{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,27]],"date-time":"2026-04-27T12:49:22Z","timestamp":1777294162780,"version":"3.51.4"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,6,10]],"date-time":"2024-06-10T00:00:00Z","timestamp":1717977600000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Epigenome-wide association studies (EWAS) are susceptible to widespread confounding caused by population structure and genetic relatedness. Nevertheless, kinship estimation is challenging in EWAS without genotyping data. Here, we proposed MethylGenotyper, a method that for the first time enables accurate genotyping at thousands of single nucleotide polymorphisms (SNPs) directly from commercial DNA methylation microarrays. We modeled the intensities of methylation probes near SNPs with a mixture of three beta distributions corresponding to different genotypes and estimated parameters with an expectation-maximization algorithm. We conducted extensive simulations to demonstrate the performance of the method. When applying MethylGenotyper to the Infinium EPIC array data of 4662 Chinese samples, we obtained genotypes at 4319 SNPs with a concordance rate of 98.26%, enabling the identification of 255 pairs of close relatedness. Furthermore, we showed that MethylGenotyper allows for the estimation of both population structure and cryptic relatedness among 702 Australians of diverse ancestry. We also implemented MethylGenotyper in a publicly available R package (https:\/\/github.com\/Yi-Jiang\/MethylGenotyper) to facilitate future large-scale EWAS.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzae044","type":"journal-article","created":{"date-parts":[[2024,6,10]],"date-time":"2024-06-10T19:45:06Z","timestamp":1718048706000},"source":"Crossref","is-referenced-by-count":5,"title":["MethylGenotyper: Accurate Estimation of SNP Genotypes and Genetic Relatedness from DNA Methylation Data"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1196-0280","authenticated-orcid":false,"given":"Yi","family":"Jiang","sequence":"first","affiliation":[{"name":"Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030,","place":["China"]},{"name":"Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-3155-679X","authenticated-orcid":false,"given":"Minghan","family":"Qu","sequence":"additional","affiliation":[{"name":"Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030,","place":["China"]},{"name":"Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7888-2408","authenticated-orcid":false,"given":"Minghui","family":"Jiang","sequence":"additional","affiliation":[{"name":"Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030,","place":["China"]},{"name":"Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-1580-3186","authenticated-orcid":false,"given":"Xuan","family":"Jiang","sequence":"additional","affiliation":[{"name":"Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030,","place":["China"]},{"name":"Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4881-245X","authenticated-orcid":false,"given":"Shane","family":"Fernandez","sequence":"additional","affiliation":[{"name":"Centre for Precision Health, Edith Cowan University , Perth, WA 6027,","place":["Australia"]},{"name":"Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University , Perth, WA 6027,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7887-6622","authenticated-orcid":false,"given":"Tenielle","family":"Porter","sequence":"additional","affiliation":[{"name":"Centre for Precision Health, Edith Cowan University , Perth, WA 6027,","place":["Australia"]},{"name":"Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University , Perth, WA 6027,","place":["Australia"]},{"name":"Curtin Medical School , Bentley, WA 6102,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4355-7082","authenticated-orcid":false,"given":"Simon M","family":"Laws","sequence":"additional","affiliation":[{"name":"Centre for Precision Health, Edith Cowan University , Perth, WA 6027,","place":["Australia"]},{"name":"Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University , Perth, WA 6027,","place":["Australia"]},{"name":"Curtin Medical School , Bentley, WA 6102,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3072-7940","authenticated-orcid":false,"given":"Colin L","family":"Masters","sequence":"additional","affiliation":[{"name":"The Florey Institute of Neuroscience and Mental Health, University of Melbourne , Melbourne, VIC 3052,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7838-2585","authenticated-orcid":false,"given":"Huan","family":"Guo","sequence":"additional","affiliation":[{"name":"Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030,","place":["China"]},{"name":"Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2676-7341","authenticated-orcid":false,"given":"Shanshan","family":"Cheng","sequence":"additional","affiliation":[{"name":"Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and 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