this clinician a hospital doctor was not aware well about uh genetic causes of syndromic cleft lip ap- lip cleft lip and palate, so this is one of the problem the second one, he gave a wrong recurrence risks for- to the family, and in fact the risk he gave, one in fifty, was ten times eh less that than the actual risk as it's know from the literature in the Van de Woude syndrome if one parent has lip pits, the recurrence risks to have lip pits plus cleft lip and palate in the offspring , is em- empiric risk in one in five so there is a huge difference between these two risks. so these problems can uh cause a lot of um results in future so the problems we can face in future , could be delay in early diagnosis, and increase in incidence of er syndromic cleft lip and palette. and eh Van de Woude syndrome is autosomal dominant er syndrome, that's why it would increase the incidence of syndrome in the population. if cleft lip and palate was associated with the recessive syndrome, then it would uh be able to get more carrier, so carrier frequency would increase in the population. the second could be eh because of this incorrect risk er the family was deprived from the right to make an informed choice. so if they know that they have high risk for the for the next pregnancy they would chose prenatal diagnosis or PGD but they had uh they were given wrong risk. this third one is , when this family gets second baby in the family with dysmorphic features, that kind of cause anger in the family. tha- and this can lead to legal issues between the patients and clinicians in future. and overall all these like um, the this family just would lose their belief in the professionalism of healthcare providers. so how we could improve this situation? we could er give more information to medical students during their studies at medical school, we could er make them familiar more about eh syndromic cleft lip and palate, it's genetic causes, and also about databases as London Dysmorphology database OMIN and others. the second we could erm work out rules in which conditions in which situations, to uh refer the patient with cleft lip and palate to the clinical geneticist. for example in this case scenario if there were rules that for example er if patient has cleft lip and palate and in his family there is even more er l- l- me- minor dysmorphic features as cl- eh lip pits, that patient would be referred to the clinician , er cl- erm to the clinical geneticist. and the third one we could write guidelines [?desk] references books for clinicians and also leaflets , for clinicians and patients. why for patients? because this family just ignore they have lip pits during the three four generations , so if they had some more information about syndromic cleft lip and palate about erm dysmorphic syndromic dysmorphic cases maybe they would spot this minor uhm minor difference in their pheno- phenotype. so while searching for uh guidelines for clinicians and patients i came across with very interesting project. which was um in two thousand seven, by university of Manchester. and it's called dyscerne, the good thing about this project is that they uh they allow the sharing expertise and experience between clinicians and er dysmorphology experts also they produce leaflets for patients and referring clinicians so by submitting case to the database clinicians gets feedback from the dysmorphology expert about ehm a diagnosis and the management of dysmorph- dysmorphology case. and also, patients get more information about that. in conclusion i want to say that in when a clinicians see the patient in clinic with cleft lip and palate er before referring this patient to the surgery unit for uh plastic operation or something else, he or she should bear in mind that even is first case in the family, this could be syndromic cleft lip and palate. and er clinicians and um also clinical geneticists work- should work together in order to provide a patient with correct diagnosis and better management, thank you. OTHER_COMMENTS: [1806.139] [clapping][clears throat] S38T6_12_2: [1813.828] are there any questions for S20? OTHER_COMMENTS: [1818.012] [laughter] S38T6_12_2: [1823.022] okay i'll start then er so could you define erm, what you mean by non syndromic cleft lip and palate S20_12_2: [1829.511] it's not caused by a mutation it's caused by variation and both environmental and genetic factors. and it occurs on it's own whereas syndromic there tends to be other abnormalities that come up with it, but um non syndromic it's on it's own and it's just variation rather than mutations. OTHER_COMMENTS: [1834.203] [sneeze] S22_12_2: [1849.461] can i also answer that question because i also had syndrome [laughs]so in OTHER_COMMENTS: [1852.291] [laughter] S22_12_2: [1857.222] because i also had about syndromic cleft lip and palate, and briefly saying syndromic means associated with the syndrome non syndromic means it's not associated with any syndrome. so in this case it's syndromic because it's associated with , Van de Woude syndrome and besi- besides cleft lip and palate these patients also could have other abnormalities and ca- also cardio abnormalities [?], or em, problems with thumb and so it's associated with syndrome. it comes with many phenotypic features, but when er non syndromic means it's just cleft lip and palate there is no other abnormalities. OTHER_COMMENTS: [1898.594] [inaudible] S38T6_12_2: [1899.222] any [?] S9_T1_12_2: [1900.871] ehm i was just going to ask about um i i didn't catch see monozygotic twins, i mean what did you say the concordance was? S4_12_2: [1907.108] eh three to, oh wait eh twenty five to forty percent yeah S9_T1_12_2: [1911.442] so obviously you're doing [?which ] and environmental factors, does the environment invitro different [?for] monozygotic twins what's the, what's the kind of thought on that S4_12_2: [1913.558] [nods head] [1922.062] well, i'm not entirely sure about how it sort of happens but, there must be something, in there that's different i i don't know exactly what it i don't know whether they're getting more, of the nutrients or, i i'm not i don't i it's not really been shown yet how exactly that works it's just, it happens [laughs] OTHER_COMMENTS: [1941.407] [inaudible] S38T6_12_2: [1944.871] right any other questions for, S20? (4) [pause] if not we'll take questions for S4. OTHER_COMMENTS: [1953.820] [background noise] S38T6_12_2: [1956.680] um okay nobody else wants to start, you showed a , er a picture of um IR six expression in a in an embryo, can you tell me what what are you actually looking at there expressions of [inaudible] OTHER_COMMENTS: [1958.828] [laughter] [1960.995] [cough] S4_12_2: [1970.115] it's the R and E levels [inaudible] it's in situ, ehm i think it's eh R and- R and E. so ehm, here ehm, these are tissues [points to board] that form the, i'll pu- i'll put out the light, will i? S38T6_12_2: [1970.928] it's the R and E S4_12_2: [1983.557] [puts out light] S38T6_12_2: [1984.536] i think we can actually s- uh, S4_12_2: [1985.448] can you see it? S38T6_12_2: [1986.312] it does show up yeah, okay OTHER_COMMENTS: [1987.032] [cough] S4_12_2: [1987.812] so this is actually hair follicles, up here, and these thi- this is the, the formation of the secondary palate i think right here. OTHER_COMMENTS: [1996.608] [slapping noise as if something falls] S38T6_12_2: [1997.839] so have they actually looked at the protein? S4_12_2: [2000.365] ehm i, no ah, not in that paper i looked at. i don't think. they've done ehm, what they've done is ehm, stru- ehm, it's all predicted protein ehm, (2) it's- it's based on computer database. OTHER_COMMENTS: [2004.189] [cough] S38T6_12_2: [2017.689] yeah i meant sorry i meant the protein levels they've , obviously they've looked at the R and A levels on this [inaudible] protein levels. would you expect the protein levels to to follow the R and A levels [?in this?]. S4_12_2: [2021.149] so that's the R and A [2030.425] no, well yeah [laughs] (2) yes. (6) yeah. OTHER_COMMENTS: [2033.158] [laughing] [2042.653] [laughter] S38T6_12_2: [2046.642] okay right uhm any o- any other questions for[laughs] for S4? (2) uhm if not we will move on to S22. any questions for, S22? (3) uhm S31_12_2? S4_12_2: [2057.360] [switches light on] SFLOOR: [2064.462] [S26] hi ehm , you were just mentioning at the end about that database just ehm S22_12_2: [2065.106] hi [2069.222] dyscerne project? SFLOOR: [2070.177] [SE] yes. S22_12_2: [2070.800] uhuh SFLOOR: [2070.800] [S26] ehm i was just wondering is that, can anyone sort of , is that something anyone can access or is it just clinicians themselves are sharing information about dysmorphology? S22_12_2: [2079.033] okay this project involves um, centres from fifty European countries so from fifty European countries clinicians in those centres , submitted case to database. patients or other people cannot submit it eh a case clinicians submit a case, then this case go for the first um review, then it goes to a expert panel, which is eh consisted thirty-seven uh dysmorphology experts uh from different countries, um it goes again to coordinating centre, they produce leaflets, ca- expert case reports and, management guidelines and then eh clinician and patients can get those leaflets and clinician gets feedback , but patients no they cannot submit case to this SFLOOR: [2129.436] [S26_12_2] so it's [?a sort of?] database [?that anyone can access?] [inaudible] S22_12_2: [2130.756] yeah it's er purely um sharing experience between clinicians and , dysmorphology experts SFLOOR: [2138.393] [S26_12_2] okay, thank you. S9_T1_12_2: [2142.569] it's a wee bit more general but, you talked about educating doctors at the level of when they were medical students, which is something that i'm very interested in because i do quite a lot of a bit of undergraduate teaching, you mentioned that maybe you should teach them about, specific syndromes or maybe you should teach them about databases, OMIN that kind of thing, how would you prioritise what you teach to medical students in today's world about genetics? what what do you think they need to know? S22_12_2: [2149.378] hmm mmm [2172.050] okay at least um because it's cleft lip and palate and it's co- commonly i mean why the incident of cleft lip in adult is one in seven hundred. but, by the ignoring syndromic cleft lip and palate we will just erm, increase the incidence of this syndrome in our population, so at least if, the, in dysmorphology phase the, mmm disease that are more common, we could give more information to, students about more common genetic disease. (2) so probably that would reduce er the incidence of syndromic cleft lip and palate in the population. S9_T1_12_2: [2214.739] do you think it do you think it'll reduce the incidence, what like what mechani- like, (2) do you mean like that people would terminate, pregnan- S22_12_2: [2225.210] at least we eh at least people would have right to pass this syndrome to their future generation or not. (2) so this family we- were not given right , er to decide for their future generation. so that's just depriving people's right. S38T6_12_2: [2241.183] [inaudible] SFLOOR: [2244.607] [S16_12_2] uh yeah i have a question, uhm you you mentioned empiric risk so how is that one out of fifty generated? S22_12_2: [2252.038] one in five SFLOOR: [2253.513] [SF] one in fifty S22_12_2: [2254.200] eh one fifty was the risk that hospital doctor gave to this family SFLOOR: [2257.793] [S16_12_2] yeah so how was it generated S22_12_2: [2260.181] one in fifty risk or one in five risk, anyway it's eh both of them are empiric risk so empiric risk is calculated based on the, for example if we have hundred families, with that syndrome, we take these hundred families and we calculate in which cases for example if parent has lip pits , how many cases from the hundred had lip pits offspring have lip pits plus cleft lip and palate, so they took all Van de Woude syndrome cases, and they generated that one in five risk. and also one in fifty risk, i guess it was calculated because, um hospital doctor told them it's sporadic case no one before the fam- uh in the family had cleft lip and palate and it's just uh, because first eh in general eh the risk is one in seven hundred, but because they already had one child with cleft lip and palate so risk eh just increased to one in fifty. (5) are you satisfied with answer [laughs] SFLOOR: [2260.750] [SF] yeah OTHER_COMMENTS: [2323.212] [laughter] S38T6_12_2: [2325.524] right i think we'll move on. thank you PBL group one S22_12_2: [2327.515] thank you OTHER_COMMENTS: [2327.868] [clapping] S38T6_12_2: [2333.204] and PL group four is next i think OTHER_COMMENTS: [2335.996] [background noise / inaudible chatter / coughing; groups changing over] [2368.250] [N.B. speaker refers to group members' names S40, SJ, SM, SS, SV, SA and SK SC S + initial- not all have speaker code; not recorded] S39_12_2: [2368.973] good morning ehm i'd like to talk to you today about the screening of IRF six ehm in non syndromic cleft palate, cleft lip palate cases and i'll refer to this as OFC oral facial clefts from now on throughout the talk. okay i'd just like to say who i'm representing PBL group four that the other members are, well it's myself, S40, SJ, SM, SS, SV, SA and SK [inaudible] SC [laughs] [inaudible]. okay. (2) right i'll start by giving you a brief overview of my talk today. ehm, first of all i'll talk about OFC, what the causes of it are, how it occurs, the development of it, [?the embriology?] of it, ehm then talk about environmental causes versus genetic causes. talk a wee bit about syndromic versus non syndromic. syndromic atr- specifically about Van de Woude syndrome since it was relevant in our case study. and then i want to concentrate on a recent research article that was , published in two thousand and ten, last year, and it was looking at screening for IRF gene fact- ehm mutations, ehm non syndromic cases, and syndromic cases. okay, first of all this shows you really, the development of the palate, how it comes about the different processes on any, ehm come together to form, first of all the primary palate and then behind that [?] secondary palate. (2) okay you can see here, in figure B, [sniffs; referring to slides/visuals] you've got the the nose and the upper lip, eh the primary palate and the different areas they're, kind of medium purple in the middle shows you the primary palate , and sorry shows you the secondary palate primary palate is the white blue [?at the beginning?], and the darker purple area is actually the soft palate. it's the secondary palate split into hard palate, and soft palate. briefly, just circled , more severe cleft [?lip?] and palates here [?this is the?] unilateral ehm cleft lip and palate, so here's bilateral ehm cleft lip and palate. and this one's an isolated cleft palate, it's just mmm it's just the cleft [?palate?] that's involved no cleft lip. okay, what are the causes, of OFC ehm, as we've heard before it's environmental causes and there's also, whi- which can be split into you know things that happen [?when] the mother's pregnant like maternal smoke that has a detrimental effect , on developing embryo. ehm folic acid deficiency for example as well. teratogenic effects the things that actually happen to the the mother when she's pregnant, could be like if she ha- [clears throat] excuse me had an infection of any kind either bacterial or viral that would have a, detrimental effect on develop embryo. ehm i think this is [?cause- ] this is a cause of linked it- it's ehm through association studies [have less effect on patient's lives]. (2) ehm and the other cause is obviously genetic, and IRF six is the gene , which is in locus the chromosome one, locus thirty-two Q [?Q?] three two to Q four one and it's been associated [?or ] it's being proven to be linked to Van der Woude syndrome. which is relevant in our case. (2) ehm the research article that i'm going to talk to you about their hypothesis was , that some families are classified as non syndromic cleft lip and palate cases of facial clefting, could have the IRF six mutation and so they screened individuals for, this mutation in IRF six. [clears throat] excuse me. it's a hundred and seventy, ehm patients in total were screened, and out of this ehm, (2) seventy five were diagnosed, non syndromic, and there was IRF six mutation [?] identified in sixty-two point three seven percent and thirteen point three percent respectively. so they looked at more detail at the non syndromic cases were, (2) that were diagnosed with this IRF six mutation, and they looked at the more ehm in more detail clinically as well as going through the the family history, (2) and in the end up they were reclassified as having Van de Woude syndrome. and and they also, through the clinical examination spotted a new, minor clinical sign of Van de Woude syndrome which is notching eh nodules just below the lip, and eh two of the patients [?were] two different families, okay that were very similar. (2) now summary ehm, so [?the?] identified the IRF six mutation, in two cases two families ehm previously they'd been diagnosed as having non syndromic ehm oral facial clefting so it was reclassified and they identified eh also in one sporadic case. which wasn't in any other members of the family. eh this quite easily done because fifty percent of Van de Woude cases do not show lip pits, and they also suggest, (2) that you do screening for IRF, six mutation ehm if there's any doubts of the [?abnormality] of the lip or, [?when there's?] ehm, non syndromic oral facial clefts ehm within auto domiso- do- autosomal dominant inheritance, which is suggested by family history. okay? (2) that's me and that's my references. thanks very much. OTHER_COMMENTS: [2399.513] [laughs] [clears throat] [2401.530] [clears throat] [2555.778] [coughs] [2738.781] [clapping] S39_12_2: [2742.508] [?any] questions S38T6_12_2: [2744.581] um can we actually have the second [inaudible] S39_12_2: [2747.261] oh sorry, sorry. [inaudible] S40_12_2: [2753.579] eh hello everyone, so we have been seeing eh seeing about all the genetic and the clinical aspects of, a patient with Van de Woude , syndrome. now loo- let's look at the next uh well loo- lets look at the er what psycho problems psycho-[?social?] problems he or she undergoes, when, (2) they get the disease. so now, who doesn't want to be loved, cared, have friends. everybody wants friends, everybody wants to be loved. but, what is given to an OFC patient, rejection. rejection from the very early stage of their life. (2) now society, society is a place where, a pat- a child grows up, and the society is the one who should support the patient or the child or any normal child. and the society starts from the home. parents and family, parents and family parents should uh parents want their to be perfect, but er you cannot like force perfection into the child and er , in some families like where i come from in India, if the child is born, and if eh they had the cleft lip palate, mainly the mother's blamed and pressurised that she is the cause for the er cleft lip. so when she is pressu- pressurised, there is a hatred that forms for the child the mother kind of er, pressurises the child, and er that eh [?] gives a differ- a distance between the mother and the child. so um , that is uh now there are awareness like, people are educated they you know they are they now know that, i- it's not in fact entirely the lady's problem, but then yeah, still some [?orthodox ] family has this problem. and then it's the health professionals. in this syndrome uh there is the GP, the dentist, the psychologist, all of them should put the child's need first. what the child wants, and uh nn- no- noth- nothing should be done for the sake of doing. no treatment or counselling should be done if the, if the child is not okay with it. and then the child goes to the school. in school, teachers and fellow [?mates] , teachers should not discriminate er the child from the other, children or sympathise them if they sympathise them they take advantage of it they can take advantage of the [?sympathisers]. and then uh teasing and bullying in school. uh when you ask the patients uh with eh VWS, they are they are not concerned about the cleft lip they are more hurt or depressed by the teasing or the bullying that they receive from their fellow [?mates?]. so that should be uh, should uh d- uh fellow [?m- mates?] should be give awareness about how they feel. and then it's, they go for a job, colleagues, employers. Er when they go for a job the, the um employer should not, be biased they should not be ev- evaluated according to their appearance or er, if they deserve a promotion they cou- they should be given. so now, answer for all [?of?]]this, is surgery. now surgery has been done. and this a child with a cleft lip palate and after surgery that's the child. she's fourteen years old and, and er, so, the eh all the er problems i've been talking about can be corrected with this. but, this is a plastic surgery and it's costly. in developed countries like UK US, the government funds it. but there are underdeveloped and er developing countries where these uh these things cannot be done. er because it's costly. er so then comes the ethical problem. er a survey was done with one sixty-five parents and uh, questions were asked according to their religion, er the child the [?recurrence] risk, er record of [?] family environment, and the most parents thought it's not a severe condition, why should i abort it. so that's what the- this study, in Argentina when they made a questionnaire like this that's what parents felt. (3) now, studies were done on the social uh psycho-social problems by professor Hunt and one sixty children with OFC and one thirty-nine children were, er, were looked at uh were looked into with these er, anxiety self esteem depression behavioural problems, and they sai- they saw that depression and the behavioural pro- problems the main thing , that er flagged the er i mean they were more depressed and more er they had more behavioural problems than the, er normal children anxiety and self esteem were, er okay with them and like it was as same as the normal kids. but this information va- mmm- can vary in different group of patients. like, these are a few er pa- uh this a review done by professor Hunt em, er in few er group of patients facial appearance attachment, it was not a problem but in few it was. in behavioural problems same. in self esteem behaviour some thought it's not [?good?]. so, what is the answer for all this. encourage them, support them, friendly environment give them friendly environment awareness, give them attention not rejection. thank you. OTHER_COMMENTS: [3075.129] [clapping] [3080.902] [laughing] S38T6_12_2: [3082.261] can we have eh questions for S39 S1_12_2: [3086.508] um you said that um the testing for the IRF six they found ehm thirteen point three percent ehm and they subsequently found a [?minor clinical ] sign so were and how many [? ]. S39_12_2: [3097.555] two families, two families. S1_12_2: [3098.994] so do you think that uhm perhaps maybe a more thorough clinical examination would've produced the the need for testing so that other families could who they didn't find the mutation. S39_12_2: [3102.395] yeah [3109.013] no the reason why i mean in IF six it's obviously causal for van de woudes syndrome, so that's the reason why they tested, ehm [?] of people that've been , diagnosed as having non syndromic cleft lip and palate they've tested for IRF six to see whether [?i mean?] that's flagged up in fact it's probably not non syndromic, it's probably Van der Woude syndrome so it's syndromic so it's been misdiagnosed. (3) do you see what i mean S1_12_2: [3137.707] yeah S38T6_12_2: [3139.582] can i ask you a related question? so this uhm i think you said it was notch the [?cli- minor clinical?] feature was notching the [inaudible] S39_12_2: [3146.886] uhuh it was the nose basically underneath the lower lip. S38T6_12_2: [3151.145] yeah so if they then look back at the rest of the Van der Woude patients how many of those, what percentage actually do [?show] S39_12_2: [3158.712] well that's that's the good point and [?] they didn't look back] at that so, it's a good point it could be could actually have these minor signs that they've not picked up on. but also ehm i forgot to mention that the second patient in family B, that is actually brother of the [?], his ehm, you know his nodules underneath the lower lip were similar to the first one , and they also found a l- a lower missing tooth, as well although it's not the one that's usually associated, with Van der Woude it's the lower incisor rather than the lower [?pre-molar]. so that might have been part of the, minor s- ehm sign as well. S38T6_12_2: [3202.938] are there other questions for S39? (2) nope are there questions for, S40? (3) uhm no OTHER_COMMENTS: [3213.923] [laughter] S1_12_2: [3214.881] what possible solutions could you think of for getting people treatment for cleft lip and palate in countries where it's not currently available for free. S40_12_2: [3225.767] uh, in my country it's in [?like?], in some er hospitals they give er free er, surgery, erm you know er in some it it is like er, trial or something, it is there but without that it's money so maybe i don't know the government has to decide something [?i mean ]the the financial government or something S9_T1_12_2: [3251.071] and see in the first study you mentioned about, there was parents looking at was it different social factors of parents and different religious views or whatever of parents, wha- what did they find with regards to the view of say social status as what parents thought about? did they look at that did they look at, i do- can y- can you go back to that slide [?you put up] OTHER_COMMENTS: [3272.464] [background noise] S40_12_2: [3280.547] this one? S9_T1_12_2: [3281.410] yeah that one. ehm, yeah so they had socio- social demographic information, on the questionnaire, did they find [?they said?] most parents didn't see it was severe but did that change with how the parents were, social status did rich pa- rich people or poor people [? think it was more of an issue]? S40_12_2: [3299.724] er it was like, the er the er the questionnaire in [?] like hundred and fifteen of them, er like in two hundred a hundred and fify said ,er it was okay with it and er yeah, both these social status, er i mean people who were in high status and low thought that it wasn't a severe condition S9_T1_12_2: [3319.155] so there wasn't there wasn't actually any difference between the, between groups or was any difference like between religious levels of religion-ness, and what they thought of cleft palate no? S40_12_2: [3331.696] um maybe yeah, um, some thought like, er in these er six, you know the, some thought abortion was okay but in like three categories it was like okay if i had a great [?social] status and my religion is o- uh says oh i it's fine, and uh, the characteristics i can address to it [?that?], but i er the risk er er , of something my my attitude to the abortion is like i don't want it, like er for the different questions they had er er for some they were okay with the abortion for some, they were not. [3371.129] any other qustions? S38T6_12_2: [3373.090] [?inaudible] SFLOOR: [3374.861] [S23_12_2] can i just check with you, just i was saying there's a comparison between the, the child with cleft lip and palate and a normal group S40_12_2: [3381.695] yeah SFLOOR: [3382.248] [S23_12_2] you're saying that they are having more er they experienced more, behaviour problems and er depresssion, do do they have [?gone into] what cause, them to feel more depressed and why they had [?most?] behavioural problems S40_12_2: [3388.128] uhum [3389.576] uhum [3397.043] yeah, they em er when you look at er normal kids and with cleft lip palate, er like the picture i showed before the surgery er she was given interview she was like i didn't have any friends. there were like very few friends and that made her depressed or mmm er, if she would have had some cousins with normal er in the- in the- inside the family it's if there'll be er discrimination that made her depressed. that kind of thing. SFLOOR: [3427.642] [S14_12_2] is there any difference i mean, at the time of the surgery [inaudible] S40_12_2: [3432.559] oh before and after, yeah there is there is. people recognised ehm, pe- people uh the er person with the cleft lip palate after the surgery. you know that's what you asked for right? OTHER_COMMENTS: [3433.601] [cough] SFLOOR: [3434.137] [S14_12_2] yeah [3444.608] [S14_12_2] i'm asking the- is there any difference in the effect of [?surgery ??] i understand from you that, this lady did the surgery late. S40_12_2: [3447.430] of the [3455.852] er, yeah, that's SFLOOR: [3459.816] [S23-12-2] [inaudible] i think her question is that is this surgery at a younger age or older age, is there a difference? S22_12_2: [3462.337] what age SFLOOR: [3467.227] [S34_12_2] [?yeah like?] if it's earlier do you get do you reduce depression and reduce [inaudible] S40_12_2: [3470.665] yeah yeah yeah it does reduce depression, that what, i mean there's an interview of hers, so she says that when er when i was before the surgery, i i was isolated, i was teased, by mmm some of my own friends even tease me but after the surgery, she's fine she's happy she's confident. (4) [pause] okay, okay.] SFLOOR: [3490.899] [two students raise their hands] OTHER_COMMENTS: [3491.864] [laughter] S38T6_12_2: [3494.124] [inaudible] S26 was maybe first by a millisecond and then, eh is that S22 or S31_T4 [??inaudible] S26 OTHER_COMMENTS: [3497.329] [laughter] SFLOOR: [3500.718] [S26_12_2] so, so in this case she waited till she was older to have surgery is that is that what you're saying [inaudible] S40_12_2: [3506.968] eh no no, it it has s- uh you know it has the surgery has some stages, i mean it should be done when they are small, yeah. it should be done when they are small [?and?] she's fourteen OTHER_COMMENTS: [3508.148] [inaudible] SFLOOR: [3514.181] [S26_12_2] yeah. [3517.608] [S26_12_2] you said she had an interview before she had it done but she couldn't if she was a child surely? S40_12_2: [3521.620] no no no she was interviewed when she was fourteen.wh- what do you mean like OTHER_COMMENTS: [3526.750] [laughter] SFLOOR: [3528.787] [S26_12_2] so when did she have the surgery as like a baby? S40_12_2: [3531.107] er, not like a very young baby er. OTHER_COMMENTS: [3534.177] [laughter] SFLOOR: [3535.897] [S26_12_2] still quite young S40_12_2: [3536.745] i'll tell you like, surgery in OFC has kind of stages. SFLOOR: [3541.523] [S26_12-2] okay so you have to have more than one surgery to S40_12_2: [3541.939] [?you know?] [3543.855] er yeah, like first they put a mould and then er they do a grafting a bone graft you know, it's painful. OTHER_COMMENTS: [3553.433] [coughs/laughs?] S22_12_2: [3555.224] okay you said that ehm, these children with er cleft lip and palette [?or the?] facial d-, uhm defects they show, their behaviour changed, what kind of change you say in their behaviour is that aggression to their friends or their parents S40_12_2: [3572.755] uh when, i mean when they had it. S22_12_2: [3575.366] i mean eh you showed that, uhm article that, they studied, chi- normal children and children with cleft lip and palate and they showed behavioural no the previous one they showed behavioural problems. what kind of behavioural problems do they become more aggressive to, other children or to their parents, which kind of problems they show? S40_12_2: [3599.617] their behavioural problems uh , yeah n- n- like not aggressive. they they are like, they don't talk, they don't er they don't have the confidence to er go and talk to someone, or er be friendly with someone. eh they they're not aggressive. yeah they're not like aggressive, they're the opposite of aggressive they're depr- they don't do anything yeah. S22_12_2: [3618.357] okay [3623.124] [inaudible] OTHER_COMMENTS: [3626.579] [laughter] SFLOOR: [3627.829] [S?] [raises his hand] eh, what what option? S39_12_2: [3627.923] [inaudible] just to say it's usually [inaudible] should go from one year of age [??] surgery [??] S38T6_12_2: [3631.993] okay eh thank you , [inaudible] i think we'll we'll um move on [inaudible] un- unless you wanted to make a comment or anything SFLOOR: [3634.295] [S?] awww awww? OTHER_COMMENTS: [3635.366] [laughter / inaudible chatter] S40_12_2: [3642.600] oh, no S38T6_12_2: [3643.641] were you still [inaudible] was the discussion at the front [inaudible] OTHER_COMMENTS: [3644.249] [laughter] S39_12_2: [3646.860] it was just, it was just that basically i said usually the surgery happens if they're one years old, cleft lip and palate just to clarify S40_12_2: [3647.737] no no no SFLOOR: [3655.664] [S16_12_2] well i i have a question, uh wha- what, what wou- right what option would you like would the government offer to the family which has like [?affected ] like this so would would they do like offer surgery to the family or what would they do seeing it's genetically inherited ? OTHER_COMMENTS: [3657.019] [giggling] S39_12_2: [3671.081] yeah usua-, usually they're seen at a multi disciplinary clinic where there's eh orthodontists, an oral surgeon, a speech and language therapist, ehm a psychologist. SFLOOR: [3682.763] [S16_12-2] so, [?gets help?] offered S39_12_2: [3683.128] yeah, so, there's help offered there [inaudible] S40_12_2: [3686.806] they're put on the waiting list OTHER_COMMENTS: [3689.877] [laughter] [clapping] [students moving around / background noise] [chair wheeled along the floor] [laughter]; groups changing over S9_T1_12_2: [3691.584] okay thank you PBL group [inaudible] S38T6_12_2: [3718.200] actually [?can i?] can i just ask can you take that chair away from the exit cause if anyone came [?if?] the fire alarm went off [inaudible] OTHER_COMMENTS: [3733.490] [inaudible conversation] S3_12_2: [3750.449] okay good morning everybody, our group PBL group one will going to represent, some interesting issues of Van de Woude syndrome, first we'll start with variable expression and some ethical consideration, we- and then we'll go and discuss how one gene can cause two different syndromes, and finally we're going to discuss the best ways of palate development. (2) okay first of all, variable expression and incomplete penetrance. variable expression is the term used to ehm, refer to individuals that have the same genotype but they exhibit different phenotypes, (2) so expressivity of is variable in V- VWS, as you can see, eh no- all the clinical features such as lip pits cleft lips are eh [? a cleft ] palate is seen in each case, and that clefting in both direction horizontally and vertically can occur within the same family pedigree. it is well demonstrated in JS case as, she had , cleft lip in additional to lip pits in her pedigree and all the affected people in the S family only had the lip pits. yep, and about penetrance of VWS is considered to be high, but incomplete. which means that an individual can carry the mutation in an VWS case it is the IRF six mutation so A might, have t he mutation but she's still not affected. (2) and there is a significant association between the er cleft types of the parents and their child, so a parent that, oh sorry, a parent with lip pits can only transmit ehm, twenty two percent, whereas if the case was a more severe one, like lip pits in additional to the cleft lips, it will be greater than the twenty-two percent, in J's case or in other cases where the parent is unaffected but had a family history of VWS, and in J's case her parent, her eh father, had the eh cleft, had the lip pits, but also ehm there was a, mildly phenotype, so she had a greater risk than if, only the lip pit of the parent was transmitted. okay let's now move on and talk about another topic which is the legal and, ethical consideration. the abortion act in nineteen sixty-seven, in Wales England and Scotland says that, for it is legal for any medical registered medical ehm practitioner in an NH hospital, eh can er perform, abortion if two of the following criterias are met first of all the pregnancy period, shouldn't exceed twenty-fourth week, and if it it [?represents] any serious permanent harm, to physical or mental ehm, problem health problems to r- preg- to the pregnant woman, or that the risk harm of continuation for pregnancy is greater than if the eh, pregnancy was terminated, moreover, the significance risk of the unborn that might suffer throughout the duration of it's life time either mentally or physically, can eh perform abortion. (2) okay, so, what about the ethical consideration of abortion. well according the British medical association of two-thousand-seven, they divided people into three main groups, pro-abortion groups, anti-abortion group where J's mother is is considered to be a member of them, and middle ground group. (2) well back to the S's family, what are their options? P and E, well if a mutation of IRF six is detected in a future pregnancy, a lot of questions will be raised for example will the baby, mildly be affected with the syndrome is it treatable, or will the baby's phenotype more severe? well what about ultrasound ? well ultrasound is only able to detect severe dysmorphic features. so a lot of complications is [?gone/going] through in here and genetic counselling should ehm , talk through the whole options to the family and discuss all the dilemmas that it's going through here. and now I'll move on [inaudible] my co- my colleague S32 to talk to you about how one gene can cause two deferent syndromes. S32_12_2: [4001.712] good morning everybody, well confusion seems to attract me a lot i don't know why that's why i always end up choosing topics with a lot of confusion. so that's what i'm going talk , about how mutations in the same gene cause two different syndromes. that is, Van de Woude syndrome and the extremely tongue twisting popliteal er pterygium syndrome well i'd like to refer to as PPS if you don't mind. well as we know, VWS presents itself with a cleft lip cleft lip and palate, and the most prominent one is lip pits. PPS is kind of very interesting because it ho- has all the orofacial features of the VWS and also has some popliteal back webbing, and uh [?pterygium?] and mainly to mention skin deformities and genital anomalies, so what is causing this it is basically the mutations in the IRF six gene, which is causing these two syndromes. so what do we know of the IRF six. IRF six belongs to a family of nine transcription factors. all the other members in the family are involved actively involved in immune response but it's pretty strange that only the IRF six , plays the role it's required for embryonic development and [???] differentiation and proliferation. so ehm [?] differentiation is it means that eh it's it's basically the skin the outer epidermis of the skin. so uh what you need to know in this presentation at least till i finish is, you need to know that it has two domains, one protein binding domain and uh one DNA binding domain. the right hand of the slide you can see the DNA binding domain , and how it's interacting with the DNA. so as I already mentioned it has, it's role in eh embryological development and er, function so, you could ask me what is the proof how do we know that if IRF six is playing a role in [?] differentiation. well, the proof is that mouse models lacking IRF six function , show a very poor skeletal development and you can see over here there's totally no limb development. so this is more evidence so moving onto the interesting part of the discussion it's like how, how do you know how how is it possible that mutations in the same gene that's causing two different syndromes so if you'd ask me ah my hypothesis would be that, if one percent nucleotide difference can cause completely two different organisms why not mutations in the same gene, can cause two different syndromes well that's absolutely my hypothesis and er let's keep that aside and see what the scientists have to say. well findings are that that, mutations, [?VWS ] causing mutations are evenly distributed throughout the gene. whereas PPS causing mutations occur mainly in the DNA binding domain, that is right there and er this is what is more attractive and er attracting the scientists and they came up with, eh new hypothesis as what is causing VWS and PWS i can assure you that it's not going be as dumb as mine it's pretty interesting, er it is that uhm that's mostly mutations in VWS are taking place due to, it's nonsense mutations that is stop codon mutations and hence er mostly the proteins produces are truncated proteins, and hence VWS is caused due to haploinsufficiency haploinsufficiency is the case where , you don't have enough amount of the protein produced and hence you develop the condition that is what is their hypothesis for VWS, but the hypothesis for PPS is completely different. they say it's caused due to a dominant negative mutation. now what is a dominant negative mutation. here as I already told you that in PPS the mutations occur in the DNA binding domain. so the DNA binding domain the mutation is there and hence it's not active but the protein binding domain is still active and hence , that forms [?] with the normal protein and it uh prevents the normal protein from interacting with DNA which otherwise it would, and hence that causes the condition so that is what is their hypothesis on dominant negative mutation. i know it sounds really er complex and all that stuff but i'll break it down for you. so if there is a bad guy there's no place for a good guy that's a dominant negative mutation and that's is what is causing PPS syndrome. so, going onto my interesting part which is confusion uhm well, hypothesis and all that was very nice and very interesting but subsequently what they came to find is that, (2) mutations er VWS patients also had mutations some of the VWS patients actually yeah also had mutations in the DNA binding domain, so now this puts a big question mark to actually their hypothesis stating that only mutations in that domain cause PPS or VWS , so we're not still not sure what's happening and they have their hands on their heads saying oh my God this is not you know, it's like that so it's they're still not sure of what's actually happening and all the results based on on all the previous results that were published were based on, the mutations happening in the DNA binding domain. so we don't know what's happening in the protein binding domain or what effect it would cause on these two syndromes. it's s- still unclear and um maybe, due to some genetic modifiers but it's still not sure and um yes as i would say further molecular studies and biochemical studies would surely throw light as to what is really confusing about these two syndromes. and eh i could continue f- further with the confusion but i think i'm running out of time and i'd like to hand it over to , my colleague uh S1 who will slide you into the pathways of , palate development thank you. S1_12_2: [4326.587] okay so i'm going talk about how elucidating the pathways in palate development is important in um developing therapeutic strategies and for research , so we can use the different um orofacial syndromes to identify genes which are important in um palate development. (2) and so lots of different em syndromes that cause um palate features and the two- two of the genes i'm going talk about IRF six and P sixty-three which are both, um seen mutations of in several different syndromes. (2) um so they've used um mice models to look at the interaction between IRF six and P sixty-three, and in um compound heterozygote um between P sixty-three and IRF six oop. in the um wild type mice, er em thirteen and half um days in a mouse embryo dissection you can see that their compound heterozygote and the wild type have very similar um features on this um scanning microscope, but by fourteen and half days um in the wild type the palate has em come together but in our compound heterozygote the palate has still got a cleft down the middle. (2) um so it's been shown that IRF six and P sixty-three are epistatic in palate development, and what this means is that a mutation in one of them has the same em phenotypic effect as a mutation in the other. and IRF six um expression has been found to be dependant on em P sixty-three, and having a functional P sixty-three, and IRF six is activated by P sixty-three through an enhancer element. (2) um so this diagram's just an overview of the interaction between em the two products of the genes, um so um as i just said um P sixty-three um interacts with the enhancer element of IRF six and um activates the transcription of the IRF six , and interesting there's actually a negative feedback loop between IRF six um transcription factor being present and em P sixty-three so when there's IRF six present this leads to the degradation of the P sixty-three molecules. um so P sixty-three itself has is a transcription factor and it's been shown to em be involved in [?] potential and it's presence is required for this, um and p- IRF six is involved in ensuring that there's exit from a cell cycle, in palate cells so if they don't exit from the cell cycle properly they continue to proliferate and don't differentiate properly in order to close the palate. so with both of these working you get correct [?] differentiation and palate closure. (2) um so the different um mutations that are um seen in syndromes that involve palate all- ish- will interfere with several different parts of em this interaction, so EEC which is ehm one of the palate syndromes involving P- P sixty-three mutations, you end up with an abhorrent ehm P sixty-three product so you don't get correct em prolit- proliferation of the [?], and also in this syndrome therefore the P sixty-three is unable to successfully em activate the enhancer element so you get much lower levels, of IRF six ehm being produced, and therefore the um exit from the cell cycle is also em i- impacted. in PPS and VWS the mutations are in the IRF six gene and if the ehm the mutations are present you aberrant protein which isn't able to correctly exit the cells from the cell cycle, and also you don't get the correct degradation of the P sixty-three molecules um by the [?]. (2) so in conclusion we've talked about how a verbal expressivity is a main issue in several aspects of this case , and it impacts on correct [?genetic?] counselling abortion ethics and pre-natal diagnosis. eh we've also talked about how further molecular studies of IRF six are required to understand why there are phenotypic differences, to PWS- PPS and VWS, and how IRF six and P sixty-three play a critical role in the development of the palate, and understanding how em, em molecules like this work together can be important in developing therapeutic strategies for targeting cleft lip and palate . em so thank you for listening. OTHER_COMMENTS: [4580.112] [clapping] [4586.885] [background noise] S1_12_2: [4588.911] any questions [laughs] S38T6_12_2: [4589.988] questions for eh S3? S3_12_2: [4591.973] sure S39_12_2: [4594.085] can i just ask about ehm, the difference between PPS and VWS and why PPS is more severe has more, severe phenotypes than VWS S32_12_2: [4604.469] i mean is a question to me or is [inaudible] S39_12_2: [4606.349] oh it's anybody S32_12_2: [4607.942] [inaudible] it's like, the questions, oh okay [4610.186] [inaudible] S39_12_2: [4610.484] [inaudible] OTHER_COMMENTS: [4610.628] [laughter] S38T6_12_2: [4613.134] well, well answer that one but, can we um before these sessions that's generally that we ask the questions in the order of presentation so, um but [inaudible]addressed to well would S3 like to answer that oor? S39_12_2: [4620.317] okay, well okay [inaudible] OTHER_COMMENTS: [4621.930] [laughter [4626.565] [laughter] [inaudible speech from various participants] S32_12_2: [4628.567] yeah what did you ask i'm sorry S39_12_2: [4630.092] it's just, eh the difference between VWS and PPS, why do you get a more severe phenotype [?with?] PPS S32_12_2: [4634.100] yes [4636.139] yes that was their hypothesis that maybe er mutations that take place in the PPS are mainly the DNA binding domain , so the- we are not sure as to because of because it prevents DNA interaction the protein and the DNA interaction it prevents , so that's what they hypothesise but still not sure because the same mutations have also been identified in VWS and so further research is required , as to [inaudible]. S38T6_12_2: [4658.654] okay so does anyone have questions for S3? [?sorry?]. er okay S9_T1 and then S7 S9_T1_12_2: [4665.413] i was just wondered you mentioned that sometimes there might be more severe features in VWS, [?? inaudible] and then you mentioned mental retardation or something, is that common? S3_12_2: [4671.162] yeah [4676.177] it's not common and it's still unknown, but eh there is a paper that says that, it was there and they noticed this. S9_T1_12_2: [4683.844] and is, ini- about one family or is i- S3_12_2: [4686.658] yeah in one family i guess S9_T1_12_2: [4688.040] and did they think that that was associated with mutations, in the IFR six gene S3_12_2: [4693.524] cause, cause, yeah I think so. [laughs](3) cos it causea the syndrome. SFLOOR: [4701.813] [S16_12_2] er yeah, to my knowledge there is one case in the UK or in two thousand and one where, a pregnant woman with a baby who is affected by cleft lip, and the pregnancy was at the thirty four weeks and , she had the abortion, and the two doctors who ordered were taken to court but they won the case so was your take on that, since you covered the area. S3_12_2: [4725.276] yeah well for the ethics as i mentioned two of the following criterias, should be met, so not necessarily all of the four criterias that i mentioned will be met for abortion it's either like any two of them can be if they're , were there then they can proceed with the abortion. SFLOOR: [4741.483] [S16_12_2] but, the two doctors agrees that, uhm, cleft lip was this like, it it could cause severe damage to the baby, but, do you think it , it could do that or i- is it could it cause severe, symptoms or like phenotype? S40_12_2: [4751.978] yeah S3_12_2: [4760.939] i don't understand your question cause you say [inaudible] SFLOOR: [4762.560] [S16_12_2] we- S1_12_2: [4762.929] i think he's ask- i think he's asking is cleft lip justification for abortion of a pregnancy SFLOOR: [4764.084] [S16_12_2] [inaudible] [4768.686] [S16_12_2] yeah] S1_12_2: [4768.967] is it a severe enough , phenotype S3_12_2: [4770.766] if the baby is going to be handicapped or anything else if i- ee- ee- either [?going/grow up ] to have, er physical or mental health problems then yes, i guess. SFLOOR: [4780.593] [S16_12_2] wou- would cleft lip give you handicap? S3_12_2: [4784.966] yeah i i [inaudible] like j- ehm , (2) [?name] wrote in her em, ethics eh stuff about [ability?] if you would like to answer [?] because you [inaudible] OTHER_COMMENTS: [4785.894] [sneeze] S32_12_2: [4794.476] so we're not really sure actually what is happening here because of uh variable expressivity, and if it's going be like affected but we are not sure because a mental retardation could be but even though it's kind of rare, we cannot be really sure so that's what the problem is with the pregnancy we're not able to make a decision it could be the cleft lip or palate or could be, you know even more severe with another even brain development is affected yes. SFLOOR: [4817.845] [S34_12_2] it could be, when you get an IRF six mutation too it could also be PPS- like it could also be PPS right because you're getting a, i mean, [inaudible] it could also cause they're not completely sure [inaudible] S32_12_2: [4827.784] yes it could also be yeah [4831.358] yeah based on the phenotypes it's only yeah based on the phenotypes only we can come to a conclusion just on the mutation it is not possible to come to a conclusion because, the same mutations are almost observed in you know both occasions so, n- that is what's confusing about this and uh about offering a counselling to the patients because . OTHER_COMMENTS: [4840.958] [inaudible] SFLOOR: [4845.916] [S34_12_2] patients. yes S38T6_12_2: [4848.421] okay any more questions for S3. (3) [long pause] okay questions for S32. S32_12_2: [4858.485] alright S38T6_12_2: [4859.519] um who's that? oh S22 S22_12_2: [4861.972] yeah you said like um, patients Van der Woude syndrome usually they have mutations in protein binding domain and PPS in DNA binding domain, have they seen any patients who has , PPS but has mutation in protein binding domain. S38T6_12_2: [4872.058] mhum S32_12_2: [4879.774] er not really actually most of the mutations in PPS o- occur mainly in the DNA that's what er led them to a hypothesis that might be due to the mutations over there that could cause PPS because it , predominantly o- occurs only over there, mostly but maybe one or two cases i'm not really sure i didn't refer all the literature but, that's what er, causes PPS as far as i know S22_12_2: [4903.098] okay thank you S32_12_2: [4905.604] yes S38T6_12_2: [4907.630] so can i ask um , so the DNA binding domain and the protein binding domain, are these involved in different pathways or are they [inaudible] are they involved in the same pathway? OTHER_COMMENTS: [4915.361] [cough] S32_12_2: [4919.498] uhm i think as far as i'd read i think protein er the binding domain is involved in um, [?this IRF six or not has not] involved in cancer tumour suppression , so i think that is completely a different pathway, the protein the binding domain i think it's involved in tumour suppression , and eh it interacts with another protein called [?maspin ] eh in and it suppresses tumour in breast cancer, so that might be a completely different pathway and this might be completely different eh i'm not really sure about that but, based on the literature i that i've read ehm might be it's a different pathway, yes. S38T6_12_2: [4951.594] thank you. uhm any more questions for , S32? if not we'll move on to questions for S1. oh uhm, S22 springs OTHER_COMMENTS: [4960.880] [laughter] S22_12_2: [4961.820] S1 you said that eh this IR-, IRF six and P fifty-three, the phenotypes in an patient can be these two genes like mm- i understand from your talk that they work like cause and related correlated each other, were there any case in the literature when for example Van der Woude or people who has IRF six mutation, are more susceptible to cancer. let- any correlation between them? S1_12_2: [4988.989] that's not really something i looked at P sixty-three, has a really big role in in cancer and in apoptosis but it's actually two isoforms of P sixty-three it's a really, complicated molecule there's two isoforms and there's several different alternatively spliced products, so i mainly looked a the literature that was referring purely to the palate development but P sixty-three definitely does have a a large role in cancer pathways cause it is does interact with P-fifty three as well S22_12_2: [5015.907] so could could it be possible that, er patients who have mutation in P fifty-three also have polymorphisms or mutatation in in their IRF six gene. S1_12_2: [5026.224] yes it's perfectly possible that they have mutations in both, but a mutation in one would look lik- a mutation IRF six would, th- th- the same phenotype as a mutation in P sixty-three. effectively so you'd end up with a cleft palate. S22_12_2: [5039.524] okay thank you S38T6_12_2: [5044.110] i'll ask is is P fif- , sorry P sixty-three actually a P fifty-three family protein is it S1_12_2: [5046.591] [laughs] [5049.841] it's not a family protein but eh or one of the the- there's two forms there's with [?a] slightly different end terminus, and em one of them which isn't which is the different isoform, em has a group on it which does it's similar to a group on P fifty-three , and as far as i understand it is involved in the process of causing apoptosis, ehm it but i'm no sh- don't think it is the same family i'm no- i'm not sure, about that but it does have a structure that's very similar to P fifty-three. S38T6_12_2: [5079.781] any [inaudible] S9_T1_12_2: [5081.362] might be a daft question but, how similar is how good a model is the mouse for palate formation is it very similar to what happens in humans S1_12_2: [5089.424] as far as i could see it was, very similar at the kind of, cause you've got the whole palate looks very similar in total and they were using slightly different erm approaches to, to look at it but i think it is quite a good model S32_12_2: [5101.527] but we experiment mostly on mouse so i think uh, it's mostly i mean well all experiments we use mouse instead of [?] so, i think that must be S1_12_2: [5111.383] [laughs] OTHER_COMMENTS: [5111.383] [laughter] S1_12_2: [5114.225] it's definitely a cheap and easy model OTHER_COMMENTS: [5115.830] [several S'S] yes [5116.290] [laughter] S1_12_2: [5116.447] so, [laughs] you can't really do these experiments on humans so OTHER_COMMENTS: [5119.994] [laughter] S9_T1_12_2: [5122.573] okay if there are no further their questions thank you PBL group one. OTHER_COMMENTS: [5125.004] [clapping] S9_T1_12_2: [5129.994] and last but not least it's PBL group two OTHER_COMMENTS: [5132.735] [background noise / chatter / students moving around; groups chaning over] [long silence] S8_12_2: [5179.752] hello everyone i'm S8 and me and S12 are presenting PBL group two , and we are going talk about the Van der Woude syndromes some aspects of it, so i'm going cover the variable expression which S3 spoke about and i'm basically going cover what underlies variable expression and S9_T1 asked if like there were o- other genes other than IR F six which will cause variable expression in, in the syndrome and i'm also going cover alternative causes of Van der Woude syndrome and S12's going cover testing. so there are a number of traits which do not follow Mendelian inheritance which are not single gene , pattern of inheritance , and what eh leads us to say that is variable penetrance or variable expressivity, or polygenic traits or gene [?genotractions?] or the , interven- i mean intervening of environment in the inheritance of these traits. so what about Van der Woude syndrome? well Van der Woude syndrome shows an autosomal dominant pattern of inheritance, and almost shows a hundred percent penetrance but it shows variable expressivity. so in this particular study by de Lima et al they considered three [?nought ] seven families and they really considered diverse families of, i mean different ethnic ethnic origins, and they found that sixty-eight percent of the cases showed an IRF six mutation, basically exonic mutations, and a range of phenotypes were identified even within a single family so that's what's variable expression. so wha- what could, be the reason for the remaining thirty-two percent of the cases , and what's the reason behind variable expression. (2) what they hypothesise was maybe there were gross deletions in the IRF six gene which they couldn't identify by the DNA sequencing strategy that they used, but that could be the least likely thing because sequencing is quite accurate. and next is mutations and introns they found some mutations and introns, in uh ex- intron one and three i think which are the most common, and mutations on other genes, uh other than the IRF six genes, and polygenic mechanisms . and variable expression they have proposed two hypothesis first there's modifier genes and second is the role of environment in, (2) we- mutations outside the exons i said they found mutations and introns, and mutations on other genes and these are the number of susceptible loci, mostly these genes are involved in cranial facial uh development during the embryological development, and main genes that they found was TGF beta TGF alpha, SMAD and BMP and MSX . so uhm i'm going talk about the TGF beta mainly which, this the pathway you can see that ho- i mean how it affects, so uh TGF beta binds to an [?exo ] cell whatever , eh cellular receptor and that activates a cell of proteins which are called SMAD proteins. these proteins bind to a Co-SMAD n- SMAD four is a co-SMAD protein and they bind and they go, er- they transport the nucleus and they interact with the genes erh s- certain genes on the nucleus which are involved in er, say like collagen gene w- expression et cetera, and they activate those genes. and TFG alpha has a similar function, SMAD as you- as i said it's involved in the pathway so maybe mutations in the SMAD genes which are producing SMAD proteins could also lead to uhm , Van der Woude syndrome. and BMP is a bone morpho genetic protein, which is responsible for the production of um, the bone proteins and the other cartilage proteins et cetera. and MSX one is the gene that activates uhm, BMP so maybe a mutation in MSX could also lead to any of these er i mean cleft lip or cleft palate, et cetera. and next polygenic mechanisms, basically TFG beta and BMP both of them, er kind of activate the similar i mean genes which perform the same function both o- i mean genes which are all responsible for the oral facial development. and both of them activates SMAD proteins which in turn activate, genes which are all responsible for oral facial development, so maybe it could be because of the pol- interaction of these genes which are all responsible for the same thing? and, now variable expression modifier genes, they have seen that in combination with er VWS mutation if you have certain polymorphisms in some other genes then that could lead to an increased risk of developing a cleft lip or cleft palate as opposed to just having er, lip pits. so, TGF alpha if you have the allele two, er and MSX if you have the allele three and TGF beta three if you have the allele two, then you could get a cleft lip or palate or you could get a just er a cleft palate, things like that and effective environment i think that most of them have covered that the teratogens in alcohol drugs smoking all that could affect the baby's development. so , er that's it. (2) thank you , i [?inaudible] S12_12_2: [5492.668] thank you. good morning ehm, i'm going to talk about testing method for Van der Woude syndrome. well eh Van der Woude syndrome can be diagnosed based on the clinical features, but because of the variable expression of phenotype, uhm th- the con- the the diagnosis must be confirmed. uhm, IRT six is is the gene associated with Van der Woude so this gene would be tested by cytogenetics and molecular analysis, to identify the abnormalities that leads to disease. for cytogenetic analysis both protein karyotype and FISH are used,. protein karyotype will detect large deletions and translocations, that inform IRT six, but because of the resolution it will not detect eh, deletions or translocations which are smaller than five megabases, and because of that eh the suitable [?] will be FISH because FISH detect a small deletion, within the gene by using a specific probes for eh the critical region. for molecular analysis DNA sequencing is a preferred technique, to diagnose Van der Woude syndrome. and it will detect eh micro deletions and eh point mutations within the gene. (2) well um why sequencing ? as i mentioned it's a preferred technique and that's because of several reasons the first reason is, uhm wide range of mutations including a nonsense missense eh, micro deletions and eh , [?friendships] have been identified across the whole gene. so there's a variable of IRT six mutations. the second reason is eh the size of the gene, IRT six is consist of eh ten exons . so it's relatively short and it can be sequenced to identify the mutation. DNA sequencing detects ah mutation in seventy percent of individual, with Van der Woude syndrome. and eighty percent of eh of these mutations are in exon uhm three four seven eight and nine. so these exons are positive to be the hotspots of IRT six gene. (2) well this iga- ah- this gives us the proof and and she was tested to diagnose eh, the disease. firstly she was tested by routine karyotype and the result was forty-six XX , which is a normal [?human?] karyotype with a normal , er set of chromosomes so there is no large deletions or translocations that inform IRT six. (2) uh, (2) second test was FISH er using specific probes er for the critical region and the result was normal so, there is no small deletions within the gene. then er she was testing by DNA sequencing and the result shows that she's she was heterozygote for this mutation in IRF six gene er , (2) and the implication is in exon four, it's which is the DNA binding domain, it's a missense mutation and the mutation leads to substitution of er proline, eh by serine [?] at position seventy-six of the protein. uhm, this mutation is uh previously reported by Kondo in two thousand and two and uh it's again be reported in two thousand and six in eh in Chinese patient, (2) well for conclusion uhm, another mutation has been identified, so we know the cause of the factor of the disease and er , (2) the the diagnosis confirmed and J is affected with Van der Woude syndrome, uh there's a possible follow up as as uh pedigree show the mutation is most likely to be inherited through the family, but, it's finding it to be uh confirmed by this thing other , other family members, also uhm effective er, the effected family members should be referred for genetic counselling. (2) yes that's it thank you OTHER_COMMENTS: [5737.586] [clapping] S38T6_12_2: [5742.684] okay are there any questions for S8 ? (2) [pause] oh yup uhm S34? SFLOOR: [5748.562] [S34_12_2 ] [?] IRF six go, how does IRF six fit into the TGF [?] pathway or does it at all. like i like that was the pathway you showed was just for, development of [?] S8_12_2: [5757.138] yeah, i was talking about the other causes other than IRF six which could lead to, Van der Woude syndrome a cleft lip or cleft palate and, which is associated with Van der Woude syndrome. SFLOOR: [5767.501] [S34_12_2 ] okay so IRF six doesn't necessarily go in that pathway. S8_12_2: [5770.700] no- but it seems to be associated with the TGF beta pathway but, i don't exactly know. SFLOOR: [5776.277] [S34_12_2 ] i don't know either that's why I asked OTHER_COMMENTS: [5777.722] [laughter] S38T6_12_2: [5779.563] okay i think S22 had a question S22_12_2: [5781.363] yeah, because this TFG beta gene is considered um a modifier gene in many diseases they also studied in CF patients cystic fibrosis patients i'm just wondering what's the main function of TGF in the body. S8_12_2: [5794.852] it's basically a signalling protein it S22_12_2: [5797.359] signalling protein S8_12_2: [5797.689] yeah it it activates certain proteins which further activate genes which are responsible mainly for the development and S22_12_2: [5805.439] so it has mainly signalling function. S8_12_2: [5807.031] yeah it's a signalling S38T6_12_2: [5813.793] um okay S8 i'll ask um you mentioned that M- MSX one was homeobox protein. you- what's a homeobox protein S8_12_2: [5823.047] a homeobox protein uhm, that was, yeah it basically activates certain genes which are and- that's also responsible in development and it activates certain other genes which are responsible for development. and it's called homeobox i think because it's, it's kind of similar in most i mean they've seen in mouse models and, [?] and it's kind of the similar gene it has similar functions S38T6_12_2: [5849.257] um, thank you em, any more questions for S8, if not, questions for S12. er S22? S22_12_2: [5859.268] S12 you showed uhm the, gene and you said like it's in the mutation is DNA binding uh [? site] right? S12_12_2: [5867.536] yep S22_12_2: [5868.262] and from the previous slides previous presentation we hear that usually uhm, Van der Woude syndrome is protein binding site mutations. am I right? S12_12_2: [5878.036] well, em yeah you're right [?chromosome] three and four] SFLOOR: [5879.556] [S?] no no no no no i though it was evenly distributed throughout the gene [5883.615] [?S?]so so you can get S32_12_2: [5884.091] yeah [??] PPS it takes place in that domain that's why they suspect something [?is wrong] SFLOOR: [5886.050] S22_12_2: [5889.466] but Van der Woude syndrome can be in both of them S32_12_2: [5891.271] yeah that's what i told you in my conclusion. S22_12_2: [5892.915] okay OTHER_COMMENTS: [5893.740] [laughter] S12_12_2: [5901.144] well yeah as [?you] say four seven three and four seven [?] domain and [?mutation] three and four can cause uh Van der Woude syndrome and can cause PPS, but for er, for er Van der Woude syndrome, uh mutation in seven and eight it's more likely to to cause eh Van der Woude syndrome OTHER_COMMENTS: [5903.287] [repeated banging sound] SFLOOR: [5920.076] [S34_12_2 ] can i answer the-, just try answer the question S12_12_2: [5923.384] yes OTHER_COMMENTS: [5923.534] [laughter] SFLOOR: [5924.121] [S34_12_2 ] with the the the DNA binding domain [??] mutations, the [??] the mutations in PPS in the DNA binding domain, i think they interact directly with the DNA [??] like protein [?-isation?] studies and stuff, but the mutations in the DNA binding domain with VWS, uh they don't uh interact directly with the DNA. the r- the residues don't actually contact the DNA that are mutated in VWS but the residues in PPS that are mutated, uh they actually are physically coming in contact with the DNA. if that helps. [5952.936] S22_12_2: [5953.242] so in Van der Woude syndrome, when you get mutation in DNA binding it doesn't change a lot SFLOOR: [5959.535] [S34_12_2 ] i i don't know what that means but that's how you can that's one way you can tell cause if you get a mutation in the DNA binding domain, the hypothesis is to determine whether it's VWS or PPS they look at whether or not the mutated residue interacts directly with the DNA like actually physically comes in contact or whether it does not. S22_12_2: [5968.153] okay [5974.896] so it doesn't matter it's eh even if in DNA binding, it depends on the mutation. SFLOOR: [5980.273] [S34_12_2 ] it depends more on [5982.219] [S?] it depends more on mutations [inaudible] [5983.846] [S34_12_2 ] it it's all hypothesis but it does, you can just because it's in the DNA binding domain doesn't mean that's it's for sure PPS or VWS, you have to analyse what residues actually mutated. and, but they don't know why or how they just like did it comparitively, you know? S22_12_2: [5993.574] okay then it's not it's not DNA binding or protein binding it's mutation residue cause like eh [inaudible] SFLOOR: [6000.627] [S34_12_2 ] within the within the DNA binding domain you can still say, PPS mutations i think are mostly in the DNA binding domain, but some VWS mutations like S32 was saying they're distributed throughout the gene. so if you get one, in a case like this where the mutation does occur in the DNA binding domain, you can determine whether it's PPS or VWS based on what residue is actually mutated, yeah. S22_12_2: [6019.536] ah okay it depends on [inaudible]. Thank you S12_12_2: [6021.716] but yeah, you're right uh, it's not one hundred per cent accurate that, yeah so it's not [?all] accurate [??inaudible; overlap] em, they, there is a [?] mutations that cause eh eh Van der Woude syndrome, and they found all in one mutant amino acid that react directly with the DNA. but with PPS they told that most of the mutant amino acids, they react directly with the DNA, so it's it's not one hundred percent, but in a way it's can give you a clue that the mutation going to to cause eh Van der Woude syndrome or going to cause PPS. Okay? yeah. SFLOOR: [6027.043] no [6028.595] no it's not, even [inaudible] OTHER_COMMENTS: [6029.143] laughter SFLOOR: [6047.758] [S34-12_2] yeah S3_12_2: [6065.030] yeah, eh you mentioned uh eh the chinese study, is it similar to J's case? S12_12_2: [6070.450] well it's quite similar it's er it's the same er, the same phenotype er, i cant remember female or male but the patient has er, er cleft lip also has er, a lip er pits the same as as er J. so as as as far it's only reported twice, once in two thousand and two and once in two thousand and six. S3_12_2: [6097.870] and did they have future pregnancy in whe- where it terminated or not S12_12_2: [6101.424] well no they they have discussed the, the [?diagnosing part] but eh, in J's case, the doctor as [?mentioned in scenario] they gave the family a risk of one in fifty, based on that J er doesn't have er, another affected member of family [?it's a mistake] so, uhm, the risk of of future family sorry future pregnancy to be increased so it will be fifty percent and it's likely the father is a carrier for the mutation. S3_12_2: [6104.299] oh right [6118.853] yeah [6133.151] [?] S9_T1_12_2: [6136.254] see like in the pedgiree for the family, can you bring the pedigree up? S12_12_2: [6140.561] er, (11) [pause as navigates to correct slide] yeah S9_T1_12_2: [6153.021] see the girl in the middle, er S12_12_2: [6156.860] yeah S9_T1_12_2: [6157.008] three three, [6157.634] hmm mmm, ehm, what age is she sorry? oh yeah right she's the [?SNP]- sorry, yeah. (2) are you, what're going do for her, anything or nothing or, S12_12_2: [6169.194] well um, (2) i think no i will do something for her OTHER_COMMENTS: [6173.900] [laughter] S12_12_2: [6178.012] she can be she can be affected. and the sign that that she show, it's hasn't been identified, so maybe because uh, the doctor is not er is not one hundred percent eh professional so, it should be [?this stage] to identify mutation S9_T1_12_2: [6193.272] say [6196.765] say in the family, say she comes asking for, (2) you know she wants to know if she's got a chance of having a child with the same, the cleft palette or whatever, and say, the parent suggested i don't want any, they don't want you to tell, (2) her anything about a mutation or anything in fa- in the family, (2) is she at risk of having an affected child and who's information is it, is she does she have a right to, (2) to know? SFLOOR: [6196.765]  S12_12_2: [6228.113] well, (2) she ha- she has the right and, J's parents maybe had the right also, so maybe i will [?with her] that her mother or sorry, her father is affected, and he can pass or transmit the mutation to her without mentioning that J and her parents or her father is affected with the mutation. so we can deliver the mu- information to her without mentioning that the parents, sorry that J and her father are affected. S9_T1_12_2: [6261.498] good thank you S12_12_2: [6262.652] [?] S38T6_12_2: [6264.142] any more questions? S3_12_2: [6266.257] can i also add something , to your question, see um, three three person is [?A] as i'd mentioned due to the high penetrance in the family, eh the person might carry the mutation but might not be affected so there is still be a chance that they still can transmit the mutation to their offspring, so she should be counselled S12_12_2: [6286.277] [??] S38T6_12_2: [6288.665] okay well i'd like to to th- eh finish by thanking all the speakers i think actually this year's set of presentations for this PBL scenario i think, have outdone all the previous sets of presentations for this so well done all the presenters OTHER_COMMENTS: [6305.443] [clapping] S38T6_12_2: [6311.968] [?thanks?] to the group members who contributed to the the beautiful presentations we've seen today, uhm the the staff i think will now eh go and have a a conference and we will um come up with some feedback and some marks and stuff which you will know in due course, at some point. S9_T1_12_2: [6328.461] probably not today OTHER_COMMENTS: [6329.688] [laughter] S38T6_12_2: [6329.753] not today S9_T1_12_2: [6331.386] and also there's an exam on here in this room from twelve till two not for you guys for another [?] OTHER_COMMENTS: [6336.083] [laughter] S9_T1_12_2: [6347.201] so if you try and not come in between twelve and two because they'll all be doing their exam S38T6_12_2: [6351.490] how many of you have a party back there OTHER_COMMENTS: [6353.146] [laughter / chatter; students all packing up to go] END of PBL 6362.436536/106.04 mins]