The Illumina BeadStudio 3.0 software package was used for initial CNV detection analysis. LRRs and B allele frequencies were first exported from BeadStudio. LRR values were used as an additional sample-wide genotype quality control measure, and LRRs with a standard deviation above 0.35 were excluded from the study. Chromosomes were segmented on the basis of LRRs, using the circular binary segmentation algorithm implemented in the R statistical package module DNAcopy 1.7 (http://www.bioconductor.org/). We used the reference clusters for each SNP that were supplied by Illumina from a set of HapMap samples. As these samples are a mixture of males and females, the Log R Ratio distribution for the X chromosome differs from that of the autosomal chromosomes. Accordingly, differing thresholds were chosen based on known samples with X chromosome deletions and duplications. For autosomal chromosomes, we used threshold of acceptance values of −2, −0.3 and 0.25 for the mean LRRs of potential homozygous deletions, hemizygous deletions and duplications, respectively. For males, X chromosome thresholds of −2 and 0.1 were used for hemizygous deletions and duplications, respectively. For females, X chromosome
