Hearing loss is the most common sensory deficit in humans. It is diagnosed in 1 in 500 newborns and affects half of all octogenarians. Although causality is multifactorial, in developed countries a large fraction of hearing loss is genetic and non-syndromic, i.e. not associated with other phenotypes. During the prior granting period, we implemented and integrated comprehensive genetic testing as a cornerstone in the evaluation of the deaf and hard-of-hearing person. The American College of Medical Genetics has recognized the merit of this approach, and in 2014 included comprehensive genetic testing for the evaluation of deafness in their newest treatment guidelines. In the largest study to date to corroborate this decision, we found an underlying genetic cause for hearing loss in 440 (39%) of 1119 sequentially accrued patients chosen without exclusion criteria. Pathogenic variants were present in 49 genes and included missense variants (49%), copy number changes (18%), indels (18%), nonsense variants (8%), splice-site alterations (6%) and promoter variants (<1%), making comprehensive genetic testing the single best test to order in the diagnosis of hearing loss after an audiogram. In this competitive renewal, we will build on these accomplishments by completing the following aims: ? Specific Aim 1: To optimize phenotype-genotype integration in the analysis of hereditary hearing loss by refining the use of hierarchical surface clustering and audioprofile surface analysis to determine which types of genetic hearing loss are associated with clinically meaningful sub-clusters ? Specific Aim 2: To validate and integrate physics-based protein modeling as a tool within the Deafness Variation Database to predict variant effect and the molecular and patient phenotype ? Specific Aim 3: To identify genetic modifiers of specific deafness-causing genes predicted by hierarchical surface clustering and validated by physics-based potential free-energy modeling The successful completion of this grant will improve the clinical care of persons with hearing loss by enhancing phenome-genome integration and by making variant interpretation more robust. Knowledge gained from this proposal will also lay the foundation for refined studies focused on the identification of genetic modifiers ? both positive and negative ? associated with complex phenotypes such as noise- induced and age-related hearing loss.

Public Health Relevance

This competitive renewal addresses the increasingly daunting challenge of variant interpretation. We will seamlessly integrate AudioGene into the OtoSCOPE pipeline, explore hierarchical surfaces clustering at all loci, enhance the utility of the Deafness Variation Database by adding physics-based potential free-energy modeling, and using these tools, identify genetic modifiers of select types of genetic hearing loss. The completion of these aims will lay the foundation for more refined studies focused on the identification of genetic modifiers ? both positive and negative ? associated with complex hearing loss phenotypes including noise-induced and age-related hearing loss.

Agency
National Institute of Health (NIH)
Institute
National Institute on Deafness and Other Communication Disorders (NIDCD)
Type
Research Project (R01)
Project #
5R01DC012049-07
Application #
9393258
Study Section
Auditory System Study Section (AUD)
Program Officer
Watson, Bracie
Project Start
2011-09-21
Project End
2021-11-30
Budget Start
2017-12-01
Budget End
2018-11-30
Support Year
7
Fiscal Year
2018
Total Cost
Indirect Cost
Name
University of Iowa
Department
Otolaryngology
Type
Schools of Medicine
DUNS #
062761671
City
Iowa City
State
IA
Country
United States
Zip Code
52246
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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