The Illumina 1 M array has 1,072,820 probes (which includes 23,812 non-SNP “intensity-only” markers) that were used for CNV detection. Three widely-used programs were used for CNV calling: CNVPartition (Illumina StudioBead software), PennCNV [35], and QuantiSNP [36]. Genomic waves were adjusted for CNVs called by PennCNV and QuantiSNP [37]. Both PennCNV and QuantiSNP report a metric score for quality control purposes and CNV calls with a Log Bayes Factor less than ten were removed as well as poor quality samples based on quality control measures for CNV analysis as described in our previous work [38]. CNV calls from the three programs were compared and integrated using Combined CNV (CNVision.org) [39]. To increase the positive predicative rate [38], only CNVs that were called by at least two programs, as defined by ≥ 50% reciprocal overlap, were analyzed. Given that calls in centromeric, telomeric and immunoglobin regions are prone to harbor false positives, CNV calls in those regions were removed from analyses (33 regions, 13941 calls) [35, 40].
