Additional value of screening for minor genes and copy number variants in hypertrophic cardiomyopathy

PLoS One. 2017 Aug 3;12(8):e0181465. doi: 10.1371/journal.pone.0181465. eCollection 2017.

Abstract

Introduction: Hypertrophic cardiomyopathy (HCM) is the most prevalent inherited heart disease. Next-generation sequencing (NGS) is the preferred genetic test, but the diagnostic value of screening for minor and candidate genes, and the role of copy number variants (CNVs) deserves further evaluation.

Methods: Three hundred and eighty-seven consecutive unrelated patients with HCM were screened for genetic variants in the 5 most frequent genes (MYBPC3, MYH7, TNNT2, TNNI3 and TPM1) using Sanger sequencing (N = 84) or NGS (N = 303). In the NGS cohort we analyzed 20 additional minor or candidate genes, and applied a proprietary bioinformatics algorithm for detecting CNVs. Additionally, the rate and classification of TTN variants in HCM were compared with 427 patients without structural heart disease.

Results: The percentage of patients with pathogenic/likely pathogenic (P/LP) variants in the main genes was 33.3%, without significant differences between the Sanger sequencing and NGS cohorts. The screening for 20 additional genes revealed LP variants in ACTC1, MYL2, MYL3, TNNC1, GLA and PRKAG2 in 12 patients. This approach resulted in more inconclusive tests (36.0% vs. 9.6%, p<0.001), mostly due to variants of unknown significance (VUS) in TTN. The detection rate of rare variants in TTN was not significantly different to that found in the group of patients without structural heart disease. In the NGS cohort, 4 patients (1.3%) had pathogenic CNVs: 2 deletions in MYBPC3 and 2 deletions involving the complete coding region of PLN.

Conclusions: A small percentage of HCM cases without point mutations in the 5 main genes are explained by P/LP variants in minor or candidate genes and CNVs. Screening for variants in TTN in HCM patients drastically increases the number of inconclusive tests, and shows a rate of VUS that is similar to patients without structural heart disease, suggesting that this gene should not be analyzed for clinical purposes in HCM.

MeSH terms

  • Base Sequence
  • Calcium-Binding Proteins / genetics
  • Cardiomyopathy, Hypertrophic / diagnosis
  • Cardiomyopathy, Hypertrophic / genetics*
  • Carrier Proteins / genetics
  • Cohort Studies
  • Connectin / genetics
  • DNA Copy Number Variations*
  • Female
  • Genetic Testing*
  • Heterozygote
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Male
  • Middle Aged
  • Sarcomeres / genetics

Substances

  • Calcium-Binding Proteins
  • Carrier Proteins
  • Connectin
  • TTN protein, human
  • myosin-binding protein C
  • phospholamban

Grants and funding

This work was supported by: ió “Obra social La Caixa”: Ramon Brugada; Instituto de Salud Carlos III (Fondo Investigación Sanitaria -FIS- (PI14/01773): Ramon Brugada; Sociedad Española de Cardiología (Proyecto Investigación Básica Cardiología 2015 de los Socios Estratégicos SEC): Oscar Campuzano; Instituto de Salud Carlos III (Fondo Investigación Sanitaria -FIS- (PI15/02222; BA16/00032): Raquel Yotti. The funder provided support in the form of salaries for authors CF-C, PA and SC, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.