Whole-Exome Sequencing Efficiently Detects Rare Mutations in Autosomal Recessive Nonsyndromic Hearing Loss

Oscar Diaz-Horta, Duygu Duman, Joseph Foster, Asli Sirmaci, Michael Gonzalez, Nejat Mahdieh, Nikou Fotouhi, Mortaza Bonyadi, Filiz Başak Cengiz, Ibis Menendez, Rick H. Ulloa, Yvonne J K Edwards, Stephan L Zuchner, Susan H Blanton, Mustafa Tekin

Research output: Contribution to journalArticle

96 Citations (Scopus)

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.

Original languageEnglish
Article numbere50628
JournalPLoS One
Volume7
Issue number11
DOIs
StatePublished - Nov 30 2012

Fingerprint

Exome
Audition
hearing
mutation
Genes
Mutation
deafness
Deafness
genes
Exons
exons
Nonsyndromic Deafness
Base Composition
Hearing

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Whole-Exome Sequencing Efficiently Detects Rare Mutations in Autosomal Recessive Nonsyndromic Hearing Loss. / Diaz-Horta, Oscar; Duman, Duygu; Foster, Joseph; Sirmaci, Asli; Gonzalez, Michael; Mahdieh, Nejat; Fotouhi, Nikou; Bonyadi, Mortaza; Cengiz, Filiz Başak; Menendez, Ibis; Ulloa, Rick H.; Edwards, Yvonne J K; Zuchner, Stephan L; Blanton, Susan H; Tekin, Mustafa.

In: PLoS One, Vol. 7, No. 11, e50628, 30.11.2012.

Research output: Contribution to journalArticle

Diaz-Horta, O, Duman, D, Foster, J, Sirmaci, A, Gonzalez, M, Mahdieh, N, Fotouhi, N, Bonyadi, M, Cengiz, FB, Menendez, I, Ulloa, RH, Edwards, YJK, Zuchner, SL, Blanton, SH & Tekin, M 2012, 'Whole-Exome Sequencing Efficiently Detects Rare Mutations in Autosomal Recessive Nonsyndromic Hearing Loss', PLoS One, vol. 7, no. 11, e50628. https://doi.org/10.1371/journal.pone.0050628
Diaz-Horta, Oscar ; Duman, Duygu ; Foster, Joseph ; Sirmaci, Asli ; Gonzalez, Michael ; Mahdieh, Nejat ; Fotouhi, Nikou ; Bonyadi, Mortaza ; Cengiz, Filiz Başak ; Menendez, Ibis ; Ulloa, Rick H. ; Edwards, Yvonne J K ; Zuchner, Stephan L ; Blanton, Susan H ; Tekin, Mustafa. / Whole-Exome Sequencing Efficiently Detects Rare Mutations in Autosomal Recessive Nonsyndromic Hearing Loss. In: PLoS One. 2012 ; Vol. 7, No. 11.
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