platform and algorithm combinations. In general, the most recently released arrays perform better, resulting in more CNV calls reproducibly obtained between replicates. Of the CGH arrays, the Agilent (2 × 244K) platform produced the largest number of CNV calls (an average of 377 and 387 calls per individual for the TCAG and WTSI sites, respectively, using the ADM-2 algorithm, Fig. 2b) with a con-comitant high percentage of CNV calls that were reproducible (67% and 62% for the two sites, respectively, Fig. 2a). For SNP arrays, the largest number of CNVs was called for the new CNV-focused Illumina arrays (an average of 263 and 240 calls per individual for Illumina 660W and OMNI, respectively, for the site showing the highest replicate reproducibility). In terms of reproducibility, the Affymetrix 6.0 and the three newest Illumina arrays (1M, 660W and OMNI) showed very similar values, around 80%, when analyzed with the best performing algorithms.
