Genetic variants and risk of gastric cancer: a pathway analysis of a genome-wide association study

Ju Han Lee, Younghye Kim, Jung Woo Choi, Young Sik Kim

    Research output: Contribution to journalArticlepeer-review

    10 Citations (Scopus)

    Abstract

    This study aimed to discover candidate single nucleotide polymorphisms (SNPs) for hypothesizing significant biological pathways of gastric cancer (GC). We performed an Identify Candidate Causal SNPs and Pathways (ICSNPathway) analysis using a GC genome-wide association study (GWAS) dataset, including 472,342 SNPs in 2,240 GC cases and 3,302 controls of Asian ethnicity. By integrating linkage disequilibrium analysis, functional SNP annotation, and pathway-based analysis, seven candidate SNPs, four genes and 12 pathways were selected. The ICSNPathway analysis produced 4 hypothetical mechanisms of GC: (1) rs4745 and rs12904 → EFNA1 → ephrin receptor binding; (2) rs1801019 → UMPS → drug and pyrimidine metabolism; (3) rs364897 → GBA → cyanoamino acid metabolism; and (4) rs11187870, rs2274223, and rs3765524 → PLCE1 → lipid biosynthetic process, regulation of cell growth, and cation homeostasis. This pathway analysis using GWAS dataset suggests that the 4 hypothetical biological mechanisms might contribute to GC susceptibility.

    Original languageEnglish
    Article number215
    JournalSpringerPlus
    Volume4
    Issue number1
    DOIs
    Publication statusPublished - 2015 Dec 18

    Keywords

    • Gastric cancer
    • Genome-wide association study
    • Pathway-based analysis

    ASJC Scopus subject areas

    • General

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