All associated CNV regions recurrent in MDD cases.

Listed are all loci with CNVs of at least 10 SNPs and 100 kb that were observed to be recurrent among MDD patients and not found in any controls of substantial overlap. All CNVs happened to be duplications and directly impact the genes indicated except
*CDH10 which is proximal 440 kb and involved in axon outgrowth and guidance and
**GFRA2 which is proximal 275 kb and involved in neuronal survival and differentiation. Note also ICA1 which is involved in neurotransmitter secretion. Given the PCR saturation of Perlegen 600 K processing, it is fitting that the intensity signal is diminished. However, the genotype signal is very clear and duplication calls leverage the AAB and ABB calls to deliver reliable calling. The observation of a run of homozygosity is quite common by chance so a lower intensity is important for deletion calls but diluted in this case.