For the gastric cancer GWAS, the nongenotyped variants were imputed on the basis of the 1000 Genomes Project (phase 1 integrated release 3, March 2012) using IMPUTE (31). The imputed SNPs were then excluded on the basis of the criteria of a minor allele frequency of <0.01, a genotype call rate of <95%, and P < 0.001 for Hardy-Weinberg equilibrium (HWE). A total of 4,817,140 variants were included in the analysis of the association with gastric cancer using a probabilistic dosage model in SNPTEST v2.5 (32).

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