Impact of SNPs on methylation readouts by Illumina HM450K Array. Methylation profiles in European and Asian populations. Homo sapiens

We performed a comparative study of European and Asian populations using Illumina HM450K. We found that the majority of Infinium probes, which differentiated two examined groups, had SNPs in their target sequence. We investigated the impact of those SNPs on methylation readouts by Illumina HM450K Array. Our study clearly demonstrates that SNP variation existing in the genome, if not accounted for, may lead to false interpretation of the methylation signal differences suggested by some of the Illumina Infinium probes. Overall design: Human B-lymphocyte cell lines representing Caucasian from Georgia (n=18), further referred to as Europeans and Chinese from Bejing, further referred to as East Asians (n=18) populations were used in the study. All lines were derived from unrelated healthy adults males.