Analysis of 51 proposed hypertrophic cardiomyopathy genes from genome sequencing data in sarcomere negative cases has negligible diagnostic yield

Abstract

Purpose: Increasing numbers of genes are being implicated in Mendelian disorders and incorporated into clinical test panels. However, lack of evidence supporting the gene-disease relationship can hinder interpretation. We explored the utility of testing 51 additional genes for hypertrophic cardiomyopathy (HCM), one of the most commonly tested Mendelian disorders.

Methods: Using genome sequencing data from 240 sarcomere gene negative HCM cases and 6229 controls, we undertook case-control and individual variant analyses to assess 51 genes that have been proposed for HCM testing.

Results: We found no evidence to suggest that rare variants in these genes are prevalent causes of HCM. One variant, in a single case, was categorized as likely to be pathogenic. Over 99% of variants were classified as a variant of uncertain significance (VUS) and 54% of cases had one or more VUS.

Conclusion: For almost all genes, the gene-disease relationship could not be validated and lack of evidence precluded variant interpretation. Thus, the incremental diagnostic yield of extending testing was negligible, and would, we propose, be outweighed by problems that arise with a high rate of uninterpretable findings. These findings highlight the need for rigorous, evidence-based selection of genes for clinical test panels.

Keywords: HCM; VUS; evidence-based; genetic testing; variant interpretation.

Fig. 1

Frequency of the 51 selected candidate genes in current commercial test panels. All genes listed in the Genomics England hypertrophic cardiomyopathy (HCM) panel that were not in the Oxford Medical Genetics Laboratory (OMGL) clinical HCM test panel at the time of this study were selected for analysis. The bar chart displays the number of times each of the 51 selected candidate genes was included in a commercial test panel. Data was extracted from the National Center for Biotechnology Information (NCBI) Gene Tests website (October 2016) and Genetic Test Registry (December 2017). This included 10 clinical HCM panels and 11 clinical cardiomyopathy panels. Information on laboratories and available test panels is in Table S5. The gene labels are colored according to the review status as annotated by Genomics England, which gives an indication of the level of evidence supporting each gene–disease relationship: Green = high evidence, the gene is very likely be the cause of the disease and can be reported back to patients. Amber = moderate evidence, and should not yet be used for genome interpretation. Red = low evidence for a role in disease, or not suitable for clinical diagnosis at this time.

Fig. 2

Odds ratios with 95% confidence interval (CI) in hypertrophic cardiomyopathy (HCM) cases (n=240) compared with National Institute for Health Research Bioresource Rare Disease HCM project (BRRD) controls (n=6229). All = all rare variants. Nontruncating = missense, in-frame insertions and deletions, and other variants annotated as MODERATE impact by SNPEff. . Truncating = variants predicted to result in a truncated transcript (nonsense, frameshift, canonical splice site). Rare is defined as gnomAD minor allele frequency (MAF) <0.0001. Data plotted using log10 scale. Genes in which no rare variants were detected in cases have not been plotted. A single truncating variant in TCAP was found in cases and no truncating variants were detected in controls; this result is not significant when corrected for multiple testing.

Fig. 3

Proportions of cases with different classes of reportable variants. Confirmed genes: proportion of cases with a reportable variant in confirmed hypertrophic cardiomyopathy (HCM) genes (n=16). Comparison data from Oxford Medical Genetics Laboratory clinical HCM 16-gene panel from HCM cases (n=1082) referred for genetic testing from period January 2014 to September 2015. Candidate genes: proportion of cases with a reportable variant in the genes tested in this study in 240 HCM cases in whom no likely pathogenic or pathogenic variant was detected in confirmed genes. *N=50 variants detected in the TTN gene are not shown (TTN OR was 0.9 [95%CI 0.68–1.18]. TTN VUS are found in an additional 20% of cases). Note that for the 16 confirmed genes, case excess data indicate that the majority of VUS will in fact be disease causing, whereas the absence of any excess in cases in the 50 candidate genes indicates that the vast majority of VUS will not be disease causing. CI confidence interval, OR odds ratio, VUS variants of uncertain significance