A variant detection pipeline for inherited cardiomyopathy-associated genes using next-generation sequencing

Théo G.M. Oliveira, Miguel Mitne-Neto, Louise T. Cerdeira, Julia D.C. Marsiglia, Edmundo Arteaga-Fernandez, José E. Krieger, Alexandre C. Pereira

Research output: Contribution to journalArticleResearchpeer-review

4 Citations (Scopus)

Abstract

In inherited cardiomyopathies, genetic testing is recognized as an enriching procedure in the diagnostic closure of a cardiac condition. Many genetic mutations have been described as pathogenically related to cardiomyopathies, turning next-generation sequencing into an extremely reliable scenario. Here we describe the validation process of a pipeline constructed with a target panel of 74 cardiomyopathy-related genes sequenced using a next-generation sequencing system. Fifty-two samples from a hypertrophic cardiomyopathy casuistic with previous molecular diagnostics (Sanger-sequenced for MYH7, MYBCP3, and TNNT2; 19 positives and 33 negatives) were processed in parallel with a HapMap reference sample (NA12878) applied for a complete panel assessment. Sequencing coverage values were satisfactory, with a mean of 250× (95% CI, 226.03-273.91) and 95.2% of target bases with a coverage of ≥10×. With a total of 567 variants, variant call sensitivity was tested in five scenarios of coverage and variant allele frequency cutoffs. Maximum achieved sensitivity was 96.7% for single-nucleotide variants and 28.5% for indels, and positive predictive values remained above 0.959 during the whole process. Inter- and intra-assay reproducibility values were 89.5% and 87.3%, respectively. After a careful assessment of analytical performance, we infer that the assay presents potential feasibility for application in diagnostic routines, with minimal time requirements and a simple bioinformatics structure.

Original languageEnglish
Pages (from-to)420-430
Number of pages11
JournalThe Journal of Molecular Diagnostics
Volume17
Issue number4
DOIs
Publication statusPublished - 1 Jul 2015
Externally publishedYes

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