Valentina Iotchkova | bioRxiv Science

bioRxiv2015

MultiMeta: an R package for meta-analysing multi-phenotype genome-wide association studies

SummaryAs new methods for multivariate analysis of Genome Wide Association Studies (GWAS) become available, it is important to be able to combine results from different cohorts in a meta-analysis. The R package MultiMeta provides an implementation of the inverse-variance based method for meta-analysis, generalized to an n-dimensional setting.\n\nAvailabilityThe R package MultiMeta can be downloaded from CRAN Contact: dragana.vuckovic@burlo.trieste.it

Bioinformatics↗

bioRxiv2014

FORGE : A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions.

Genome wide association studies provide an unbiased discovery mechanism for numerous human diseases. However, a frustration in the analysis of GWAS is that the majority of variants discovered do not directly alter protein-coding genes. We have developed a simple analysis approach that detects the tissue-specific regulatory component of a set of GWAS SNPs by identifying enrichment of overlap with DNase I hotspots from diverse tissue samples. Functional element Overlap analysis of the Results of GWAS Experiments (FORGE) is available as a web tool and as standalone software and provides tabular and graphical summaries of the enrichments. Conducting FORGE analysis on SNP sets for 260 phenotypes available from the GWAS catalogue reveals numerous overlap enrichments with tissue-specific components reflecting the known aetiology of the phenotypes as well as revealing other unforeseen tissue involvements that may lead to mechanistic insights for disease.

Bioinformatics↗