TY - JOUR
T1 - Genetic variants and risk of gastric cancer
T2 - a pathway analysis of a genome-wide association study
AU - Lee, Ju Han
AU - Kim, Younghye
AU - Choi, Jung Woo
AU - Kim, Young Sik
N1 - Publisher Copyright:
© 2015, Lee et al.; licensee Springer.
PY - 2015/12/18
Y1 - 2015/12/18
N2 - 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.
AB - 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.
KW - Gastric cancer
KW - Genome-wide association study
KW - Pathway-based analysis
UR - http://www.scopus.com/inward/record.url?scp=84929340032&partnerID=8YFLogxK
U2 - 10.1186/s40064-015-1005-8
DO - 10.1186/s40064-015-1005-8
M3 - Article
AN - SCOPUS:84929340032
VL - 4
JO - SpringerPlus
JF - SpringerPlus
SN - 2193-1801
IS - 1
M1 - 215
ER -
