Validation of a subset of copy number variants from GSE24424 by aCGH

This dataset was used to validate CNV predictions from GSE24424. We designed a custom CGH array to interrogate a total of 4,420 individual CNVs and their flanks predicted in 17 individuals. On the basis of a test that compares signals of probes located within to those mapping outside of CNVs (two-tailed P<0.05, Mann-Whitney U test), we could confirm about 77% of the tested predictions and thus establish a set of 3,383 validated CNVs. The vast majority of confirmed CNVs (3,299 of 3,383 or 97.5%) show a consistent direction of change between the initial array (GSE24424) and the custom array, suggesting a false-confirmation rate of approximately 5%. We interrogated a total of 4,420 individual CNVs and their flanks predicted in 17 individuals from the GSE24424 dataset by rehybridizing their DNAs on a high-resolution custom CGH array (median probe spacing 350 bp).