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      Biological insights from multi-omic analysis of 31 genomic risk loci for adult hearing difficulty

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          Abstract

          Age-related hearing impairment (ARHI), one of the most common medical conditions, is strongly heritable, yet its genetic causes remain largely unknown. We conducted a meta-analysis of GWAS summary statistics from multiple hearing-related traits in the UK Biobank (n = up to 330,759) and identified 31 genome-wide significant risk loci for self-reported hearing difficulty (p < 5x10 -8), of which eight have not been reported previously in the peer-reviewed literature. We investigated the regulatory and cell specific expression for these loci by generating mRNA-seq, ATAC-seq, and single-cell RNA-seq from cells in the mouse cochlea. Risk-associated genes were most strongly enriched for expression in cochlear epithelial cells, as well as for genes related to sensory perception and known Mendelian deafness genes, supporting their relevance to auditory function. Regions of the human genome homologous to open chromatin in epithelial cells from the mouse were strongly enriched for heritable risk for hearing difficulty, even after adjusting for baseline effects of evolutionary conservation and cell-type non-specific regulatory regions. Epigenomic and statistical fine-mapping most strongly supported 50 putative risk genes. Of these, 39 were expressed robustly in mouse cochlea and 16 were enriched specifically in sensory hair cells. These results reveal new risk loci and risk genes for hearing difficulty and suggest an important role for altered gene regulation in the cochlear sensory epithelium.

          Author summary

          The genetic architecture of age-related hearing impairment (ARHI), a strongly heritable condition, has not been well studied. We present a systems genetics analysis of risk loci for ARHI. We performed a joint GWAS analysis of four hearing related traits from the UK Biobank and identified 31 genome-wide significant risk loci for hearing difficulty, eight of which have not been previously reported. By integrating these risk loci with transcriptomic and epigenomic data from the mouse cochlea, we discovered that risk loci are strongly enriched at genes and open chromatin regions that are active in cochlear sensory epithelial cells. Our results suggest an important role in ARHI for altered gene regulation in cochlear hair cells and supporting cells.

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          Most cited references67

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          ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

          High-throughput sequencing platforms are generating massive amounts of genetic variation data for diverse genomes, but it remains a challenge to pinpoint a small subset of functionally important variants. To fill these unmet needs, we developed the ANNOVAR tool to annotate single nucleotide variants (SNVs) and insertions/deletions, such as examining their functional consequence on genes, inferring cytogenetic bands, reporting functional importance scores, finding variants in conserved regions, or identifying variants reported in the 1000 Genomes Project and dbSNP. ANNOVAR can utilize annotation databases from the UCSC Genome Browser or any annotation data set conforming to Generic Feature Format version 3 (GFF3). We also illustrate a ‘variants reduction’ protocol on 4.7 million SNVs and indels from a human genome, including two causal mutations for Miller syndrome, a rare recessive disease. Through a stepwise procedure, we excluded variants that are unlikely to be causal, and identified 20 candidate genes including the causal gene. Using a desktop computer, ANNOVAR requires ∼4 min to perform gene-based annotation and ∼15 min to perform variants reduction on 4.7 million variants, making it practical to handle hundreds of human genomes in a day. ANNOVAR is freely available at http://www.openbioinformatics.org/annovar/ .
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            UK Biobank: An Open Access Resource for Identifying the Causes of a Wide Range of Complex Diseases of Middle and Old Age

            Cathie Sudlow and colleagues describe the UK Biobank, a large population-based prospective study, established to allow investigation of the genetic and non-genetic determinants of the diseases of middle and old age.
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              LD Score regression distinguishes confounding from polygenicity in genome-wide association studies.

              Both polygenicity (many small genetic effects) and confounding biases, such as cryptic relatedness and population stratification, can yield an inflated distribution of test statistics in genome-wide association studies (GWAS). However, current methods cannot distinguish between inflation from a true polygenic signal and bias. We have developed an approach, LD Score regression, that quantifies the contribution of each by examining the relationship between test statistics and linkage disequilibrium (LD). The LD Score regression intercept can be used to estimate a more powerful and accurate correction factor than genomic control. We find strong evidence that polygenicity accounts for the majority of the inflation in test statistics in many GWAS of large sample size.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: InvestigationRole: Methodology
                Role: Data curationRole: Formal analysisRole: InvestigationRole: SoftwareRole: Writing – review & editing
                Role: Formal analysisRole: SoftwareRole: Supervision
                Role: Formal analysis
                Role: Formal analysis
                Role: Formal analysisRole: Investigation
                Role: ConceptualizationRole: Data curationRole: Funding acquisitionRole: InvestigationRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS Genet
                PLoS Genet
                plos
                plosgen
                PLoS Genetics
                Public Library of Science (San Francisco, CA USA )
                1553-7390
                1553-7404
                28 September 2020
                September 2020
                : 16
                : 9
                : e1009025
                Affiliations
                [1 ] Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
                [2 ] Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
                [3 ] Department of Otorhinolaryngology-Head & Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States of America
                [4 ] Physician Scientist Training Program, University of Maryland School of Medicine, Baltimore, MD, United States of America
                [5 ] Program in Molecular Epidemiology, University of Maryland School of Medicine, Baltimore, MD, United States of America
                [6 ] Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States of America
                [7 ] Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, United States of America
                University of Miami School of Medicine, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-4176-6489
                http://orcid.org/0000-0001-6873-7867
                http://orcid.org/0000-0002-5910-9647
                http://orcid.org/0000-0002-2276-4066
                http://orcid.org/0000-0002-2454-8498
                http://orcid.org/0000-0003-1537-5481
                http://orcid.org/0000-0001-6443-7509
                Article
                PGENETICS-D-20-00474
                10.1371/journal.pgen.1009025
                7544108
                32986727
                1bab8770-ef2c-497a-88aa-a0e86f501b00
                © 2020 Kalra et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 2 April 2020
                : 4 August 2020
                Page count
                Figures: 5, Tables: 1, Pages: 32
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000025, National Institute of Mental Health;
                Award ID: R24 MH114815
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000055, National Institute on Deafness and Other Communication Disorders;
                Award ID: R01 DC013817
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000055, National Institute on Deafness and Other Communication Disorders;
                Award ID: R00 DC013107
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100002046, Hearing Health Foundation;
                Award ID: Hearing Restoration Project (#5)
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100002046, Hearing Health Foundation;
                Award ID: Hearing Restoration Project (#4)
                Award Recipient :
                This project was supported by National Institute of Mental Health, BRAIN Initiative (R24 MH114815, R.H.) ( https://projectreporter.nih.gov/project_info_description.cfm?aid=9766403&icde=49381344&ddparam=&ddvalue=&ddsub=&cr=3&csb=default&cs=ASC&pball=); National Institute of Deafness and Other Communication Disorders (R01 DC013817, R.H.) ( https://projectreporter.nih.gov/project_info_description.cfm?aid=9654735&icde=49381326&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC&pball=); National Institute of Deafness and Other Communication Disorders (R00 DC013107, Thomas Coate, PI) ( https://projectreporter.nih.gov/project_info_description.cfm?aid=9304158&icde=49381320&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC&pball=); Hearing Health Foundation Hearing Restoration Project, Project #5 (S.A.A.) ( https://hearinghealthfoundation.org/hearing-restoration-project); Hearing Health Foundation Hearing Restoration Project, Project #4 (R.H.) ( https://hearinghealthfoundation.org/hearing-restoration-project). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Genetics
                Single Nucleotide Polymorphisms
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Genome-Wide Association Studies
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Genome-Wide Association Studies
                Biology and Life Sciences
                Genetics
                Human Genetics
                Genome-Wide Association Studies
                Medicine and Health Sciences
                Epidemiology
                Medical Risk Factors
                Biology and Life Sciences
                Genetics
                Genetic Loci
                Biology and Life Sciences
                Cell Biology
                Chromosome Biology
                Chromatin
                Biology and Life Sciences
                Genetics
                Epigenetics
                Chromatin
                Biology and Life Sciences
                Genetics
                Gene Expression
                Chromatin
                Medicine and Health Sciences
                Otorhinolaryngology
                Otology
                Hearing Disorders
                Deafness
                Biology and Life Sciences
                Anatomy
                Head
                Ears
                Inner Ear
                Cochlea
                Medicine and Health Sciences
                Anatomy
                Head
                Ears
                Inner Ear
                Cochlea
                Biology and Life Sciences
                Genetics
                Genomics
                Animal Genomics
                Mammalian Genomics
                Custom metadata
                vor-update-to-uncorrected-proof
                2020-10-08
                ATAC-seq (GSE126129), mRNA-seq (GSE158325), and scRNA-seq (GSE135737) data have been deposited in the Gene Expression Omnibus. Bed files depicting ATAC-seq peaks, processed and annotated single-cell RNA-seq data, and GWAS summary statistics from the MTAG GWAS meta-analysis are available on the Neuroscience Multi-Omic Archive (NeMO Archive), an NIH-funded genomics data repository for the BRAIN Initiative, at: http://data.nemoarchive.org/other/grant/sament/sament/hearing_gwas/. A web browser enabling visualization and analysis of the scRNAseq, mRNA-seq, ATAC-seq, and hearing difficulty GWAS data is available on gEAR ( umgear.org) within the profile: https://umgear.org/p?l=3a70e6e7. All other relevant data are within the manuscript and its Supporting Information files.

                Genetics
                Genetics

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