Several genetic variants for gastric cancer have been reported, however further study to find more novel genetic markers are still needed. This study was conducted to discover candidate single nucleotide polymorphisms (SNPs) for gastric cancer in Korean population.

We conducted a genome-wide association study (GWAS) with 551,842 SNPs in 803 gastric cancer cases and 3675 controls from the Korea Biobank Project (KBP). Regional association plots of candidate SNPs were generated and linkage disequilibrium (LD) correlation coefficient values (r²) between candidate SNPs and other SNPs were also calculated.

We discovered a total of thirty-eight candidate SNPs, which are associated with gastric cancer. Among 38 candidate SNPs, a SNP (rs13361707; P=1.95×10⁻¹⁰) is located in the PRKAA1 gene and another SNP (rs11125033; P=2.08×10⁻⁸) is located in the PRKCE gene. These two genes (PRKAA1 and PRKCE) were previously reported to be associated with gastric cancer and gastritis or gastric ulcer, respectively. We also found that three genetic variants having strong LD (r²>0.8) with rs13361707. One of these three SNPs was also significantly associated gastric cancer (rs1345778 in PTGER4; P=8.00×10⁻⁸).

This study suggests gastric cancer susceptibility loci represented by rs13361707 in PRKAA1, rs11125033 in PRKCE, and rs1345778 in PTGER4 in Korean population. Fine mapping around these potential SNPs in PRKAA1, PRKCE, and PTGER4 gene may help to confirm susceptible genetic variants for gastric cancer.