After completing quality control and case-control matching, a total of 460 cases (148 trios) and 1131 controls (436 trios) were included in our analyses (Figure 1; see also Table S1, Figure S1-2 in Supplement 1). PCA of genotypic data yielded a genomic inflation factor (λ) of 1.14. We further corrected for residual differences in batch effects by adjusting LogR values for 9 principal components (Figure S3 in Supplement 1). From this matched sample, using the set of probes shared by all array platforms, we identified a total of 745 rare high confidence CNVs in cases and 1910 in controls (Table S2 in Supplement 2). Among these, we found 4 cases (2.7%) and 5 controls (1.1%) carrying at last one rare de novo CNV (Table S3 in Supplement 1). The rate of de novo CNVs in our control sample was highly consistent with that found in prior studies (38, 57).
