title: Whole-exome sequencing efficiently detects rare mutations in autosomal recessive nonsyndromic hearing loss.
abstract: Identification of the pathogenic mutations underlying autosomal recessive nonsyndromic hearing loss (ARNSHL) is difficult, since causative mutations in 39 different genes have so far been reported. After excluding mutations in the most common ARNSHL gene, GJB2, via Sanger sequencing, we performed whole-exome sequencing (WES) in 30 individuals from 20 unrelated multiplex consanguineous families with ARNSHL. Agilent SureSelect Human All Exon 50 Mb kits and an Illumina Hiseq2000 instrument were used. An average of 93%, 84% and 73% of bases were covered to 1X, 10X and 20X within the ARNSHL-related coding RefSeq exons, respectively. Uncovered regions with WES included those that are not targeted by the exome capture kit and regions with high GC content. Twelve homozygous mutations in known deafness genes, of which eight are novel, were identified in 12 families: MYO15A-p.Q1425X, -p.S1481P, -p.A1551D; LOXHD1-p.R1494X, -p.E955X; GIPC3-p.H170N; ILDR1-p.Q274X; MYO7A-p.G2163S; TECTA-p.Y1737C; TMC1-p.S530X; TMPRSS3-p.F13Lfs*10; TRIOBP-p.R785Sfs*50. Each mutation was within a homozygous run documented via WES. Sanger sequencing confirmed co-segregation of the mutation with deafness in each family. Four rare heterozygous variants, predicted to be pathogenic, in known deafness genes were detected in 12 families where homozygous causative variants were already identified. Six heterozygous variants that had similar characteristics to those abovementioned variants were present in 15 ethnically-matched individuals with normal hearing. Our results show that rare causative mutations in known ARNSHL genes can be reliably identified via WES. The excess of heterozygous variants should be considered during search for causative mutations in ARNSHL genes, especially in small-sized families.
authors.affiliation: John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America.
authors.forename: Oscar
authors.initials: O
authors.lastname: Diaz-Horta
authors.forename: Duygu
authors.initials: D
authors.lastname: Duman
authors.forename: Joseph
authors.initials: J
authors.lastname: Foster
authors.forename: Aslı
authors.initials: A
authors.lastname: Sırmacı
authors.forename: Michael
authors.initials: M
authors.lastname: Gonzalez
authors.forename: Nejat
authors.initials: N
authors.lastname: Mahdieh
authors.forename: Nikou
authors.initials: N
authors.lastname: Fotouhi
authors.forename: Mortaza
authors.initials: M
authors.lastname: Bonyadi
authors.forename: Filiz Başak
authors.initials: FB
authors.lastname: Cengiz
authors.forename: Ibis
authors.initials: I
authors.lastname: Menendez
authors.forename: Rick H
authors.initials: RH
authors.lastname: Ulloa
authors.forename: Yvonne J K
authors.initials: YJ
authors.lastname: Edwards
authors.forename: Stephan
authors.initials: S
authors.lastname: Züchner
authors.forename: Susan
authors.initials: S
authors.lastname: Blanton
authors.forename: Mustafa
authors.initials: M
authors.lastname: Tekin
mesh_terms: D000072259:Connexin 26; D017630:Connexins; D004252:DNA Mutational Analysis / Q000379:methods*; D059472:Exome / Q000235:genetics*; D005260:Female; D005808:Genes, Recessive / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D034381:Hearing Loss / Q000235:genetics*; D006801:Humans; D008297:Male; D010375:Pedigree
chemical_list: D017630:Connexins; C000607042:GJB2 protein, human; D000072259:Connexin 26