title: Systematic permutation testing in GWAS pathway analyses: identification of genetic networks in dilated cardiomyopathy and ulcerative colitis.
abstract: BACKGROUND
  Genome wide association studies (GWAS) are applied to identify genetic loci, which are associated with complex traits and human diseases. Analogous to the evolution of gene expression analyses, pathway analyses have emerged as important tools to uncover functional networks of genome-wide association data. Usually, pathway analyses combine statistical methods with a priori available biological knowledge. To determine significance thresholds for associated pathways, correction for multiple testing and over-representation permutation testing is applied.
  
  
  RESULTS
  We systematically investigated the impact of three different permutation test approaches for over-representation analysis to detect false positive pathway candidates and evaluate them on genome-wide association data of Dilated Cardiomyopathy (DCM) and Ulcerative Colitis (UC). Our results provide evidence that the gold standard - permuting the case-control status - effectively improves specificity of GWAS pathway analysis. Although permutation of SNPs does not maintain linkage disequilibrium (LD), these permutations represent an alternative for GWAS data when case-control permutations are not possible. Gene permutations, however, did not add significantly to the specificity. Finally, we provide estimates on the required number of permutations for the investigated approaches.
  
  
  CONCLUSIONS
  To discover potential false positive functional pathway candidates and to support the results from standard statistical tests such as the Hypergeometric test, permutation tests of case control data should be carried out. The most reasonable alternative was case-control permutation, if this is not possible, SNP permutations may be carried out. Our study also demonstrates that significance values converge rapidly with an increasing number of permutations. By applying the described statistical framework we were able to discover axon guidance, focal adhesion and calcium signaling as important DCM-related pathways and Intestinal immune network for IgA production as most significant UC pathway.
authors: Christina
authors: C
authors: Backes
authors: Frank
authors: F
authors: Rühle
authors: Monika
authors: M
authors: Stoll
authors: Jan
authors: J
authors: Haas
authors: Karen
authors: K
authors: Frese
authors: Andre
authors: A
authors: Franke
authors: Wolfgang
authors: W
authors: Lieb
authors: H-Erich
authors: HE
authors: Wichmann
authors: Tanja
authors: T
authors: Weis
authors: Wanda
authors: W
authors: Kloos
authors: Hans-Peter
authors: HP
authors: Lenhof
authors: Eckart
authors: E
authors: Meese
authors: Hugo
authors: H
authors: Katus
authors: Benjamin
authors: B
authors: Meder
authors: Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany. ack@bioinf.uni-sb.de.
authors: Andreas
authors: A
authors: Keller
mesh_terms: D002311:Cardiomyopathy, Dilated / Q000235:genetics* / Q000473:pathology; D003093:Colitis, Ulcerative / Q000235:genetics* / Q000473:pathology; D053263:Gene Regulatory Networks; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods*; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D015398:Signal Transduction / Q000235:genetics