biostudies-literatureZheng YRRD VANIMH NIH HHSBiomedical Laboratory Research and Development, VA Office of Research and DevelopmentNational Institute of Mental Health2241-2258https://www.ebi.ac.uk/biostudies/studies/S-EPMC9665129biostudies-literatureUnknown17(13)Differentially methylated regions (DMRs) are genomic regions with specific methylation patterns across multiple loci that are associated with a phenotype. We examined the genome-wide false positive (GFP) rates of five widely used DMR methods: comb-p, Bumphunter, DMRcate, mCSEA and coMethDMR using both Illumina HumanMethylation450 (450 K) and MethylationEPIC (EPIC) data and simulated continuous and dichotomous null phenotypes (i.e., generated independently of methylation data). coMethDMR provided well-controlled GFP rates (~5%) except when analysing skewed continuous phenotypes. DMRcate generally had well-controlled GFP rates when applied to 450 K data except for the skewed continuous phenotype and EPIC data only for the normally distributed continuous phenotype. GFP rates for mCSEA were atEpigeneticsAn evaluation of the genome-wide false positive rates of common methods for identifying differentially methylated regions using illumina methylation arrays.PMC9665129R21 MH102834R21MH1028341R01MH108826R01 MH108826I50 RX003001I01BX003477Miller MWZheng YKatrinli SLogue MWLiu CLunetta KLSmith AKfalseAn evaluation of the genome-wide false positive rates of common methods for identifying differentially methylated regions using illumina methylation arrays.Differentially methylated regions (DMRs) are genomic regions with specific methylation patterns across multiple loci that are associated with a phenotype. We examined the genome-wide false positive (GFP) rates of five widely used DMR methods: comb-p, Bumphunter, DMRcate, mCSEA and coMethDMR using both Illumina HumanMethylation450 (450 K) and MethylationEPIC (EPIC) data and simulated continuous and dichotomous null phenotypes (i.e., generated independently of methylation data). coMethDMR provided well-controlled GFP rates (~5%) except when analysing skewed continuous phenotypes. DMRcate generally had well-controlled GFP rates when applied to 450 K data except for the skewed continuous phenotype and EPIC data only for the normally distributed continuous phenotype. GFP rates for mCSEA were at2022-01-01T00:00:00Z2022 Dec2026-05-28T01:31:40.956Z2025-02-19T01:18:01.749ZS-EPMC96651293604774210.1080/15592294.2022.2115600