In this goal-driven proposal, submitted in response to Funding Opportunity Announcement (FOA) Number PAR-11-003, we will make comprehensive genetic testing for deafness available to clinicians for under $500 per person. The driving force behind this initiative is the frequency of hearing impairment. As the most common sensory impairment, it is diagnosed in 1 of every 500 newborns and 50% of octogenarians (Morton Ann N Y Acad Sci 1991). With 57 genes implicated in nonsyndromic hearing loss (NSHL), it is also an extremely heterogeneous trait and presents a tremendous challenge to diagnosis. Current strategies for genetic testing for deafness are inadequate. For most, only a minority of genes is included, with selection criteria typically reflecting: 1) high prevalence as a cause of deafness (i.e. GJB2);2) association with another recognizable feature (i.e. SLC26A4 and enlarged vestibular aqueduct);or 3) a recognizable audioprofile (i.e. low frequency hearing loss as seen with WFS1) (Hilgert et al Mut Res 2009). The recent advent of powerful DNA target enrichment and sequencing technologies, however, makes it possible to provide comprehensive genetic testing for deafness that is efficient and cost-effective. We have shown that it is possible to analyze all deafness genes simultaneously on a single platform (called OtoSCOPE) (Shearer et al PNAS 2010). Related to this endeavor, we have also validated AudioGene as a phenotypic tool that uses patient audiograms to predict the genetic cause of ADNSHL (Hildebrand et al Genet Med 2008;Hildebrand et al Laryngoscope 2009). Building on these findings, in this proposal we will complete two specific aims.
Specific Aim 1 : To provide comprehensive, high-throughput, low-cost DNA sequence generation and analysis for deafness genetic testing Goal 1: Comprehensive, high-throughput, low-cost DNA sequence analysis for genetic testing for deafness is possible at sensitivities and specificities comparable to Sanger sequencing by using targeted sequence enrichment followed by massively parallel sequencing.
Specific Aim 2 : To optimize both machine learning-based audioprofiling of audiometric data and phenotypic filtering of genotypic data by expanding and improving the platform we have developed called AudioGene Goal 2: As a phenome tool, a machine-learning software system trained on an extensive set of audiometric data can be used to predict and to eliminate specific genes or gene variants as causes of deafness based on audiometric data. Achieving these specific aims will change the clinical evaluation of deaf and hard-of-hearing persons by making genetic testing the most important diagnostic test after a history, physical examination and audiological assessment.

Public Health Relevance

In this goal-driven proposal, submitted in response to Funding Opportunity Announcement (FOA) Number PAR-11-003, we will make comprehensive genetic testing for deafness available to clinicians for under $500 per person. Achieving this goal will change the clinical evaluation of deaf and hard-of-hearing persons by making genetic testing the most important diagnostic test after a history and physical exam.

Agency
National Institute of Health (NIH)
Institute
National Institute on Deafness and Other Communication Disorders (NIDCD)
Type
Research Project (R01)
Project #
1R01DC012049-01
Application #
8224101
Study Section
Special Emphasis Panel (ZDC1-SRB-L (49))
Program Officer
Watson, Bracie
Project Start
2011-09-21
Project End
2016-08-31
Budget Start
2011-09-21
Budget End
2012-08-31
Support Year
1
Fiscal Year
2011
Total Cost
$608,130
Indirect Cost
Name
University of Iowa
Department
Otolaryngology
Type
Schools of Medicine
DUNS #
062761671
City
Iowa City
State
IA
Country
United States
Zip Code
52242
Shearer, A Eliot; Eppsteiner, Robert W; Frees, Kathy et al. (2017) Genetic variants in the peripheral auditory system significantly affect adult cochlear implant performance. Hear Res 348:138-142
Booth, Kevin T; Azaiez, Hela; Kahrizi, Kimia et al. (2017) Exonic mutations and exon skipping: Lessons learned from DFNA5. Hum Mutat :
Korver, Anna M H; Smith, Richard J H; Van Camp, Guy et al. (2017) Congenital hearing loss. Nat Rev Dis Primers 3:16094
Michel, Vincent; Booth, Kevin T; Patni, Pranav et al. (2017) CIB2, defective in isolated deafness, is key for auditory hair cell mechanotransduction and survival. EMBO Mol Med 9:1711-1731
Booth, K T; Kahrizi, K; Babanejad, M et al. (2017) Variants in CIB2 cause DFNB48 and not USH1J. Clin Genet :
Sloan-Heggen, Christina M; Bierer, Amanda O; Shearer, A Eliot et al. (2016) Comprehensive genetic testing in the clinical evaluation of 1119 patients with hearing loss. Hum Genet 135:441-50
Beheshtian, Maryam; Babanejad, Mojgan; Azaiez, Hela et al. (2016) Heterogeneity of Hereditary Hearing Loss in Iran: a Comprehensive Review. Arch Iran Med 19:720-728
Sloan-Heggen, Christina M; Smith, Richard J H (2016) Navigating genetic diagnostics in patients with hearing loss. Curr Opin Pediatr 28:705-712
Taylor, Kyle R; Booth, Kevin T; Azaiez, Hela et al. (2016) Audioprofile Surfaces: The 21st Century Audiogram. Ann Otol Rhinol Laryngol 125:361-8
Moteki, Hideaki; Azaiez, Hela; Sloan-Heggen, Christina M et al. (2016) Detection and Confirmation of Deafness-Causing Copy Number Variations in the STRC Gene by Massively Parallel Sequencing and Comparative Genomic Hybridization. Ann Otol Rhinol Laryngol 125:918-923

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