Additional file 1.

Supplemental methods, tables and figures. Supplemental methods include Infinium HumanMethylation450 data pre-processing, adjustment for cell type heterogeneity, and association analysis and candidate selection. Table S1: DNA methylation profiles used to create the cell-type reference data set. Table S2: cell type-specific quantitative markers used as explanatory variables in heterogeneity adjustment. Table S3: characteristics of the 45 CpG sites that are significantly differentially methylated between the heavy and light co-twins identified using the Infinium HumanMethylation450 BeadChip. Table S4: distribution of the samples across the bead chips, detected CpGs and the corresponding call rate per sample. Table S5: reaction conditions and primer sequences of the bisulfite-PCRs. Table S6: reaction conditions and primer sequences of the SIRPH analysis. Table S7: statistical power of the twin study. Figure S1: pair-wise correlations for each pair of samples, calculated from approximately 480,000 CpGs. Figure S2: sample-independent Infinium methylation controls. Figure S3: sample-dependent Infinium methylation controls. Figure S4: pair-wise correlations for each pair of samples, including the reference dataset for whole-blood and buccal (27k), calculated from approximately 25,978 CpGs. Figure S5: mixing experiment with KG1a and K562 cells profiled on the Infinium HumanMethylation450 BeadChip. Figure S6: distribution of the correlation coefficients of the methylation values of the approximately 480,000 CpGs to the methylation values of the PTPN7 CpG (cg18384097). Figure S7: pair-wise correlations for each pair of samples after adjusting for cell type composition using the PTPN7 CpG (cg18384097). Figure S8: examples of methylation profiles generated using the deep bisulfite sequencing data of the APPL2, PPARGC1B, PHKG2 and PTPN7 amplicons. Figure S9: correlation plots in which the (unadjusted) Infinium 450K data of the validated CpGs are plotted against the (unadjusted) deep bisulfite sequencing (DBS) data for every sample separately. Figure S10: box-plot of the correlation coefficients calculated between the Infinium 450K data and the deep bisulfite sequencing (DBS) data of the validated CpGs for every individual sample. Figure S11: correlation plots of the (unadjusted) Infinium 450K data and the (unadjusted) deep bisulfite sequencing (DBS) data of the 17 discordant MZ twin pairs for each validated CpG separately. Figure S12: continuation of Figure S11. Figure S13: box-plot of the intra-pair differences in β-values of the 64 SNPs present on the Infinium HumanMethylation450 BeadChip before and after normalisation using internal controls and background subtraction by the GenomeStudio software.

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Souren et al. Genome Biology 2013 14:R44   doi:10.1186/gb-2013-14-5-r44