Identification of copy number variants through whole-exome sequencing in autosomal recessive nonsyndromic hearing loss

Genet Test Mol Biomarkers. 2014 Sep;18(9):658-61. doi: 10.1089/gtmb.2014.0121. Epub 2014 Jul 25.


Genetic variants account for more than half of the cases with congenital or prelingual onset hearing loss. Autosomal recessive nonsyndromic hearing loss (ARNSHL) is the most common subgroup. Whole-exome sequencing (WES) has been shown to be effective detecting deafness-causing single-nucleotide variants (SNVs) and insertion/deletions (INDELs). After analyzing the WES data for causative SNVs or INDELs involving previously reported deafness genes in 78 families with ARNSHL, we searched for copy number variants (CNVs) through two different tools in 24 families that remained unresolved. We detected large homozygous deletions in STRC and OTOA in single families. Thus, causative CNVs in known deafness genes explain 2 out of 78 (2.6%) families in our sample set. We conclude that CNVs can be reliably detected through WES and should be the part of pipelines used to clarify genetic basis of hearing loss.

Publication types

  • Clinical Trial
  • Multicenter Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • DNA Copy Number Variations*
  • Exome*
  • Family
  • Female
  • GPI-Linked Proteins / genetics*
  • Genetic Diseases, Inborn / genetics*
  • Genome-Wide Association Study
  • Hearing Loss / genetics*
  • Humans
  • INDEL Mutation*
  • Intercellular Signaling Peptides and Proteins
  • Male
  • Membrane Proteins / genetics*
  • Pedigree


  • GPI-Linked Proteins
  • Intercellular Signaling Peptides and Proteins
  • Membrane Proteins
  • OTOA protein, human
  • STRC protein, human