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Pathway-based analysis of primary biliary cirrhosis genome-wide association studies
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Journal Article
Pathway-based analysis of primary biliary cirrhosis genome-wide association studies
2013
Overview
Genome-wide association studies (GWAS) have successfully identified several loci associated with primary biliary cirrhosis (PBC) risk. Pathway analysis complements conventional GWAS analysis. We applied the recently developed linear combination test for pathways to datasets drawn from independent PBC GWAS in Italian and Canadian subjects. Of the Kyoto Encyclopedia of Genes and Genomes and BioCarta pathways tested, 25 pathways in the Italian dataset (449 cases, 940 controls) and 26 pathways in the Canadian dataset (530 cases, 398 controls) were associated with PBC susceptibility (
P
<0.05). After correcting for multiple comparisons, only the eight most significant pathways in the Italian dataset had FDR <0.25 with tumor necrosis factor/stress-related signaling emerging as the top pathway (
P
=7.38 × 10
−4
, FDR=0.18). Two pathways, phosphatidylinositol signaling and hedgehog signaling, were replicated in both datasets (
P
<0.05), and subjected to two additional complementary pathway tests. Both pathway signals remained significant in the Italian dataset on modified gene set enrichment analysis (
P
<0.05). In both GWAS, variants nominally associated with PBC were significantly overrepresented in the phosphatidylinositol pathway (Fisher exact
P
<0.05). These results point to established and novel pathway-level associations with inherited predisposition to PBC that, on further independent replication and functional validation, may provide fresh insights into PBC etiology.
Publisher
Nature Publishing Group UK,Nature Publishing Group
Subject
/ Analysis
/ Biomedical and Life Sciences
/ Canada
/ Datasets
/ Etiology
/ Female
/ Gene set enrichment analysis
/ Genetic Predisposition to Disease - genetics
/ Genetics
/ Genome-wide association studies
/ Genome-Wide Association Study - methods
/ Genomes
/ Genotype
/ Humans
/ Italy
/ Liver Cirrhosis, Biliary - genetics
/ Male
/ Medicine
