Genetics and genotype-phenotype correlations in Finnish patients with dilated cardiomyopathy

Abstract

Aims: Despite our increased understanding of the genetic basis of dilated cardiomyopathy (DCM), the clinical utility and yield of clinically meaningful findings of comprehensive next-generation sequencing (NGS)-based genetic diagnostics in DCM has been poorly described. We utilized a high-quality oligonucleotide-selective sequencing (OS-Seq)-based targeted sequencing panel to investigate the genetic landscape of DCM in Finnish population and to evaluate the utility of OS-Seq technology as a novel comprehensive diagnostic tool.

Methods and results: Using OS-Seq, we targeted and sequenced the coding regions and splice junctions of 101 genes associated with cardiomyopathies in 145 unrelated Finnish patients with DCM. We developed effective bioinformatic variant filtering strategy and implemented strict variant classification scheme to reveal diagnostic yield and genotype-phenotype correlations. Implemented OS-Seq technology provided high coverage of the target region (median coverage 410× and 99.42% of the nucleotides were sequenced at least 15× read depth). Diagnostic yield was 35.2% (familial 47.6% and sporadic 25.6%, P = 0.004) when both pathogenic and likely pathogenic variants are considered as disease causing. Of these, 20 (53%) were titin (TTN) truncations (non-sense and frameshift) affecting all TTN transcripts. TTN truncations accounted for 20.6% and 14.6% of the familial and sporadic DCM cases, respectively.

Conclusion: Panel-based, high-quality NGS enables high diagnostic yield especially in the familial form of DCM, and bioinformatic variant filtering is a reliable step in the process of interpretation of genomic data in a clinical setting.

Keywords: Diagnosis; Dilated cardiomyopathy; Genetics.

Figure 1

Bioinformatics variants filtering and characterization strategy. RadialSVM prediction, support vector machine (SVM)-based ensemble prediction; LR, logistic regression-based ensemble prediction.

Figure 2

Spatial distribution of titin frameshift and non-sense mutations in Finnish dilated cardiomyopathy cohort. Titin is linearly depicted with its 152 Immunoglobulin-like domains in green and 132 fibronectin type III domains in purple. TTN mutations are shown as lollipops. Depicted are non-sense (red) and frameshift (green) mutations in subjects with dilated cardiomyopathy. Variants are shown relative to the titin Uniprot Sequence identifier Q8WZ42. The dashed lines below the protein schematic indicate the location of variants within the sarcomere.

Figure 3

Pedigrees of the patients with truncating TTN mutations. All family members with available DNA samples were included. Index patients are marked with an arrow. All family members with dilated cardiomyopathy carried truncating TTN mutation. Disease penetrance increased from 53.8% at age 50 to 84.6% at age 60 and 100.0% at age 70.

Figure 4

Kaplan–Meier curve demonstrating freedom from composite endpoint (cardiac transplantation and death from cardiac causes). Panel A shows Kaplan–Meier curve for patients with and without detected disease-causing mutation and Panel B shows comparison between patients with TTN vs. LMNA mutations. Importantly, many patients are 40–60 years old at a moment and have not reached any endpoint. Hatch marks indicate patient age at last follow-up date in Finnish dilated cardiomyopathy study.