We profiled the epigenetic landscape of 990 unique donors forming the control cohort of the Assessment of Risk for Colorectal Cancer Tumours in Canada (ARCTIC) project.14 (link) Fifteen μl of lymphocyte-derived DNA extracted (at an average concentration 90 ng/μl) was bisulfite-converted using the EZ-96 DNA Methylation-Gold Kit (Zymo Research, Orange, CA); 4μl of bisulfite-treated DNA was then analyzed on the HumanMethylation450 BeadChip from Illumina according to the manufacturer’s protocol. Intensities were normalized using Illumina’s internal normalization probes and algorithms, without background subtraction. Beta values with assigned detection p-values > 0.01 were treated as missing data. CpG sites with more than 1% missing data across all samples were discarded.
We removed from analysis samples that were outliers with respect to any one of the internal control probes (excluding probes designed to evaluate the background noise and probes designed to normalize the data) and samples that were not of non-Hispanic white ancestry, either self-declared or by investigation of genetic ancestry using genome-wide SNP data. After sample exclusion, we were left with 489 adult males and 357 adult females.
We removed from analysis samples that were outliers with respect to any one of the internal control probes (excluding probes designed to evaluate the background noise and probes designed to normalize the data) and samples that were not of non-Hispanic white ancestry, either self-declared or by investigation of genetic ancestry using genome-wide SNP data. After sample exclusion, we were left with 489 adult males and 357 adult females.
