Illumina Infinium weak signals regions aligned with CpG and C + G maps. This image uses chromosome 2 to provide typical evidence of the degree of correlation between copy number inferences per SNP for samples that genotyped poorly on Illumina Infinium arrays (first data row below the ideogram), long-range averaged C + G content on a scale of 30-70% (middle data rows, data from UCSC genome browser), and the location of CpG islands (bottom data rows, data from UCSC genome browser). Weak Illumina signal regions are not simply correlated with CpG islands, nor with generally high C + G content, but only with regions containing the highest peaks of C + G content.
Veal et al. BMC Genomics 2012 13:455 doi:10.1186/1471-2164-13-455