Whole-Genome Sequencing Adds Value to Cardiomyopathy Workup

Whole-genome sequencing (WGS) identifies additional genetic causes of hypertrophic cardiomyopathy (HCM) beyond those identified through targeted gene sequencing approaches, according to a study published in the July issue of the Journal of the American College of Cardiology. This increased detection of disease-causing variants is mostly a result of screening deep into intronic regions and the identification of intronic variants that impact splicing.

Recommendations call for genetic evaluation of all HCM patients and includes sequencing of a panel of about 30 genes, although some expanded panels evaluate hundreds of genes. Given the declining cost of sequencing, some are exploring the utility of replacing panels or reflexing to whole-genome sequencing.

The current study evaluated WGS (mean read depth of 43) on 46 unrelated patients with HCM who had undergone previous genetic testing without a diagnosis (gene-elusive HCM), 14 affected family members, and 12 unaffected members of a severely affected proband. Variants in coding regions of 184 candidate cardiac hypertrophy genes, 58 autosomal dominant genes, 12 X-linked genes, and 114 autosomal recessive genes were examined, in addition to variants in deep intronic regions that alter RNA splicing, large genomic rearrangements, and mitochondrial genome variants.

The researchers found a pathogenic or likely pathogenic variant in 9 of 46 families (20 percent) for which prior genetic testing was inconclusive. Three families had variants in genes not included in prior genetic testing, while one family had a pathogenic variant that was filtered out with prior exome sequencing. Five families had pathogenic variants in noncoding regions—four with deep intronic variants that activate novel splicing and one mitochondrial genome variant.

WGS added incremental value in identifying pathogenic variants in 9 percent of gene-elusive HCM, yielding a molecular diagnosis in an additional 20 percent of patients with prior inconclusive genetic testing. When WGS is used as a first-line test, 42 percent of HCM patients (five of 12 families) received a molecular diagnosis.

“It might be expected that advancing from sequencing 30 genes to 20,000 genes would greatly improve the diagnostic rate, but the gains in this domain appear relatively muted,” writes Euan Ashley, M.B.Ch.B., D.Phil., in an accompanying editorial. Given this incremental benefit, the study authors offer the following cautious recommendations.

• First-line genetic testing using a gene panel or exome sequencing–based analysis
  • If testing is inconclusive, no further testing is needed for people with late-onset HCM and a mild phenotype.
  • For severe clinical presentation, WGS can be used to look for de novo variants, including consideration of family trio testing.
  • For gene-elusive patients with a family history of HCM, WGS-based analysis of intronic regions (MYBPC3) and the mitochondrial genome may improve diagnosis.

One of the study’s novel findings is that RNA sequencing or functional assays may be required to prove causality from novel genes variants in deep intronic regions that affect RNA splicing. To date, RNA analysis is typically not currently available in clinical settings.

Takeaway: WGS may potentially provide incremental value as part of genetic testing strategies for patients with HCM.