It is known that the genotyping error rate of CNPs is higher than that of SNPs [8]. To validate the CNP genotyping quality, we performed TaqMan gene copy number assays using real-time quantitative PCR (referred to as “TaqMan assays” throughout this manuscript) for the five CNPs at the CYP2A6 locus. Using subsamples from both the GWAS () and the replication set (), we found a concordance rate of more than 95% for all CNPs (Table S4). In particular, the CNP (rs8102683) showed the highest concordance rate (99%) in both the GWAS and the replication set.
