Abstract 18754: The Variants of Uncertain Significance Issue on Steroids: Determination of the Background Genetic Noise Rate Within the Known Channelopathy/Cardiomyopathy-Susceptibility Genes
Background: Next-Generation Sequencing (NGS) allows for sequencing of a many genes simultaneously, leading genetic testing companies to provide sequencing of all genes associated with a particular disease in large gene test panels. For example, there are over 90 distinct genes associated with premature sudden arrhythmic death. Previous publiclations have shown a background rate of rare non-synonymous single nucleotide variants (nsSNVs) in many of these genes which may be compounded when included in large gene panels. Therefore, we hoped to determine this background rate of nsSNVs in 93 genes that comprise various sudden death genetic heart disease genetic test panels.
Methods: The exomes from the 1000 Genomes Project (1kG) and the NHLBI Exome Sequencing Project (ESP) were genotyped in-silico for nsSNVs in 93 genes indentified on clinically available genetic tests available for HCM, DCM, ARVC, LQTS, SQTS, BrS, and CPVT. The number of subjects hosting an exceedingly rare and unique nsSNV was determined for each gene.
Results: Strikingly, 40.8% of the 1 kG cohort (12.5% hosted > 2 unique nsSNVs) and 41.9% of the ESP cohort possessed > 1 rare nsSNV within the entire 93 gene panel, while the yield of rare nsSNVs in individual genes only ranged from 0.02% for PLN to 2.3% for DMD. This background rate directly correlated with the number of genes on the panel (r=0.97). When limited to only those genes that account for >10% of the disease (HCM - MYBPC3, MYH7; LQTS - KCNQ1, KCNH2; ARVC - PKP2, DSG2; CPVT - RYR2; BrS - SCN5A), at least 7% of the subjects in both cohorts had at least one nsSNV. Thus, nearly 90% of the background rate is contained within the minor disease-susceptibility genes.
Conclusions: Despite not being enriched for the presence of genetic channelopathies and cardiomyopathies, two out of every 5 subjects within these cohorts hosted at least 1 ultra-rare nsSNV within the 93 known channelopathy/cardiomyopathy-susceptibility genes. Despite the anticipated transition from disease-specific genetic testing to whole exome genetic testing, great caution must be exercised to glean the true pathogenic mutation amidst this very daunting burden of background genetic noise. If handled poorly, false positive genetic test results and misguided cascade screens will increase.
- © 2013 by American Heart Association, Inc.