1Biostatistics and Research Decision Sciences, Merck Research Laboratories, Rahway, NJ, USA 070652Target Sciences, GSK, King of Prussia, Philadelphia, PA 27513, USA3OmicSoft Corporation, Cary, NC 27513, USA4Target Sciences, GSK, Stevenage, SG1 2NY UK
Checking for direct PDF access through Ovid
Summary:We developed the STOPGAP (Systematic Target OPportunity assessment by Genetic Association Predictions) database, an extensive catalog of human genetic associations mapped to effector gene candidates. STOPGAP draws on a variety of publicly available GWAS associations, linkage disequilibrium (LD) measures, functional genomic and variant annotation sources. Algorithms were developed to merge the association data, partition associations into non-overlapping LD clusters, map variants to genes and produce a variant-to-gene score used to rank the relative confidence among potential effector genes. This database can be used for a multitude of investigations into the genes and genetic mechanisms underlying inter-individual variation in human traits, as well as supporting drug discovery applications.Availability and implementation:Shell, R, Perl and Python scripts and STOPGAP R data files (version 2.5.1 at publication) are available at https://github.com/StatGenPRD/STOPGAP. Some of the most useful STOPGAP fields can be queried through an R Shiny web application at http://stopgapwebapp.com.Contact:email@example.comSupplementary information:Supplementary data are available at Bioinformatics online.