The yield on re-interpretation of genetic variants in pediatric cardiomyopathy

Background Variant interpretation can change over time as new knowledge emerges. Our aim was to determine the frequency and causes of variant reinterpretation on systematic re-evaluation in pediatric patients with cardiomyopathy.

Overall, 227 unrelated pediatric patients with cardiomyopathy enrolled in the Heart Centre Biobank harbored a pathogenic/likely pathogenic (P/LP) variant and/or a variant of uncertain significance (VUS) on clinical genetic testing (2005-2022). Variant pathogenicity was re-evaluated using the American College of Medical Genetics and Genomics (ACMG) guidelines. Additional extension cohorts (n=4547, cases) were analyzed to assess variant burden in cases versus controls (gnomAD 4.1.0).

382 variants (110 P/LP, 272 VUS) in 227 patients were re-evaluated. Forty-nine variants in 49 patients (21.6%) changed classification. Twelve (10.9%) P/LP variants were downgraded to VUS in 14 patients. Leading criteria were high population allele frequency and variant not located in mutational hotspot or critical functional gene domain. Thirty-seven (13.6%) VUS were upgraded to P/LP in 35 patients. Leading criteria were variant location in mutational hotspot for gene, and deleteriousness on in silico prediction. Only 8 reclassified variants had been reported back by the clinical genetic testing laboratory at the time of the study. Ten of the 37 VUS upgraded to P/LP were significantly enriched in cardiomyopathy cases (n=4796) versus controls.

One in five patients with cardiomyopathy had a clinically relevant change in variant pathogenicity on systematic re-evaluation that would require modifying family clinical screening and cascade genetic testing. These findings underscore the clinical importance of regular variant re-interpretation on follow-up. Competing Interest Statement Seema Mital is on the Scientific Advisory Board of Bristol Myers Squibb, Rocket Pharmaceuticals, and Tenaya Therapeutics. The remaining authors declare that they have no competing interests. Funding Statement This project received support from the Canadian Institutes of Health Researchs Canadian Heart Function Alliance Network Grant (HFN 181992) (SM), the Ted Rogers Centre for Heart Research (SM, RJ), and the Heart & Stroke Foundation of Canada / Robert M Freedom Chair of Cardiovascular Science (SM). TS was funded by the Japan Heart Foundation Research Grant, Canadian Heart Function Alliance, and Philip Witchel Research Fellowship in Heart Failure at the Hospital for Sick Children. CS was funded by the German Cardiac Society, the German Centre for Cardiovascular Research, and the Dr. Rolf M. Schwiete Foundation. PSD was funded by the Department of Biotechnology (BT/PR45262/MED/12/955/2022). VJR was funded by ICMR-SRF (3/1/1 (8)/CVD/2020-NCD-1). Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study was approved by the Institutional Research Ethics Board of The Hospital for Sick Children. Written informed consent to participate was obtained from all patients and/or their parents/legal guardians. The study protocol adhered to the Declaration of Helsinki. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Footnotes We added a burden analysis utilizing an extension cohort comprising 4547 cardiomyopathy cases and population controls from gnomAD v4.1.0. This analysis evaluated the enrichment of reclassified variants, focusing on those upgraded from variants of uncertain significance (VUS) to pathogenic/likely pathogenic (P/LP). Among the 37 VUS upgraded to P/LP, 10 variants demonstrated significant enrichment in cardiomyopathy cases compared to controls. These findings support the clinical relevance of systematic variant re-evaluation and have been incorporated into the Methods, Results, and Discussion sections of the manuscript. DATA AVAILABILITY De-identified data analyzed in this study are available in the main and supplemental tables, and additional data are available from the corresponding author on reasonable request. Abbreviations - ACM - Arrhythmogenic ventricular cardiomyopathic - AMP - The American College of Medical Genetics and Genomics/Association for Molecular Pathology - B/LB - Benign/Likely benign - CI - Confidence interval - DCM - Dilated cardiomyopathy - HCM - Hypertrophic cardiomyopathy - LVNC - Left ventricular noncompaction cardiomyopathy - OR - Odds ratio - pLI - probability of loss-of-function intolerant - P/LP - Pathogenic/Likely pathogenic - RCM - Restrictive cardiomyopathy - VUS - Variant of uncertain significance