We also analysed data on 242 HapMap samples on an Illumina Infinium genotyping platform (Human660W), developed in conjunction with the WTCCC 2 experiments, which incorporates probes in 8,914 of our CNVs (biased towards those with high frequency in CEU), using recently published CNV genotyping software21. We observed that 2,513 CNVs could be genotyped, 2,175 (87%) of which were also genotyped on the Agilent CGH microarrays. This high concordance suggests that the genomic properties of the CNV rather than the performance characteristics of the technology platform determine whether a CNV can be reliably typed. Given the extensive overlap, and the smaller number of HapMap samples run on the Illumina array, subsequent analyses of genotyped CNVs focus solely on data from the array-CGH CNV-typing.
