Development and Validation of a Next-Generation Sequencing Panel for Syndromic and Nonsyndromic Hearing Loss

Malinda Butz, Amber McDonald, Patrick A. Lundquist, Melanie Meyer, Sean Harrington, Sarah Kester, Mariam I. Stein, Nipun A. Mistry, Eric Zimmerman Zuckerman, Zhiyv Niu, Lisa Schimmenti, Linda Hasadsri, Nicole J. Boczek

Research output: Contribution to journalArticlepeer-review

Abstract

BACKGROUND: Deafness and hearing loss are common conditions that can be seen independently or as part of a syndrome and are often mediated by genetic causes. We sought to develop and validate a hereditary hearing loss panel (HHLP) to detect single nucleotide variants (SNVs), insertions and deletions (indels), and copy number variants (CNVs) in 166 genes related to nonsyndromic and syndromic hearing loss. METHODS: We developed a custom-capture next-generation sequencing (NGS) reagent to detect all coding regions, ±10 flanking bp, for the 166 genes related to nonsyndromic and syndromic hearing loss. Our validation consisted of testing 52 samples to establish accuracy, reproducibility, and analytical sensitivity. In addition to NGS, supplementary methods, including multiplex ligation-dependent probe amplification, long-range PCR, and Sanger sequencing, were used to ensure coverage of regions that had high complexity or homology. RESULTS: We observed 100% positive and negative percentage agreement for detection of SNVs (n = 362), small indels (1-22 bp, n = 25), and CNVs (gains, n = 8; losses, n = 17). Finally, we showed that this assay was able to detect variants with a variant allele frequency ≥20% for SNVs and indels and ≥30% to 35% for CNVs. CONCLUSIONS: We validated an HHLP that detects SNVs, indels, and CNVs in 166 genes related to syndromic and nonsyndromic hearing loss. The results of this assay can be utilized to confirm a diagnosis of hearing loss and related syndromic disorders associated with known causal genes.

Original languageEnglish (US)
Pages (from-to)467-479
Number of pages13
JournalThe journal of applied laboratory medicine
Volume5
Issue number3
DOIs
StatePublished - May 1 2020

Keywords

  • deafness
  • DFNA
  • DFNB
  • hearing loss
  • next generation sequencing
  • nonsyndromic hearing loss
  • syndromic hearing loss

ASJC Scopus subject areas

  • Medicine(all)

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