Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing

A Eliot Shearer; Adam P DeLuca; Michael S Hildebrand; Kyle R Taylor; José Gurrola II; Steve Scherer; Todd E Scheetz; Richard J H Smith

doi:10.1073/pnas.1012989107

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Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing

Journal article

Open access

Peer reviewed

Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing

A Eliot Shearer, Adam P DeLuca, Michael S Hildebrand, Kyle R Taylor, José Gurrola II, Steve Scherer, Todd E Scheetz and Richard J H Smith

Proceedings of the National Academy of Sciences - PNAS, Vol.107(49), pp.21104-21109

12/07/2010

DOI: 10.1073/pnas.1012989107

PMCID: PMC3000272

PMID: 21078986

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Abstract

The extreme genetic heterogeneity of nonsyndromic hearing loss (NSHL) makes genetic diagnosis expensive and time consuming using available methods. To assess the feasibility of target-enrichment and massively parallel sequencing technologies to interrogate all exons of all genes implicated in NSHL, we tested nine patients diagnosed with hearing loss. Solid-phase (NimbleGen) or solution-based (SureSelect) sequence capture, followed by 454 or Illumina sequencing, respectively, were compared. Sequencing reads were mapped using GSMAPPER, BFAST, and BOWTIE, and pathogenic variants were identified using a custom-variant calling and annotation pipeline (ASAP) that incorporates publicly available in silico pathogenicity prediction tools (SIFT, BLOSUM, Polyphen2, and Align-GVGD). Samples included one negative control, three positive controls (one biological replicate), and six unknowns (10 samples total), in which we genotyped 605 single nucleotide polymorphisms (SNPs) by Sanger sequencing to measure sensitivity and specificity for SureSelect-Illumina and NimbleGen-454 methods at saturating sequence coverage. Causative mutations were identified in the positive controls but not in the negative control. In five of six idiopathic hearing loss patients we identified the pathogenic mutation. Massively parallel sequencing technologies provide sensitivity, specificity, and reproducibility at levels sufficient to perform genetic diagnosis of hearing loss.

Software

Hearing Loss - genetics

DNA Mutational Analysis

Humans

Genotype

Polymorphism, Single Nucleotide

Genetic Testing - methods

Sequence Analysis, DNA - methods

Details

Title: Subtitle: Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing
Creators: A Eliot Shearer - Department of Otolaryngology, Head and Neck Surgery, University of Iowa, Iowa City, IA 52242, USA
Adam P DeLuca
Michael S Hildebrand
Kyle R Taylor
José Gurrola II
Steve Scherer
Todd E Scheetz
Richard J H Smith
Resource Type: Journal article
Publication Details: Proceedings of the National Academy of Sciences - PNAS, Vol.107(49), pp.21104-21109
DOI: 10.1073/pnas.1012989107
PMID: 21078986
PMCID: PMC3000272
NLM abbreviation: Proc Natl Acad Sci U S A
ISSN: 1091-6490
eISSN: 1091-6490
Publisher: United States
Grant note: R01 DC02842 / NIDCD NIH HHS R01 DC003544 / NIDCD NIH HHS T32 GM082729 / NIGMS NIH HHS R01 DC002842 / NIDCD NIH HHS
Language: English
Date published: 12/07/2010
Academic Unit: Roy J. Carver Department of Biomedical Engineering; Electrical and Computer Engineering; Molecular Physiology and Biophysics; Anatomy and Cell Biology; Stead Family Department of Pediatrics; Iowa Neuroscience Institute; Center for Bioinformatics and Computational Biology; Otolaryngology; Internal Medicine; Ophthalmology and Visual Sciences
Record Identifier: 9983980064402771

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