biostudies-literatureHecker JNational Institute of Allergy and Infectious DiseasesNIAID NIH HHSNational Heart, Lung, and Blood InstituteNHLBI NIH HHSNIMH NIH HHSNHGRI NIH HHSCure Alzheimer's FundNational Institute of Mental HealthNIGMS NIH HHS2257437https://www.ebi.ac.uk/biostudies/studies/S-EPMC11062373biostudies-literatureUnknown18(1)Background: Recent studies have identified thousands of associations between DNA methylation CpGs and complex diseases/traits, emphasizing the critical role of epigenetics in understanding disease aetiology and identifying biomarkers. However, association analyses based on methylation array data are susceptible to batch/slide effects, which can lead to inflated false positive rates or reduced statistical powerResults: We use multiple DNA methylation datasets based on the popular Illumina Infinium MethylationEPIC BeadChip array to describe consistent patterns and the joint distribution of slide effects across CpGs, confirming and extending previous results. The susceptible CpGs overlap with the Illumina Infinium HumanMethylation450 BeadChip array content.Conclusions: Our findings reveal systematic patterns in slide effects. The observations provide further insights into the characteristics of these effects and can improve existing adjustment approaches.EpigeneticsA consistent pattern of slide effects in Illumina DNA methylation BeadChip array data.PMC11062373K99HL159234K99 HL159234R01 HL120393P01HL132825R01 HL117626U01 HL091528R01 AI154470R01AI154470P01 HL114501P01 HL132825R01 HG011393R01HG011393U01 HL120393HHSN268201800001CR35 GM131802U01HL091528P01HL114501R01MH129337R01 MH129337HHSN268201600038CLutz SMHecker JLee SHahn GProkopenko DMaaser-Hecker AIrizarry RLange CWeiss STKachroo PDeMeo DLfalseA consistent pattern of slide effects in Illumina DNA methylation BeadChip array data.Background: Recent studies have identified thousands of associations between DNA methylation CpGs and complex diseases/traits, emphasizing the critical role of epigenetics in understanding disease aetiology and identifying biomarkers. However, association analyses based on methylation array data are susceptible to batch/slide effects, which can lead to inflated false positive rates or reduced statistical powerResults: We use multiple DNA methylation datasets based on the popular Illumina Infinium MethylationEPIC BeadChip array to describe consistent patterns and the joint distribution of slide effects across CpGs, confirming and extending previous results. The susceptible CpGs overlap with the Illumina Infinium HumanMethylation450 BeadChip array content.Conclusions: Our findings reveal systematic patterns in slide effects. The observations provide further insights into the characteristics of these effects and can improve existing adjustment approaches.2023-01-01T00:00:00Z2023 Dec2026-04-21T03:16:50.582Z2026-04-21T03:13:38.216ZS-EPMC110623733773136710.1080/15592294.2023.2257437