Deafness gene variations in a 1120 nonsyndromic hearing loss cohort: molecular epidemiology and deafness mutation spectrum of patients in Japan

The Annals of Otology, Rhinology, and Laryngology
Shin-Ya Nishio, Shin-Ichi Usami

Abstract

To elucidate the molecular epidemiology of hearing loss in a large number of Japanese patients analyzed using massively parallel DNA sequencing (MPS) of target genes. We performed MPS of target genes using the Ion PGM system with the Ion AmpliSeq and HiSeq 2000 systems using SureSelect in 1389 samples (1120 nonsyndromic hearing loss cases and 269 normal hearing controls). We filtered the variants identified using allele frequencies in a large number of controls and 12 predication program scores. We identified 8376 kinds of variants in the 1389 samples, and 409 835 total variants were detected. After filtering the variants, we selected 2631 kinds of candidate variants. The number of GJB2 mutations was exceptionally high among these variants, followed by those in CDH23, SLC26A4, MYO15A, COL11A2, MYO7A, and OTOF. We performed a large number of MPS analyses and clarified the genetic background of Japanese patients with hearing loss. This data set will be a powerful tool to discover rare causative gene mutations in highly heterogeneous monogenic diseases and reveal the genetic epidemiology of deafness.

References

May 19, 2006·The New England Journal of Medicine·Cynthia C Morton, Walter E Nance
Apr 23, 2008·Human Mutation·A OshimaW J Kimberling
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
May 26, 2010·Clinical Genetics·K TsukadaUNKNOWN Deafness Gene Study Consortium
Jul 6, 2010·Nucleic Acids Research·Kai WangHakon Hakonarson
Nov 17, 2010·Proceedings of the National Academy of Sciences of the United States of America·A Eliot ShearerRichard J H Smith
Jun 22, 2012·Journal of Medical Genetics·Xiao Chang, Kai Wang
Nov 7, 2012·Nature·UNKNOWN 1000 Genomes Project ConsortiumGil A McVean
Dec 5, 2012·American Journal of Medical Genetics. Part a·Isabelle SchrauwenMatthew J Huentelman
Nov 16, 2013·Nucleic Acids Research·Melissa J LandrumDonna R Maglott
May 31, 2014·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Barbara VonaThomas Haaf
Sep 30, 2014·American Journal of Human Genetics·A Eliot ShearerRichard J H Smith

❮ Previous
Next ❯

Citations

Aug 16, 2016·BioMed Research International·Shin-Ya NishioHela Azaiez
Jun 9, 2017·Expert Review of Molecular Diagnostics·Manou SommenGuy Van Camp
Oct 7, 2017·Otology & Neurotology : Official Publication of the American Otological Society, American Neurotology Society [and] European Academy of Otology and Neurotology·Pavlina PlevovaEva Mrazkova
Nov 3, 2016·Current Opinion in Pediatrics·Christina M Sloan-Heggen, Richard J H Smith
Oct 28, 2018·European Archives of Oto-rhino-laryngology : Official Journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : Affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery·Tianni XuPing Wang
Nov 4, 2016·EMBO Molecular Medicine·Takehiko UeyamaShin-Ichiro Kitajiri
Aug 23, 2019·The Journal of Laryngology and Otology·R Larsen-ReindorfG J Basura
Sep 17, 2019·Intractable & Rare Diseases Research·Mahbobeh KoohiyanMorteza Hashemzadeh-Chaleshtori
Sep 19, 2019·International Journal of Molecular Sciences·Tomohiro KitanoShin-Ichi Usami
Feb 7, 2020·The Anatomical Record : Advances in Integrative Anatomy and Evolutionary Biology·Shin-Ichi UsamiHidekane Yoshimura
Sep 13, 2019·Annals of Human Genetics·Mahbobeh KoohiyanFatemeh Azadegan-Dehkordi
Dec 13, 2019·European Journal of Human Genetics : EJHG·Lilian DownieDavid J Amor
Mar 11, 2016·International Journal of Audiology·Kathleen C M CampbellDaniel J Fox
Oct 1, 2019·Journal of Audiology & Otology·Mahbobeh KoohiyanMorteza Hashemzadeh-Chaleshtori
Oct 19, 2017·Annals of Human Genetics·Juliana Sampaio-SilvaKarina Lezirovitz
Mar 7, 2020·Acta Oto-laryngologica·Hidekane YoshimuraShin-Ichi Usami
Dec 26, 2019·International Journal of Pediatric Otorhinolaryngology·Raja A H KuchayMustafa Tekin

❮ Previous
Next ❯

Methods Mentioned

BETA
AmpliSeq
genotyping

Software Mentioned

SIFT
Torrent Variant Caller
Mutation Assessor
Mut Taster
FATHMM
GERP
Polyphen2 HVAR
PhyloP
BWA
SiPhy

Related Concepts

Related Feeds

Auditory Perception

Auditory perception is the ability to receive and interpret information attained by the ears. Here is the latest research on factors and underlying mechanisms that influence auditory perception.