biostudies-literatureLyu CNational Heart, Lung and Blood InstituteEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNICHD NIH HHSNIDCR NIH HHSNational Institute of Dental and Craniofacial Research under award numberNIEHS NIH HHSNHLBI NIH HHS3853-3862https://www.ebi.ac.uk/biostudies/studies/S-EPMC9364381biostudies-literatureUnknown38(16)<h4>Motivation</h4>CpG sites within the same genomic region often share similar methylation patterns and tend to be co-regulated by multiple genetic variants that may interact with one another.<h4>Results</h4>We propose a multi-trait methylation random field (multi-MRF) method to evaluate the joint association between a set of CpG sites and a set of genetic variants. The proposed method has several advantages. First, it is a multi-trait method that allows flexible correlation structures between neighboring CpG sites (e.g. distance-based correlation). Second, it is also a multi-locus method that integrates the effect of multiple common and rare genetic variants. Third, it models the methylation traits with a beta distribution to characterize their bimodal and interval properties. Through siBioinformatics (Oxford, England)Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci.PMC9364381R01 HD039054R03 HD092854R03DE025646K01 HL140333R01HD039054R03 DE025646R03HD092854P30 ES030285K01HL140333R03 DE024198Witte JSChen ZLiu NHuang MLyu CLi MLupo PJTycko BHobbs CAfalseRandom field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci.<h4>Motivation</h4>CpG sites within the same genomic region often share similar methylation patterns and tend to be co-regulated by multiple genetic variants that may interact with one another.<h4>Results</h4>We propose a multi-trait methylation random field (multi-MRF) method to evaluate the joint association between a set of CpG sites and a set of genetic variants. The proposed method has several advantages. First, it is a multi-trait method that allows flexible correlation structures between neighboring CpG sites (e.g. distance-based correlation). Second, it is also a multi-locus method that integrates the effect of multiple common and rare genetic variants. Third, it models the methylation traits with a beta distribution to characterize their bimodal and interval properties. Through si2022-01-01T00:00:00Z2022 Aug2025-04-21T22:12:48.043Z2025-04-21T22:12:48.043ZS-EPMC93643813578131910.1093/bioinformatics/btac443