Detection of rare CNVs was performed using MeZOD as follows. For each CNV region that was defined in our whole-genome scans, we computed the median Z score of tiling array probes in each individual. The median of a region was then standardized vertically across all individuals. We then assign deletion genotypes using a Z score threshold of ≤ −2 and duplication genotypes using a Z score threshold of ≥ +2. Positive CNV calls were further verified by manual inspection of log2 ratios in the subject, mother, and father. Representative examples of validated de novo deletions are shown in Figure 1 and Figure 2. The details of the number of putative de novo CNVs identified in BD, SCZ, and controls and their validation by tiling array CGH are described in Table S3. The rates of validations are presented in Table S4. The overall validation rate of putative de novo CNVs was 16% (23/145). As expected, the validation rate was highest for CNVs > 100 kb in size and lowest (3%) for CNVs that were < 20 kb in size.
