TY - JOUR
T1 - Pathway analysis of genome-wide association studies for Parkinson's disease
AU - Song, Gwan Gyu
AU - Lee, Young Ho
N1 - Copyright:
Copyright 2014 Elsevier B.V., All rights reserved.
PY - 2013/3
Y1 - 2013/3
N2 - The study was done to identify the candidate causal single nucleotide polymorphisms (SNPs) and candidate causal mechanisms that contribute to Parkinson's disease (PD) susceptibility and to generate a SNP to ene to pathway hypothesis using an analytical pathway-based approach. We used a PD genome-wide association study (GWAS) meta-analysis data of the genotypes of 2,525,705 SNPs in 4,238 PD cases and 4,239 controls. Identify candidate Causal SNPs and Pathways (ICSNPathway) analysis was applied to the PD GWAS dataset. The first stage involved the pre-selection of candidate causal SNPs by linkage disequilibrium analysis and the functional SNP annotation of the most significant SNPs found. The second stage involved the annotation of biological mechanisms for the pre-selected candidate causal SNPs using improved-gene set enrichment analysis. ICSNPathway analysis identified three candidate SNPs, two genes, twenty-one pathways, and three hypothetical biological mechanisms: (1) rs17651549 to microtubule-associated protein tau (MAPT) to protein domain specific binding (nominal p < 0.001, false discovery rate (FDR) < 0.001), neurogenesis (nominal p < 0.001, FDR < 0.001), regulation of neurogenesis (nominal p < 0.001, FDR = 0.001), positive regulation of axonogenesis (nominal p < 0.001, FDR = 0.001), regulation of protein polymerization (nominal p < 0.001, FDR = 0.004), negative regulation of organelle organization (nominal p < 0.001, FDR = 0.004), hsa01510 (nominal p < 0.001, FDR = 0.005), neuron differentiation (nominal p < 0.001, FDR = 0.009), and axonogenesis (nominal p < 0.001, FDR = 0.009); (2) rs10445337 to MAPT to protein domain specific binding (nominal p < 0.001, FDR < 0.001), neurogenesis (nominal p < 0.001, FDR < 0.001), regulation of neurogenesis (nominal p < 0.001, FDR = 0.001), and positive regulation of axonogenesis (nominal p < 0.001, FDR = 0.001); (3) rs9938550 to HSD3B7 to hsa00363 (nominal p < 0.001, FDR = 0.004), bile acid metabolic process (nominal p = 0.005, FDR = 0.019), and steroid metabolic process (nominal p = 0.010, FDR = 0.039). By applying the ICSNPathway analysis to PD GWAS meta-analysis data, three candidate SNPs, two genes (MAPT and HSD3B7), and 21 pathways involving protein domain specific binding and neurogenesis were identified, which may contribute to PD susceptibility.
AB - The study was done to identify the candidate causal single nucleotide polymorphisms (SNPs) and candidate causal mechanisms that contribute to Parkinson's disease (PD) susceptibility and to generate a SNP to ene to pathway hypothesis using an analytical pathway-based approach. We used a PD genome-wide association study (GWAS) meta-analysis data of the genotypes of 2,525,705 SNPs in 4,238 PD cases and 4,239 controls. Identify candidate Causal SNPs and Pathways (ICSNPathway) analysis was applied to the PD GWAS dataset. The first stage involved the pre-selection of candidate causal SNPs by linkage disequilibrium analysis and the functional SNP annotation of the most significant SNPs found. The second stage involved the annotation of biological mechanisms for the pre-selected candidate causal SNPs using improved-gene set enrichment analysis. ICSNPathway analysis identified three candidate SNPs, two genes, twenty-one pathways, and three hypothetical biological mechanisms: (1) rs17651549 to microtubule-associated protein tau (MAPT) to protein domain specific binding (nominal p < 0.001, false discovery rate (FDR) < 0.001), neurogenesis (nominal p < 0.001, FDR < 0.001), regulation of neurogenesis (nominal p < 0.001, FDR = 0.001), positive regulation of axonogenesis (nominal p < 0.001, FDR = 0.001), regulation of protein polymerization (nominal p < 0.001, FDR = 0.004), negative regulation of organelle organization (nominal p < 0.001, FDR = 0.004), hsa01510 (nominal p < 0.001, FDR = 0.005), neuron differentiation (nominal p < 0.001, FDR = 0.009), and axonogenesis (nominal p < 0.001, FDR = 0.009); (2) rs10445337 to MAPT to protein domain specific binding (nominal p < 0.001, FDR < 0.001), neurogenesis (nominal p < 0.001, FDR < 0.001), regulation of neurogenesis (nominal p < 0.001, FDR = 0.001), and positive regulation of axonogenesis (nominal p < 0.001, FDR = 0.001); (3) rs9938550 to HSD3B7 to hsa00363 (nominal p < 0.001, FDR = 0.004), bile acid metabolic process (nominal p = 0.005, FDR = 0.019), and steroid metabolic process (nominal p = 0.010, FDR = 0.039). By applying the ICSNPathway analysis to PD GWAS meta-analysis data, three candidate SNPs, two genes (MAPT and HSD3B7), and 21 pathways involving protein domain specific binding and neurogenesis were identified, which may contribute to PD susceptibility.
KW - Genome-wide association study
KW - Parkinson's disease
KW - Pathway-based analysis
UR - http://www.scopus.com/inward/record.url?scp=84878393854&partnerID=8YFLogxK
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U2 - 10.1007/s11033-012-2346-9
DO - 10.1007/s11033-012-2346-9
M3 - Article
C2 - 23238920
AN - SCOPUS:84878393854
SN - 0301-4851
VL - 40
SP - 2599
EP - 2607
JO - Molecular Biology Reports
JF - Molecular Biology Reports
IS - 3
ER -