RT Journal Article SR Electronic T1 FORGE: multivariate calculation of gene-wide p-values from Genome-Wide Association Studies JF bioRxiv FD Cold Spring Harbor Laboratory SP 023648 DO 10.1101/023648 A1 Inti Pedroso A1 Michael R Barnes A1 Anbarasu Lourdusamy A1 Ammar Al-Chalabi A1 Gerome Breen YR 2015 UL http://biorxiv.org/content/early/2015/07/31/023648.abstract AB Genome-wide association studies (GWAS) have proven a valuable tool to explore the genetic basis of many traits. However, many GWAS lack statistical power and the commonly used single-point analysis method needs to be complemented to enhance power and interpretation. Multivariate region or gene-wide association are an alternative, allowing for identification of disease genes in a manner more robust to allelic heterogeneity. Gene-based association also facilitates systems biology analyses by generating a single p-value per gene. We have designed and implemented FORGE, a software suite which implements a range of methods for the combination of p-values for the individual genetic variants within a gene or genomic region. The software can be used with summary statistics (marker ids and p-values) and accepts as input the result file formats of commonly used genetic association software. When applied to a study of Crohn’s disease susceptibility, it identified all genes found by single SNP analysis and additional genes identified by large independent metaanalysis. FORGE p-values on gene-set analyses highlighted association with the Jak-STAT and cytokine signalling pathways, both previously associated with CD. We highlight the software’s main features, its future development directions and provide a comparison with alternative available software tools. FORGE can be freely accessed at https://github.com/inti/FORGE.