The Illumina 1M array has a total of 1,072,820 probes, predominantly indexed by polymorphic SNPs. 23,812 of these probes are non-SNP “intensity-only” markers for CNV detection. All of the 1,072,820 probes were used for the CNV analyses. Three common programs were used to call CNVs: CNVPartition, PennCNV (Wang et al., 2007), and QuantiSNP (Colella et al., 2007). Genomic waves were also adjusted when we called CNVs by PennCNV and QuantiSNP (Diskin et al., 2008). Both PennCNV and QuantiSNP report a metric score for quality control purposes. As recommended by QuantiSNP documentation, we removed all CNV calls that had Log Bayes Factor (LBF) less than 10, as well as poor quality samples based on quality control measures for CNV analysis, following the approaches described in our previous work (Lin et al., 2011). In total, we genotyped 2,583 non-Hispanic European American samples in SAGE and among them 95 samples failed to pass quality controls for CNV analysis.
