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Bioinformatics DOI:10.1093/bioinformatics/bts191

INRICH: interval-based enrichment analysis for genome-wide association studies.

Publication TypeJournal Article
Year of Publication2012
AuthorsLee, PH, O'Dushlaine, C, Thomas, B, Purcell, SM
JournalBioinformatics
Volume28
Issue13
Pages1797-9
Date Published2012 Jul 01
ISSN1367-4811
KeywordsGenes, Genome-Wide Association Study, Genomics, Humans, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Software
Abstract

SUMMARY: Here we present INRICH (INterval enRICHment analysis), a pathway-based genome-wide association analysis tool that tests for enriched association signals of predefined gene-sets across independent genomic intervals. INRICH has wide applicability, fast running time and, most importantly, robustness to potential genomic biases and confounding factors. Such factors, including varying gene size and single-nucleotide polymorphism density, linkage disequilibrium within and between genes and overlapping genes with similar annotations, are often not accounted for by existing gene-set enrichment methods. By using a genomic permutation procedure, we generate experiment-wide empirical significance values, corrected for the total number of sets tested, implicitly taking overlap of sets into account. By simulation we confirm a properly controlled type I error rate and reasonable power of INRICH under diverse parameter settings. As a proof of principle, we describe the application of INRICH on the NHGRI GWAS catalog.

AVAILABILITY: A standalone C++ program, user manual and datasets can be freely downloaded from: http://atgu.mgh.harvard.edu/inrich/.

URLhttp://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=22513993
DOI10.1093/bioinformatics/bts191
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/22513993?dopt=Abstract

Alternate JournalBioinformatics
PubMed ID22513993
PubMed Central IDPMC3381960
Grant ListU01MH0855513 / MH / NIMH NIH HHS / United States