Genome-wide pathway analysis in glioma

Y. H. Lee, G. G. Song

    Research output: Contribution to journalArticlepeer-review

    11 Citations (Scopus)


    The aim of this study was to identify candidate single-nucleotide polymorphisms (SNPs) that may play a role in the susceptibility to glioma, to elucidate their potential mechanisms, and to generate SNP-to-gene-to-pathway hypotheses. A genome-wide association study (GWAS) dataset of glioma including 509,345 SNPs from 1,856 glioma patients and 4,955 control subjects of European descent was used in this study. Identify candidate Causal SNPs and Pathways (ICSNPathway) analysis was applied to the GWAS dataset. ICSNPathway analysis identified 6 candidate SNPs, 5 genes, and 9 pathways, which revealed 5 hypothetical biological mechanisms. The hypothetical mechanisms, beginning with the strongest, are summarized as follows: (i) rs667128 alters the role of taste receptor, type 2, member 8 (TAS2R8) in taste receptor activity and taste transduction pathways (p < 0.001, false discovery rate (FDR) < 0.001; p = 0.001, FDR = 0.012, respectively), (ii) rs619381 modulates the effect of taste receptor, type 2, member 7 (TAS2R7) on taste receptor activity and taste transduction (p < 0.001, FDR < 0.001; p = 0.001, FDR = 0.012), (iii) rs1033583 modulates delta-like protein 1 (DLL1), regulating cell adhesion and segment specification (p < 0.001, FDR = 0.011; p = 0.001, FDR = 0.032), (iv) rs2232580 affects the role of lipopolysaccharide binding protein (LBP) in the response to lipopolysaccharide, positive regulation of interleukin-6 production, acute inflammatory response, and in macrophage activation (0.002 ≤ p ≤ 0.013; 0.012 ≤ FDR ≤ 0.030), and (v) rs4644 and rs4652 regulate lectin, galactoside-binding, soluble, 3 (LGALS3), affecting immunoglobulin binding (p = 0.010; FDR = 0.040). Using the ICSNPathway to analyze glioma GWAS data, 6 candidate SNPs, 5 genes (TAS2R8, TAS2R7, DLL1, LBP, and LGALS3), and 9 pathways that may contribute to the susceptibility of glioma were identified.

    Original languageEnglish
    Pages (from-to)230-238
    Number of pages9
    Issue number2
    Publication statusPublished - 2015

    Bibliographical note

    Publisher Copyright:
    © 2015, Cancer Research Institute Slovak Acad. of Sciences. All rights reserved.


    • Genome-wide association study
    • Glioma
    • Pathway-based analysis

    ASJC Scopus subject areas

    • Cancer Research


    Dive into the research topics of 'Genome-wide pathway analysis in glioma'. Together they form a unique fingerprint.

    Cite this