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Artomov M, Loboda AA, Artyomov MN, Daly MJ. Public platform with 39,472 exome control samples enables association studies without genotype sharing. Nat Genet 2024; 56:327-335. [PMID: 38200129 PMCID: PMC10864173 DOI: 10.1038/s41588-023-01637-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/01/2023] [Indexed: 01/12/2024]
Abstract
Acquiring a sufficiently powered cohort of control samples matched to a case sample can be time-consuming or, in some cases, impossible. Accordingly, an ability to leverage genetic data from control samples that were already collected elsewhere could dramatically improve power in genetic association studies. Sharing of control samples can pose significant challenges, since most human genetic data are subject to strict sharing regulations. Here, using the properties of singular value decomposition and subsampling algorithm, we developed a method allowing selection of the best-matching controls in an external pool of samples compliant with personal data protection and eliminating the need for genotype sharing. We provide access to a library of 39,472 exome sequencing controls at http://dnascore.net enabling association studies for case cohorts lacking control subjects. Using this approach, control sets can be selected from this online library with a prespecified matching accuracy, ensuring well-calibrated association analysis for both rare and common variants.
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Affiliation(s)
- Mykyta Artomov
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute, Cambridge, MA, USA.
| | - Alexander A Loboda
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- ITMO University, St. Petersburg, Russia
- Almazov National Medical Research Center, St. Petersburg, Russia
| | - Maxim N Artyomov
- Department of Immunology and Pathology, Washington University in St. Louis, St. Louis, MO, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute, Cambridge, MA, USA.
- Institute for Molecular Medicine Finland, Helsinki, Finland.
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Escalera-Balsera A, Parra-Perez AM, Gallego-Martinez A, Frejo L, Martin-Lagos J, Rivero de Jesus V, Pérez-Vázquez P, Perez-Carpena P, Lopez-Escamez JA. Rare Deletions or Large Duplications Contribute to Genetic Variation in Patients with Severe Tinnitus and Meniere Disease. Genes (Basel) 2023; 15:22. [PMID: 38254912 PMCID: PMC10815708 DOI: 10.3390/genes15010022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Meniere disease (MD) is a debilitating disorder of the inner ear defined by sensorineural hearing loss (SNHL) associated with episodes of vertigo and tinnitus. Severe tinnitus, which occurs in around 1% of patients, is a multiallelic disorder associated with a burden of rare missense single nucleotide variants in synaptic genes. Rare structural variants (SVs) may also contribute to MD and severe tinnitus. In this study, we analyzed exome sequencing data from 310 MD Spanish patients and selected 75 patients with severe tinnitus based on a Tinnitus Handicap Inventory (THI) score > 68. Three rare deletions were identified in two unrelated individuals overlapping the ERBB3 gene in the positions: NC_000012.12:g.56100028_56100172del, NC_000012.12:g.56100243_56101058del, and NC_000012.12:g.56101359_56101526del. Moreover, an ultra-rare large duplication was found covering the AP4M1, COPS6, MCM7, TAF6, MIR106B, MIR25, and MIR93 genes in another two patients in the NC_000007.14:g.100089053_100112257dup region. All the coding genes exhibited expression in brain and inner ear tissues. These results confirm the contribution of large SVs to severe tinnitus in MD and pinpoint new candidate genes to get a better molecular understanding of the disease.
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Affiliation(s)
- Alba Escalera-Balsera
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain; (A.E.-B.); (A.M.P.-P.); (A.G.-M.); (L.F.); (J.M.-L.); (P.P.-C.)
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, 18016 Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
| | - Alberto M. Parra-Perez
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain; (A.E.-B.); (A.M.P.-P.); (A.G.-M.); (L.F.); (J.M.-L.); (P.P.-C.)
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, 18016 Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
| | - Alvaro Gallego-Martinez
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain; (A.E.-B.); (A.M.P.-P.); (A.G.-M.); (L.F.); (J.M.-L.); (P.P.-C.)
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, 18016 Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
| | - Lidia Frejo
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain; (A.E.-B.); (A.M.P.-P.); (A.G.-M.); (L.F.); (J.M.-L.); (P.P.-C.)
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, 18016 Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
- Meniere’s Disease Neuroscience Research Program, Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, NSW 2065, Australia
| | - Juan Martin-Lagos
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain; (A.E.-B.); (A.M.P.-P.); (A.G.-M.); (L.F.); (J.M.-L.); (P.P.-C.)
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, 18016 Granada, Spain
- Department of Otorhinolaryngology, Hospital Clinico Universitario San Cecilio, 18016 Granada, Spain
| | | | - Paz Pérez-Vázquez
- Servicio de Otorrinolaringología, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain;
| | - Patricia Perez-Carpena
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain; (A.E.-B.); (A.M.P.-P.); (A.G.-M.); (L.F.); (J.M.-L.); (P.P.-C.)
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, 18016 Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
- Department of Otorhinolaryngology, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
| | - Jose A. Lopez-Escamez
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain; (A.E.-B.); (A.M.P.-P.); (A.G.-M.); (L.F.); (J.M.-L.); (P.P.-C.)
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, 18016 Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
- Meniere’s Disease Neuroscience Research Program, Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, NSW 2065, Australia
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