Toward an effective exome-based genetic testing strategy in pediatric dilated cardiomyopathy

Johanna C. Herkert*, Kristin M. Abbott, Erwin Birnie, Martine T. Meems-Veldhuis, Ludolf G. Boven, Marloes Benjamins, Gideon J. du Marchie Sarvaas, Daniela Q. C. M. Barge-Schaapveld, J. Peter van Tintelen, Paul A. van der Zwaag, Yvonne J. Vos, Richard J. Sinke, Maarten P. van den Berg, Irene M. van Langen, Jan D. H. Jongbloed

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

18 Citations (Scopus)

Abstract

Purpose: We evaluated the diagnostic yield in pediatric dilated cardiomyopathy (DCM) of combining exome sequencing (ES)based targeted analysis and genome-wide copy-number variation (CNV) analysis. Based on our findings, we retrospectively designed an effective approach for genetic testing in pediatric DCM.

Methods: We identified 95 patients (in 85 families) with pediatric onset of DCM. We initially excluded 13 of these families because they already had a genetic diagnosis, leaving a total of 31 probands for singlenucleotide polymorphism (SNP) array and trio-ES. We used Human Phenotype Ontology (HPO)-based filtering for our data analysis.

Results: We reached a genetic diagnosis in 15/31 (48.4%) families. ES yielded a diagnosis in 13 probands (13/15; 86.7%), with most variants being found in genes encoding structural cardiomyocyte components. Two large deletions were identified using SNP array. If we had included the 13 excluded families, our estimated yield would have been 54%.

Conclusion: We propose a standardized, stepwise analysis of (i) wellknown cardiomyopathy genes, (ii) CNVs, (iii) all genes assigned to HPO cardiomyopathy, and (iv) if appropriate, genes assigned to other HPO terms. This diagnostic approach yields the highest increase at each subsequent step and reduces analytic effort, cost, the number of variants of unknown clinical significance, and the chance of incidental findings.

Original languageEnglish
Pages (from-to)1374-1386
Number of pages13
JournalGenetics in Medicine
Volume20
Issue number11
DOIs
Publication statusPublished - Nov-2018

Keywords

  • copy-number variation analysis
  • diagnostic approach
  • dilated cardiomyopathy
  • exome sequencing
  • pediatric cardiomyopathy
  • HUMAN PHENOTYPE ONTOLOGY
  • DEVELOPMENTAL DELAY
  • POSITION STATEMENT
  • WORKING GROUP
  • MUTATIONS
  • TITIN
  • DELETION
  • INFANT
  • COHORT
  • FORM

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