Reevaluating the Genetic Contribution of Monogenic Dilated Cardiomyopathy

Abstract

Background: Dilated cardiomyopathy (DCM) is genetically heterogeneous, with >100 purported disease genes tested in clinical laboratories. However, many genes were originally identified based on candidate-gene studies that did not adequately account for background population variation. Here we define the frequency of rare variation in 2538 patients with DCM across protein-coding regions of 56 commonly tested genes and compare this to both 912 confirmed healthy controls and a reference population of 60 706 individuals to identify clinically interpretable genes robustly associated with dominant monogenic DCM.

Methods: We used the TruSight Cardio sequencing panel to evaluate the burden of rare variants in 56 putative DCM genes in 1040 patients with DCM and 912 healthy volunteers processed with identical sequencing and bioinformatics pipelines. We further aggregated data from 1498 patients with DCM sequenced in diagnostic laboratories and the Exome Aggregation Consortium database for replication and meta-analysis.

Results: Truncating variants in TTN and DSP were associated with DCM in all comparisons. Variants in MYH7, LMNA, BAG3, TNNT2, TNNC1, PLN, ACTC1, NEXN, TPM1, and VCL were significantly enriched in specific patient subsets, with the last 2 genes potentially contributing primarily to early-onset forms of DCM. Overall, rare variants in these 12 genes potentially explained 17% of cases in the outpatient clinic cohort representing a broad range of adult patients with DCM and 26% of cases in the diagnostic referral cohort enriched in familial and early-onset DCM. Although the absence of a significant excess in other genes cannot preclude a limited role in disease, such genes have limited diagnostic value because novel variants will be uninterpretable and their diagnostic yield is minimal.

Conclusions: In the largest sequenced DCM cohort yet described, we observe robust disease association with 12 genes, highlighting their importance in DCM and translating into high interpretability in diagnostic testing. The other genes analyzed here will need to be rigorously evaluated in ongoing curation efforts to determine their validity as Mendelian DCM genes but have limited value in diagnostic testing in DCM at present. This data will contribute to community gene curation efforts and will reduce erroneous and inconclusive findings in diagnostic testing.

Keywords: ExAC; Mendelian genetics; dilated cardiomyopathy; genetic testing; rare variant association testing.

Figure 1.

Number of dilated cardiomyopathy (DCM) cases sequenced for each gene and cohort. The primary cohort is the outpatient DCM cohort. The secondary clinical genetic testing referral cohort was composed of cases that had been previously reported (light orange) along with data reported here for the first time (dark orange).

Figure 2.

Overview of the cohorts and rare variant burden analyses performed in this study. The primary cohort (n=1040) was compared with 912 healthy controls sequenced on the same platform and with the Exome Aggregation Consortium (ExAC) reference dataset. A further 1498 cases were sequenced in diagnostic laboratories on a range of platforms over a decade, and compared with ExAC (n=60 706). Comparing both cohorts with the ExAC reference population dataset, extensive quality control was performed to minimize differences caused by sequencing technologies.

Figure 3.

Comparison of the prevalence of rare protein-altering variation between dilated cardiomyopathy (DCM) cases and the Exome Aggregation Consortium (ExAC) reference dataset. Genes with a statistically significant association with disease are highlighted in red. Results are shown separately for truncating and nontruncating variants, and for primary and secondary cohorts. Truncating variants in TTN, robustly associated with DCM (prevalence 11.3% in primary DCM cohort and 11.7% in secondary cohort, vs 0.55% ExAC frequency), are not shown on these axes.

Figure 4.

Case excess of rare variants in genes significantly enriched in dilated cardiomyopathy (DCM). The excess burden of rare protein-altering variation (above the population background rate) provides an estimate of the proportion of cases attributable to variation in each gene under a dominant monogenic inheritance model. Genes with a significant enrichment of rare truncating (A) and nontruncating (B) variants in patients with DCM compared with controls are shown (with the exceptions of ACTC1, PLN, and NEXN, where we detected an enrichment of joint truncating and nontruncating variation in DCM but not when the 2 variant classes were analyzed separately). Results are summarized for 3 comparisons as shown in Figure 2. Statistically significant enrichments are shown in saturated hues. ExAC indicates Exome Aggregation Consortium; NS, not significant; and S, significant.

Figure 5.

Known and interpretable classes of genetic variants in dilated cardiomyopathy (DCM). The case excess (the difference in rare variant prevalence between cases and controls) provides an estimate of the contribution of a gene/variant class to DCM (proportion of cases explained by that gene/variant class) and is plotted against the etiological fraction, a measure of the interpretability of rare variants detected in patients (the proportion of cases with a variant where that variant is likely causative). Truncating and nontruncating variants are shown separately for each DCM cohort.