title: Reliability of DNA methylation measures from dried blood spots and mononuclear cells using the HumanMethylation450k BeadArray.
abstract: The reliability of methylation measures from the widely used HumanMethylation450 (HM450K) microarray has not been assessed for DNA from dried blood spots (DBS) or peripheral blood mononuclear cells (PBMC), nor for combined data from different studies. Repeated HM450K methylation measures in DNA from DBS and PBMC samples were available from participants in six case-control studies nested within the Melbourne Collaborative Cohort Study. Reliability was assessed for individual CpGs by calculating the intraclass correlation coefficient (ICC) based on technical replicates (samples repeated in a single study; 126 PBMC, 136 DBS) and study duplicates (samples repeated across studies; 280 PBMC, 769 DBS) using mixed-effects models. Reliability based on technical replicates was moderate for PBMC (median ICC = 0.42), but lower for DBS (median ICC = 0.20). Study duplicates gave lower ICCs than technical replicates. CpGs that were either highly methylated or unmethylated generally had lower ICCs, which appeared to be mostly related to their lower variability. The ICCs for global methylation measures were high, typically greater than 0.70. The reliability of methylation measures determined by the HM450K microarray is wide-ranging and depends primarily on the variability in methylation at individual CpG sites. The power of association studies is low for a substantial proportion of CpGs in the HM450K assay.
authors.affiliation: Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia.|Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia.
authors.forename: Pierre-Antoine
authors.initials: PA
authors.lastname: Dugué
authors.affiliation: Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia.|Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia.
authors.forename: Dallas R
authors.initials: DR
authors.lastname: English
authors.affiliation: Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia.|Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: MacInnis
authors.affiliation: VLSCI Life Sciences Computation Centre, University of Melbourne, Carlton VIC, Australia.
authors.forename: Chol-Hee
authors.initials: CH
authors.lastname: Jung
authors.affiliation: Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia.
authors.forename: Julie K
authors.initials: JK
authors.lastname: Bassett
authors.affiliation: Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia.
authors.forename: Liesel M
authors.initials: LM
authors.lastname: FitzGerald
authors.affiliation: Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, VIC, Melbourne.
authors.forename: Ee Ming
authors.initials: EM
authors.lastname: Wong
authors.affiliation: Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, VIC, Melbourne.
authors.forename: Jihoon E
authors.initials: JE
authors.lastname: Joo
authors.affiliation: Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia.
authors.forename: John L
authors.initials: JL
authors.lastname: Hopper
authors.affiliation: Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, VIC, Melbourne.
authors.forename: Melissa C
authors.initials: MC
authors.lastname: Southey
authors.affiliation: Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia.|Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia.
authors.forename: Graham G
authors.initials: GG
authors.lastname: Giles
authors.affiliation: Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia.|Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia.
authors.forename: Roger L
authors.initials: RL
authors.lastname: Milne
mesh_terms: D018899:CpG Islands; D019175:DNA Methylation; D059788:Dried Blood Spot Testing / Q000379:methods / Q000592:standards*; D006801:Humans; D009000:Monocytes / Q000737:chemistry / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods / Q000592:standards*; D011933:Reagent Kits, Diagnostic / Q000592:standards; D015203:Reproducibility of Results
chemical_list: D011933:Reagent Kits, Diagnostic