QuantiSNP analysis was applied to each Human-1 and HumanHap300 datasets, and the combined dataset. Figure 4 shows two examples of the QuantiSNP analysis results output (for data visualization see Supplementary Figure S1). QuantiSNP identified 8/9 deletions (no SNP mapping on the deletion on chromosome 5 for sample 17) and 3/3 duplications in either one (1 case) or both (9 cases) array platforms, and always in the combined dataset (11 cases). In 7/11 of identified cases, (combined data analysis) the validated event was identified together with one or more unvalidated CNV events. Several of these additional events were found in more than one sample. A detailed analysis compared the additional CNVs with the Database of Genomic Variants (http://projects.tcag.ca/variation/—12th October 2006 Release) and 11/15 of these mapped to previously discovered CNV events (sample No.10 was excluded due to unusually high noise in the sample data). In Figure 5, we have plotted the average number of unvalidated CNV events detected in samples No. 2–9, 11–18 by QuantiSNP at different Bayes Factor thresholds (). This is not a true false call rate, as some
