CANADIAN COLLEGE OF MEDICAL GENETICISTS (CCMG) Molecular Genetics Specialty Examination. May 6, 2008

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1 NDIN OLLEGE OF MEDIL GENEIISS (MG) Molecular Genetcs Specalty Examnaton Duraton: 3 hours otal Pages: 9 otal Marks: 91 Instructons: May 6, Please ensure that your canddate number s on each page of your answer booklet. Do not use your name. 2. Please wrte n dark blue or black nk. Do not use pencl. 3. Each queston may be answered n pont form wth tables and dagrams where approprate. Please show all calculatons. 4. Please return all exam materals at the end of the examnaton. 1

2 1. ompare and contrast two dfferent methods for DN extracton from whole blood. Your answer should nclude knowledge of the dfferent steps n the processes but does not need to nclude statements about the advantages and dsadvantages of the methods or detals such as volumes of reagents used. Begn wth blood collecton and end pror to begnnng a PR reacton. (12 marks) 2. patent wth an unconfrmed famly hstory of Huntngton dsease (HD) s tested, along wth two presumably affected sblngs, to determne hs rsk of developng HD. he patent s mother, who was reported to have had HD, s deceased and no molecular testng was performed. he patent s father, who was reported to also have a neurologcal dsorder, s estranged from the famly. he results of the HD testng are gven below n the famly pedgree. HD results from an expanson of a polymorphc G repeat n the I-15 gene, where affected ndvduals carry 36 or more G repeats. 46, 16 19, 19 47, 19 Interpret the results of the HD testng as t relates to the neurologcal health of ths famly. Explore possble explanatons for the results. (12 marks) 2

3 3. he sequence below s for a mrn of a hypothetcal gene. he G start codon begns at nucleotde 75. he stop codon ends at nucleotde For the followng varants, gve the codng sequence (c) desgnaton and the proten (p) desgnaton usng Human Genome Varaton Socety recommendatons for mutaton nomenclature. 1 agttcctgct ttgatgtgac ctgtgactcc ccagaataca ccttgcttct gtagaccagc 61 tccaacagga ttccatggta gctgggatgt tagggctcag ggaagaaaag tcagaagacc 121 aggacctcca gggcctcaag gacaaacccc tcaagtttaa aaaggtgaag aaagataaga 181 aagaagagaa agagggcaag catgagcccg tgcagccatc agcccaccac tctgctgagc 241 ccgcagaggc aggcaaagca gagacatcag aagggtcagg ctccgccccg gctgtgccgg 301 aagcttctgc ctcccccaaa cagcggcgct ccatcatccg tgaccgggga cccatgtatg 361 atgaccccac cctgcctgaa ggctggacac ggaagcttaa gcaaaggaaa tctggccgct 421 ctgctgggaa gtatgatgtg tatttgatca atccccaggg aaaagccttt cgctctaaag 481 tggagttgat tgcgtacttc gaaaaggtag gcgacacatc cctggaccct aatgattttg 541 acttcacggt aactgggaga gggagcccct cccggcgaga gcagaaacca cctaagaagc 601 ccaaatctcc caaagctcca ggaactggca gaggccgggg acgccccaaa gggagcggca 661 ccacgagacc caaggcggcc acgtcagagg gtgtgcaggt gaaaagggtc ctggagaaaa 721 gtcctgggaa gctccttgtc aagatgcctt ttcaaacttc gccagggggc aaggctgagg 781 ggggtggggc caccacatcc acccaggtca tggtgatcaa acgccccggc aggaagcgaa 841 aagctgaggc cgaccctcag gccattccca agaaacgggg ccgaaagccg gggagtgtgg 901 tggcagccgc tgccgccgag gccaaaaaga aagccgtgaa ggggtcttct atccgatctg 961 tgcaggagac cgtactcccc atcaagaagc gcaagacccg ggagacggtc agcatcgagg 1021 tcaaggaagt ggtgaagccc ctgctggtgt ccaccctcgg tgagaagagc gggaaaggac 1081 tgaagacctg taagagccct gggcggaaaa gcaaggagag cagccccaag gggcgcagca 1141 gcagcgcctc ctcacccccc aagaaggagc accaccacca tcaccaccac tcagagtccc 1201 caaaggcccc cgtgccactg ctcccacccc tgcccccacc tccacctgag cccgagagct 1261 ccgaggaccc caccagcccc cctgagcccc aggacttgag cagcagcgtc tgcaaagagg 1321 agaagatgcc cagaggaggc tcactggaga gcgacggctg ccccaaggag ccagctaaga 1381 ctcagcccgc ggttgccacc gccgccacgg ccgcagaaaa gtacaaacac cgaggggagg 1441 gagagcgcaa agacattgtt tcatcctcca tgccaaggcc aaacagagag gagcctgtgg 1501 acagccggac gcccgtgacc gagagagtta gctgacttta cacggagcgg attgcaaagc 1561 ctctgacaaa gcttcccgat taactgaaat aaaaaatatt tttttttctt tca a) to nucleotde change at # 664 b) to nucleotde change at #837 c) Deleton of G at nucleotdes 731 and 732 d) he followng sequence (compare to same poston above): 1261 ccgaggaggccc e) patent has the mutaton descrbed n a and the mutaton descrbed n b as does hs mother. What s the correct nomenclature for these changes n ths patent usng the codng sequence desgnaton? f) Mutatons n ths gene cause an autosomal recessve dsorder. he patent beng analysed has the mutaton descrbed n c and n d. Hs unaffected father 3

4 carres the c mutaton and hs unaffected mother carres the d mutaton. What s the correct genotype nomenclature for the patent and hs parents usng the codng sequence desgnaton? (12 marks) Second Poston of odon G F r s t P o s t o n G Phe [F] Phe [F] Leu [L] G Leu [L] Leu [L] Leu [L] Leu [L] G Leu [L] Ile [I] Ile [I] Ile [I] G Met [M] G Val [V] G Val [V] G Val [V] GG Val [V] Ser [S] Ser [S] Ser [S] G Ser [S] Pro [P] Pro [P] Pro [P] G Pro [P] hr [] hr [] hr [] G hr [] G la [] G la [] G la [] GG la [] yr [Y] yr [Y] er [end] G er [end] Hs [H] Hs [H] Gln [Q] G Gln [Q] sn [N] sn [N] Lys [K] G Lys [K] G sp [D] G sp [D] G Glu [E] GG Glu [E] G ys [] G ys [] G er [end] GG rp [W] G rg [R] G rg [R] G rg [R] GG rg [R] G Ser [S] G Ser [S] G rg [R] GG rg [R] GG Gly [G] GG Gly [G] GG Gly [G] GGG Gly [G] G G G G h r d P o s t o n 4

5 4. You are asked to provde a resdual carrer rsk for the partner of a woman who s known to be a carrer of SM. pproxmately 98% of ndvduals affected wth SM have a homozygous deleton of the SMN1 gene; ~2% have a deleton of one SMN1 gene and a pont mutaton n the other SMN1 gene; a small percentage have 2 pont mutatons. hs regon s known to have multple copes of SMN1 n cs and the followng values represent the frequences of the varous SMN1 copy number per chromosome n the populaton: 0 SMN SMN SMN he frequency of SMN1 pont mutatons s ssume he has no famly hstory of SM. a) What s hs pror rsk of beng a carrer of SM? (3 marks) b) He s shown by molecular analyss to have 2 copes of SMN1. What s hs resdual carrer rsk? (4 marks) c) He s shown to have 3 copes of SMN1. What s hs resdual carrer rsk? (3 marks) 5. You are the Drector of a Molecular laboratory. a) What should a Molecular laboratory drector consder when decdng whether to ntroduce a new dagnostc test versus referrng the test out? (6 marks) b) What steps should be taken to ntroduce a new test? (6 marks) 6. Your lab s screenng for mutatons n the breast cancer genes BR1 and BR2. hey fnd a varant n BR2 exon 11: c.6455>, whch alters a serne codon to tyrosne n the proten. hs varant has not been reported n the breast cancer nformaton core (BI) onlne database. Brefly descrbe at least 5 steps that could be taken to determne the pathogencty (clncal relevance) of ths varant. (10 marks) 5

6 7. patent has been sent to your lab wth the request to test for unparental dsomy (UPD) for chromosome 15. he followng mcrosatellte markers were analyzed, gvng the results (repeat szes) lsted below: Marker Parent 1 Parent 2 hld Dstance from the p arm telomere D15S , , Mb D15S11 95, 97 95, Mb D15S10 102, , Mb GBRβ3 300, , Mb a) Defne unparental dsomy (UPD). (2 marks) b) Interpret the results for each marker tested (4 marks) c) Gven these results, are there any other tests that you would recommend on your fnal report to the physcan? (2 marks) d) What mechansms have been postulated to account for UPD? (3 marks) e) Lst 4 chromosomes (or syndromes) that have been shown to be caused by UPD and lst the parent nvolved (maternal or paternal). (2 marks) 6

7 PLESE NSWER QUESION 8 OR 8B-NO BOH 8) Your lab does multplex lgaton-dependent probe amplfcaton (MLP) for the MLH1 and MSH2 genes. DN sample from a man wth a famly hstory of Lynch syndrome gves the result shown below. Please answer the followng questons: a) Brefly descrbe how the MLP process works (you may use dagrams to help). (4 marks) b) What are the possble explanatons for the result below and brefly descrbe technques to test your theores? (4 marks) c) Lst two genetc syndromes or dseases that you could detect usng MLP (Note: the MLP does not have to be commercally avalable for ether syndrome). (2 marks) Normalzed allelc ratos MSH2 exon 8 7

8 8B. Prenatal aneuplody screenng for chromosomes 13, 18, 21, X and Y has tradtonally been done by FISH. However, you would lke to replace FISH by QF- PR (quanttatve fluorescent PR). a) Brefly descrbe how QF-PR works. (3 marks) b) he results below were obtaned on a drect amnotc flud specmen. Descrbe the result and clncal nterpretaton of ths result. (3 marks) c) Descrbe the advantages and dsadvantages of QF-PR compared to FISH. (4 marks) 8

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