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

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• 作者：Ju-Han Lee ; Younghye Kim ; Jung-Woo Choi ; Young-Sik Kim
• 关键词：Genome ; wide association study ; Pathway ; based analysis ; Gastric cancer
• 刊名：SpringerPlus
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：4
• 期：1
• 全文大小：552KB
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• 作者单位：Ju-Han Lee (1)
  Younghye Kim (1)
  Jung-Woo Choi (1)
  Young-Sik Kim (1)
  
  1. Department of Pathology, Korea University Ansan Hospital, 123, Jeokgeum-Ro, Danwon-Gu, Ansan-Si, Gyeonggi-Do, 425-707, Republic of Korea
  
• 刊物类别：Science, general;
• 刊物主题：Science, general;
• 出版者：Springer International Publishing
• ISSN：2193-1801

文摘

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鈥夆啋鈥?em class="EmphasisTypeItalic ">EFNA1鈥夆啋鈥塭phrin receptor binding; (2) rs1801019鈥夆啋鈥?em class="EmphasisTypeItalic ">UMPS鈥夆啋鈥塪rug and pyrimidine metabolism; (3) rs364897鈥夆啋鈥?em class="EmphasisTypeItalic ">GBA鈥夆啋鈥塩yanoamino acid metabolism; and (4) rs11187870, rs2274223, and rs3765524鈥夆啋鈥?em class="EmphasisTypeItalic ">PLCE1鈥夆啋鈥塴ipid 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. Keywords Genome-wide association study Pathway-based analysis Gastric cancer