Interpreting secondary cardiac disease variants in an exome cohort

Abstract

Background: Massively parallel sequencing to identify rare variants is widely practiced in medical research and in the clinic. Genome and exome sequencing can identify the genetic cause of a disease (primary results), but it can also identify pathogenic variants underlying diseases that are not being sought (secondary or incidental results). A major controversy has developed surrounding the return of secondary results to research participants. We have piloted a method to analyze exomes to identify participants at risk for cardiac arrhythmias, cardiomyopathies, or sudden death.

Methods and results: Exome sequencing was performed on 870 participants not selected for arrhythmia, cardiomyopathy, or a family history of sudden death. Exome data from 22 cardiac arrhythmia- and 41 cardiomyopathy-associated genes were analyzed using an algorithm that filtered results on genotype quality, frequency, and database information. We identified 1367 variants in the cardiomyopathy genes and 360 variants in the arrhythmia genes. Six participants had pathogenic variants associated with dilated cardiomyopathy (n=1), hypertrophic cardiomyopathy (n=2), left ventricular noncompaction (n=1), or long-QT syndrome (n=2). Two of these participants had evidence of cardiomyopathy and 1 had left ventricular noncompaction on echocardiogram. Three participants with likely pathogenic variants had prolonged QTc. Family history included unexplained sudden death among relatives.

Conclusions: Approximately 0.5% of participants in this study had pathogenic variants in known cardiomyopathy or arrhythmia genes. This high frequency may be due to self-selection, false positives, or underestimation of the prevalence of these conditions. We conclude that clinically important cardiomyopathy and dysrhythmia secondary variants can be identified in unselected exomes.

Keywords: arrhythmias, cardiac; cardiomyopathies; genetic susceptibility; genetic variation; genetics; genomics; long QT syndrome.

Figure 1

Framework for Variant Interpretation. Variants were filtered on genotype quality, coverage and allele frequency. Variants occurring at a frequency greater than the disease prevalence were designated class 2. Remaining variants were assigned pathogenicity scores based on data in HGMD and LSDBs (Table 1). dbSNP, Single Nucleotide Polymorphism Database; ESP, NHLBI Exome Sequencing Project; HGMD, Human Gene Mutation Database; LSDB, locus-specific database; MAF, minor allele frequency; MPG, most probable genotype score.

Figure 2

Whole exome gene coverage. A. Cardiomyopathy-associated genes. B. Arrhythmia-associated genes. Box and whisker plots showing base coverage for each gene across 870 probands. The bottom and top lines of the box represent the upper bounds of the first and third quartiles respectively; the mid-line represents the median. The bottom and top whiskers represent the lowest and highest values within 1.5 times the interquartile range. Outliers have been excluded. The y-axis represents the fraction of total coding bases covered by a high quality genotype call.

Figure 2

Whole exome gene coverage. A. Cardiomyopathy-associated genes. B. Arrhythmia-associated genes. Box and whisker plots showing base coverage for each gene across 870 probands. The bottom and top lines of the box represent the upper bounds of the first and third quartiles respectively; the mid-line represents the median. The bottom and top whiskers represent the lowest and highest values within 1.5 times the interquartile range. Outliers have been excluded. The y-axis represents the fraction of total coding bases covered by a high quality genotype call.

Figure 3

Summary of variants by pathogenicity class. A. Distribution of 1367 cardiomyopathy-associated variants by pathogenicity class. B. Distribution of 360 arrhythmia-associated variants by pathogenicity class.

Figure 4

Cardiac MRI. A. Four-chamber view of a normal heart. B. Four-chamber view of heart from participant 120682 with hypertrabeculation and increased noncompaction.