Identifying and correcting epigenetics measurements for systematic sources of variation.
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Authors
Perrier, FlavieNovoloaca, Alexei
Ambatipudi, Srikant
Baglietto, Laura
Ghantous, Akram
Perduca, Vittorio
Barrdahl, Myrto
Harlid, Sophia
Ong, Ken K
Cardona, Alexia
Polidoro, Silvia
Nøst, Therese Haugdahl
Overvad, Kim
Omichessan, Hanane
Dollé, Martijn
Bamia, Christina
Huerta, José Marìa
Vineis, Paolo
Herceg, Zdenko
Romieu, Isabelle
Ferrari, Pietro
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ArticleLanguage
en
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Identifying and correcting epigenetics measurements for systematic sources of variation.Published in
Clin Epigenetics 2018; 10:38Publiekssamenvatting
Methylation measures quantified by microarray techniques can be affected by systematic variation due to the technical processing of samples, which may compromise the accuracy of the measurement process and contribute to bias the estimate of the association under investigation. The quantification of the contribution of the systematic source of variation is challenging in datasets characterized by hundreds of thousands of features.In this study, we introduce a method previously developed for the analysis of metabolomics data to evaluate the performance of existing normalizing techniques to correct for unwanted variation. Illumina Infinium HumanMethylation450K was used to acquire methylation levels in over 421,000 CpG sites for 902 study participants of a case-control study on breast cancer nested within the EPIC cohort. The principal component partial R-square (PC-PR2) analysis was used to identify and quantify the variability attributable to potential systematic sources of variation. Three correcting techniques, namely ComBat, surrogate variables analysis (SVA) and a linear regression model to compute residuals were applied. The impact of each correcting method on the association between smoking status and DNA methylation levels was evaluated, and results were compared with findings from a large meta-analysis.PMID
29588806ae974a485f413a2113503eed53cd6c53
10.1186/s13148-018-0471-6
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