Genome-wide pathway analysis in amyotrophic lateral sclerosis

Y. H. Lee, G. G. Song

    Research output: Contribution to journalArticlepeer-review

    3 Citations (Scopus)


    The aims of this study were to identify candidate single-nucleotide polymorphisms (SNPs) and mechanisms of amyotrophic lateral sclerosis (ALS) and to generate SNP-to-gene-to-pathway hypotheses. An ALS genome-wide association study (GWAS) dataset that included 483,051 SNPs in 276 patients with ALS and 271 controls of European descent was used in this study. Identify Candidate Causal SNPs and Pathway (ICSNPathway) analysis was applied to the GWAS dataset. ICSNPathway analysis identified 19 candidate SNPs, 8 genes, and 9 pathways, which provided 8 hypothetical biological mechanisms. The strongest hypothetical biological mechanism was that rs9352 alters the role of chromatin assembly factor 1 subunit A in the context of the pathways of chromatin and nucleosome assembly (nominal P < 0.001, false discovery rate (FDR) ≤ 0.001, 0.018, respectively). The second strongest was rs1046329 → HILS1 → chromatin assembly (nominal P < 0.001, FDR = 0.018). The third was rs11100790 → SMARCA5 → chromatin and nucleosome assembly (nominal P < 0.001, FDR ≤ 0.001, 0.018, respectively). The application of ICSNPathway analysis to the ALS GWAS dataset resulted in the identification of candidate SNPs, pathways, and biological mechanisms that might contribute to ALS susceptibility.

    Original languageEnglish
    Pages (from-to)6429-6438
    Number of pages10
    JournalGenetics and Molecular Research
    Issue number2
    Publication statusPublished - 2015 Jun 11

    Bibliographical note

    Publisher Copyright:
    © FUNPEC-RP.


    • Amyotrophic lateral sclerosis
    • Genome-wide association study
    • Pathway-based analysis

    ASJC Scopus subject areas

    • Molecular Biology
    • Genetics


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