CNP genotyping for the GWAS and replication sets was performed using the PlatinumCNV [8], which uses a Bayesian Gaussian mixture model for SNP array signal intensity data. We ran PlatinumCNV on the raw signal intensity data from the Illumina 610K platform (GWAS set) and obtained 4,256 CNP loci that passed the following quality control criteria: call rate (), HWE test () and minor allele frequency of total aneuploidy haplotypes () (calculated as described in [8]). For the replication set, we ran PlatinumCNV on the signal intensity data of markers within the CYP2A6 locus. The five CNPs that satisfied the genome-wide significance level () in the GWAS were successfully genotyped using the signal intensity data from the OmniExpress II platform (see Figure S8 for detailed clustering results).
