Targeted Exon Sequencing Successfully Discovers Rare Causative Genes and Clarifies the Molecular Epidemiology of Japanese Deafness Patients
Open Access
- 13 August 2013
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 8 (8), e71381
- https://doi.org/10.1371/journal.pone.0071381
Abstract
Target exon resequencing using Massively Parallel DNA Sequencing (MPS) is a new powerful strategy to discover causative genes in rare Mendelian disorders such as deafness. We attempted to identify genomic variations responsible for deafness by massive sequencing of the exons of 112 target candidate genes. By the analysis of 216randomly selected Japanese deafness patients (120 early-onset and 96 late-detected), who had already been evaluated for common genes/mutations by Invader assay and of which 48 had already been diagnosed, we efficiently identified causative mutations and/or mutation candidates in 57 genes. Approximately 86.6% (187/216) of the patients had at least one mutation. Of the 187 patients, in 69 the etiology of the hearing loss was completely explained. To determine which genes have the greatest impact on deafness etiology, the number of mutations was counted, showing that those in GJB2 were exceptionally higher, followed by mutations in SLC26A4, USH2A, GPR98, MYO15A, COL4A5 and CDH23. The present data suggested that targeted exon sequencing of selected genes using the MPS technology followed by the appropriate filtering algorithm will be able to identify rare responsible genes including new candidate genes for individual patients with deafness, and improve molecular diagnosis. In addition, using a large number of patients, the present study clarified the molecular epidemiology of deafness in Japanese. GJB2 is the most prevalent causative gene, and the major (commonly found) gene mutations cause 30–40% of deafness while the remainder of hearing loss is the result of various rare genes/mutations that have been difficult to diagnose by the conventional one-by-one approach. In conclusion, target exon resequencing using MPS technology is a suitable method to discover common and rare causative genes for a highly heterogeneous monogenic disease like hearing loss.Keywords
This publication has 26 references indexed in Scilit:
- A Low-Cost Exon Capture Method Suitable for Large-Scale Screening of Genetic Deafness by the Massively-Parallel Sequencing ApproachGenetic Testing and Molecular Biomarkers, 2012
- Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platformBMC Medical Genomics, 2012
- Simultaneous Screening of Multiple Mutations by Invader Assay Improves Molecular Diagnosis of Hereditary Hearing Loss: A Multicenter StudyPLOS ONE, 2012
- Applications of targeted gene capture and next-generation sequencing technologies in studies of human deafness and other genetic disabilitiesHearing Research, 2012
- Exome sequencing as a tool for Mendelian disease gene discoveryNature Reviews Genetics, 2011
- Application of Deafness Diagnostic Screening Panel Based on Deafness Mutation/Gene Database Using Invader AssayGenetic Testing, 2007
- Comprehensive splice-site analysis using comparative genomicsNucleic Acids Research, 2006
- Newborn Hearing Screening — A Silent RevolutionThe New England Journal of Medicine, 2006
- Identification of CRYM as a Candidate Responsible for Nonsyndromic Deafness, through cDNA Microarray Analysis of Human Cochlear and Vestibular Tissues**Nucleotide sequence data reported herein are available in the DDBJ/EMBL/GenBank databases; for details, see the Electronic-Database Information section of this article.American Journal of Human Genetics, 2003
- Mechanisms of fidelity in pre-mRNA splicingCurrent Opinion in Cell Biology, 2000