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Several methods have been developed to predict CpG methylation levels from genotypes when the direct measurements of methylation are unavailable. To date, the published methods have mostly used datasets from populations of European ancestry to train prediction models for methylations, which limits the generalizability of methylome-wide association study to non-European populations. To address this gap, we proposed a new model by incorporating local ancestry (LA) information, called LA Methylation Predictor with Preselection (LAMPP), to improve the prediction accuracy of DNA methylation in admixed populations. We showed that LAMPP outperformed the conventional model and other LA models in prediction accuracy using an admixed African American population. We further applied our model to identify significant CpG sites for seven complex traits. Together, our LAMPP model is a valuable tool to reveal epigenetic underpinnings of complex traits in the admixed populations.<\/jats:p>","DOI":"10.1093\/bib\/bbaf325","type":"journal-article","created":{"date-parts":[[2025,7,7]],"date-time":"2025-07-07T13:55:44Z","timestamp":1751896544000},"source":"Crossref","is-referenced-by-count":0,"title":["Incorporating local ancestry information to predict genetically associated DNA methylation in admixed populations"],"prefix":"10.1093","volume":"26","author":[{"given":"Youshu","family":"Cheng","sequence":"first","affiliation":[{"name":"Department of Biostatistics, Yale School of Public Health , 47 College St, New Haven, CT 06510 ,","place":["United States"]},{"name":"VA Connecticut Healthcare System , 950 Campbell Ave, West Haven, CT 06516 ,","place":["United States"]}]},{"given":"Geyu","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Yale School of Public Health , 47 College St, New Haven, CT 06510 ,","place":["United States"]}]},{"given":"Hongyu","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Yale School of Public Health , 47 College St, New Haven, CT 06510 ,","place":["United States"]}]},{"given":"Xinyu","family":"Zhang","sequence":"additional","affiliation":[{"name":"VA Connecticut Healthcare System , 950 Campbell Ave, West Haven, CT 06516 ,","place":["United States"]},{"name":"Department of Psychiatry, Yale School of Medicine , 300 George St, New Haven, CT 06510 ,","place":["United States"]}]},{"given":"Amy","family":"Justice","sequence":"additional","affiliation":[{"name":"VA Connecticut Healthcare System , 950 Campbell Ave, West Haven, CT 06516 ,","place":["United States"]},{"name":"Department of Internal Medicine, Yale School of Medicine , 333 Cedar St, New Haven, CT 06510 ,","place":["United States"]}]},{"given":"Claudia","family":"Martinez","sequence":"additional","affiliation":[{"name":"Cardiovascular Division, Department of Medicine, University of Miami Miller School of Medicine , 1600 NW 10th Ave, Miami, FL 33136 ,","place":["United States"]}]},{"given":"Bradley E","family":"Aouizerat","sequence":"additional","affiliation":[{"name":"Bluestone Center for Clinical Research, College of Dentistry, New York University , 421 1st Ave, New York, NY 10010 ,","place":["United States"]},{"name":"Department of Oral and Maxillofacial Surgery, College of Dentistry, New York University , 421 1st Ave, New York, NY 10010 ,","place":["United States"]}]},{"given":"Ke","family":"Xu","sequence":"additional","affiliation":[{"name":"VA Connecticut Healthcare System , 950 Campbell Ave, West Haven, CT 06516 ,","place":["United States"]},{"name":"Department of Psychiatry, Yale School of Medicine , 300 George St, New Haven, CT 06510 ,","place":["United States"]}]},{"given":"Hongyu","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Yale School of Public Health , 47 College St, New Haven, 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