A consistent pattern of slide effects in Illumina DNA methylation BeadChip array data
Julian Hecker,
Sanghun Lee,
Priyadarshini Kachroo,
Dmitry Prokopenko,
Anna Maaser-Hecker,
Sharon M. Lutz,
Georg Hahn,
Rafael Irizarry,
Scott T. Weiss,
Dawn L. DeMeo,
Christoph Lange
Affiliations
Julian Hecker
Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
Sanghun Lee
Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
Priyadarshini Kachroo
Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
Dmitry Prokopenko
Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
Anna Maaser-Hecker
Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
Sharon M. Lutz
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
Georg Hahn
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
Rafael Irizarry
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
Scott T. Weiss
Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
Dawn L. DeMeo
Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
Christoph Lange
Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
ABSTRACTBackground: 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.
