Using BeadStudio LOH+ and HumanHap300 data, we identified 7/9 known deletions and 3/3 known duplications in either one or both of the array platforms in samples 4–18. As the study was conducted in a blind fashion after the analysis we realized that the sample 17 deletion (mapped by PCR) could not be identified, as there are no SNPs on the arrays that map to the deleted region on chromosome 5. In all samples, using HumanHap300 arrays, BeadStudio LOH+ discovered the validated event together with one or more unvalidated CNV events (Supplementary Table S1). Many of the additional events were mapped to chromosome X (52/105). At present, the sample sheet for the BeadStudio LOH+ module (version 2.3.41; Autobookmarking version 1.0) does not include a column to give information of the gender of the samples and therefore some of the X chromosome events may be solely due to differing copy numbers of X between genders. No new events around the translocation breakpoints were identified in cases 11,12 and 13.
