for Affymetrix 250K to >95% for Illumina 660W. As the arrays differ substantially in resolution and in distribution of probes, it is also relevant to investigate the distribution of probes within the CNV call made for each platform (Supplementary Fig. 5). This analysis shows that arrays that specifically target CNVs detected in previous studies (e.g., Illumina 660W) have a very uniform distribution of number of probes per CNV call compared to arrays such as Illumina 1M and Affymetrix 6.0. Another aspect of the CNV calls that differ widely between platforms is the ratio of copy number gains to losses. Certain arrays are very biased toward detection of deletions, with the Illumina 660W showing the highest ratio of deletions to duplications (Supplementary Figs. 4 and 5).
