title: Comparison of pathway analysis approaches using lung cancer GWAS data sets.
abstract: Pathway analysis has been proposed as a complement to single SNP analyses in GWAS. This study compared pathway analysis methods using two lung cancer GWAS data sets based on four studies: one a combined data set from Central Europe and Toronto (CETO); the other a combined data set from Germany and MD Anderson (GRMD). We searched the literature for pathway analysis methods that were widely used, representative of other methods, and had available software for performing analysis. We selected the programs EASE, which uses a modified Fishers Exact calculation to test for pathway associations, GenGen (a version of Gene Set Enrichment Analysis (GSEA)), which uses a Kolmogorov-Smirnov-like running sum statistic as the test statistic, and SLAT, which uses a p-value combination approach. We also included a modified version of the SUMSTAT method (mSUMSTAT), which tests for association by averaging χ(2) statistics from genotype association tests. There were nearly 18000 genes available for analysis, following mapping of more than 300,000 SNPs from each data set. These were mapped to 421 GO level 4 gene sets for pathway analysis. Among the methods designed to be robust to biases related to gene size and pathway SNP correlation (GenGen, mSUMSTAT and SLAT), the mSUMSTAT approach identified the most significant pathways (8 in CETO and 1 in GRMD). This included a highly plausible association for the acetylcholine receptor activity pathway in both CETO (FDR≤0.001) and GRMD (FDR = 0.009), although two strong association signals at a single gene cluster (CHRNA3-CHRNA5-CHRNB4) drive this result, complicating its interpretation. Few other replicated associations were found using any of these methods. Difficulty in replicating associations hindered our comparison, but results suggest mSUMSTAT has advantages over the other approaches, and may be a useful pathway analysis tool to use alongside other methods such as the commonly used GSEA (GenGen) approach.
authors.affiliation: Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
authors.forename: Gordon
authors.initials: G
authors.lastname: Fehringer
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Liu
authors.forename: Laurent
authors.initials: L
authors.lastname: Briollais
authors.forename: Paul
authors.initials: P
authors.lastname: Brennan
authors.forename: Christopher I
authors.initials: CI
authors.lastname: Amos
authors.forename: Margaret R
authors.initials: MR
authors.lastname: Spitz
authors.forename: Heike
authors.initials: H
authors.lastname: Bickeböller
authors.forename: H Erich
authors.initials: HE
authors.lastname: Wichmann
authors.forename: Angela
authors.initials: A
authors.lastname: Risch
authors.forename: Rayjean J
authors.initials: RJ
authors.lastname: Hung
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D030541:Databases, Genetic; D005189:False Positive Reactions; D005260:Female; D053263:Gene Regulatory Networks / Q000235:genetics*; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study / Q000379:methods*; D060005:Genotyping Techniques; D006801:Humans; D008175:Lung Neoplasms / Q000453:epidemiology / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D016017:Odds Ratio; D011950:Receptors, Cholinergic / Q000378:metabolism; D012307:Risk Factors; D015398:Signal Transduction / Q000235:genetics*; D012984:Software; D055815:Young Adult
chemical_list: D011950:Receptors, Cholinergic