Case 3. Laura Yeates BSc (hons) Grad Dip Gen Couns. FHGSA

Transcription

1 Case 3 Laura Yeates BSc (hons) Grad Dip Gen Couns. FHGSA Genetic Counsellor & Clinic Coordinator Molecular Cardiology Program, Centenary Institute HCM & Genetic Heart Disease Clinics, RPAH ICCG 2018

2 Proband 19y female Syncopal episode whilst refereeing a soccer match Second syncope 2 months later whilst walking to class at university Both events she describes feeling dizzy and short of breath before blacking out

3 QTc = 490ms Baseline

4 9 min recovery QTc 550ms

5 NW European NW European 80 s AMI 80 s Lung Ca nc LQTS PPM in 20 s

6 Genetic testing 32 gene arrhythmia panel No mutations identified

7 Brother 1 QTc = 490ms EST Prolonged QTc >480ms at 4 and 6 minutes recovery

8 Father QTc = 440ms Normal EST

9 Mother Normal EST

10 NW European NW European 80 s AMI 80 s Lung Ca N nc N N LQTS LQTS PPM in 20 s

11 Genetic Counselling issues Acceptance of diagnosis by parents are you sure? our daughter can exaggerate things Adjustment to exercise restrictions Initial denial and non-compliance with beta-blockers in brother Further genetic testing

12 Genetic testing - MLPA Large deletions/insertions not detected by NGS panels Multiplex ligation-dependent probe amplification (MLPA) is a test used to detect large deletions/ insertions In LQTS patients with a negative gene panel, large deletions/insertions account for around 10% of LQTS gene variants NM_ (KCNQ1) c.(1032+1_1033 1)_(1128+1_1129 1)del A heterozygous in frame deletion of exon 8 of the KCNQ1 gene was identified. Classified by laboratory as likely pathogenic

13 KCNQ1 (LQT1) Loss of function variants in KCNQ1 are a known mechanism of disease Deletion is absent from population databases Reports in the literature of whole exon deletions in KCNQ1 causing LQTS (exon 3, exon 7, exon 13 14) Report of one deletion on Dicipher 100bp upstream from this deletion classified as pathogenic

14 VARIANT INFORMATION KCNQ1(NM_ : c _1129-1del; p.gly345_376glndel) Cardio VarID VAR EVIDENCE OF PATHOGENICITY PVS1 null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multiexon deletion) in a gene where LOF is a known mechanism of disease Caveats: Very Strong Beware of genes where LOF is not a known disease mechanism (e.g., GFAP, MYH7) (VS) Use caution interpreting LOF variants at the extreme 3 end of a gene Use caution with splice variants that are predicted to lead to exon skipping but leave the remainder of the protein intact Use caution in the presence of multiple transcripts PS1 Same amino acid change as a previously established pathogenic variant regardless of nucleotide change OR a well-characterised mutation at the same amino acid position Strong (S) Example: Val Leu caused by either G>C or G>T in the same codon Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level PS2 De novo (both maternity and paternity confirmed) in a patient with the disease and no family history Note: Confirmation of paternity only is insufficient. Egg donation, surrogate motherhood, errors in embryo transfer, and so on, can contribute to nonmaternity. PS3 Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product Note: Functional studies that have been validated and shown to be reproducible and robust in a clinical diagnostic laboratory setting are considered the most well established. PS4 The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls Note 1: Relative risk or OR, as obtained from case control studies, is >5.0, and the confidence interval around the estimate of relative risk or OR does not include 1.0. See the article for detailed guidance PM1 Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation PM2 Absent OR rarity (<0.001 or <0.1%) from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or ExAC Caveat: Population data for insertions/deletions may be poorly called by next-generation sequencing. PM3 For recessive disorders, detected in trans with a pathogenic variant Moderate (M) Note: This requires testing of parents (or offspring) to determine phase PM4 Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants PM5 Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before Example: Arg156His is pathogenic; now you observe Arg156Cys Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level. PM6 Assumed de novo, but without confirmation of paternity and maternity PM7 Prior observation of the variant in multiple unrelated patients with the same phenotype Note: In instances of very rare variants where case control studies may not reach statistical significance, but variant is absent in controls, this may be used as moderate level of evidence. PP1 Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease Note: May be used as stronger evidence with increasing segregation data Supporting (P) PP2 Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease PP3 Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.) Caveat: Because many in silico algorithms use the same or very similar input for their predictions, each algorithm should not be counted as an independent criterion. PP3 can be used only onceinany evaluation of a variant. PP4 Patient s phenotype or family history is highly specific for a disease with a single genetic etiology PP5 Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation

15 KCNQ1 deletion MLPA qpcr 6** * ** Long range PCR 96 base pairs WT mrna Skipped mrna Dr Richard Bagnall In frame deletion

16 PM1 Located in a mutational hot spot and/or critical and well established functional domain (e.g. active site of an enzyme) without benign variation PP1 Cosegregation with disease in multiple affected family members in a gene definitely known to cause the disease. Note: may be used as stronger evidence with increasing segregation data PP4 Patient s phenotype or family history is highly specific for a disease with a single gene etiology

17 Summary Reviewing pathogenicity of genetic tests results is challenging but important Management of the genetic heart disease families requires a multidisciplinary approach to care

18 Thank you Dr Belinda Gray A/Prof Raymond Sy Dr Caroline Medi Dr Jodie Ingles Dr Richard Bagnall Ms Charlotte Burns Prof Chris Semsarian

19 QTc = 490ms Baseline

20 9 min recovery QTc 550ms