Development and Validation of a Next-Generation Sequencing Panel for Syndromic and Nonsyndromic Hearing Loss
| Autor: | Zhiyv Niu, Eric Zimmerman Zuckerman, Nipun A. Mistry, Nicole J. Boczek, Sarah Kester, Malinda L. Butz, Mariam I Stein, Amber McDonald, Sean C. Harrington, Melanie Meyer, Patrick A. Lundquist, Lisa A. Schimmenti, Linda Hasadsri |
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| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
Genotype Hearing loss Biology DNA sequencing 03 medical and health sciences symbols.namesake 0302 clinical medicine medicine Humans Coding region Genetic Predisposition to Disease Multiplex Genetic Testing Copy-number variation Hearing Loss Indel Gene Alleles Genetic Association Studies Sanger sequencing Genetics Chromosome Mapping Computational Biology High-Throughput Nucleotide Sequencing Reproducibility of Results General Medicine 030104 developmental biology Amino Acid Substitution Molecular Diagnostic Techniques symbols medicine.symptom 030217 neurology & neurosurgery |
| Zdroj: | The Journal of Applied Laboratory Medicine. 5:467-479 |
| ISSN: | 2475-7241 2576-9456 |
| DOI: | 10.1093/jalm/jfaa021 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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