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 of these events may be real CNVs, however, it is nonetheless a useful approximation. When compared to the false call rates derived from our simulation studies, we can see that there is good matching between the two boundaries for the Human-1 dataset. The comparison using the HumanHap300 data is less favourable, however, this is likely to be due to the different versions of the HumanHap300 used in the experiments (see Supplementary Data, Materials and Methods S1 for details). No new events around the translocation breakpoints were identified in cases 11, 12 and 13 in agreement with the BeadStudio LOH+ analysis described above. All QuantiSNP analysis was performed on a 3 GHz Pentium IV PC with 512 Mb.
