- GRASP v2.0: an update on the Genome-Wide Repository of Associations between SNPs and phenotypes. [PMID: 25428361]
John D Eicher, Christa Landowski, Brian Stackhouse, Arielle Sloan, Wenjie Chen, Nicole Jensen, Ju-Ping Lien, Richard Leslie, Andrew D Johnson
Nucleic acids research 2015:43(Database issue)
9 Citations (Google Scholar as of 2015-12-24)
Abstract: Here, we present an update on the Genome-Wide Repository of Associations between SNPs and Phenotypes (GRASP) database version 2.0 (http://apps.nhlbi.nih.gov/Grasp/Overview.aspx). GRASP is a centralized repository of publically available genome-wide association study (GWAS) results. GRASP v2.0 contains ? 8.87 million SNP associations reported in 2082 studies, an increase of ? 2.59 million SNP associations (41.4% increase) and 693 studies (48.9% increase) from our previous version. Our goal in developing and maintaining GRASP is to provide a user-friendly means for diverse sets of researchers to query reported SNP associations (P ? 0.05) with human traits, including methylation and expression quantitative trait loci (QTL) studies. Therefore, in addition to making the full database available for download, we developed a user-friendly web interface that allows for direct querying of GRASP. We provide details on the use of this web interface and what information may be gleaned from using this interactive option. Additionally, we describe potential uses of GRASP and how the scientific community may benefit from the convenient availability of all SNP association results from GWAS (P ? 0.05). We plan to continue updating GRASP with newly published GWAS and increased annotation depth. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by US Government employees and is in the public domain in the US.
- GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database. [PMID: 24931982]
Richard Leslie, Christopher J O'Donnell, Andrew D Johnson
Bioinformatics (Oxford, England) 2014:30(12)
19 Citations (Google Scholar as of 2016-01-28)
Abstract: We created a deeply extracted and annotated database of genome-wide association studies (GWAS) results. GRASP v1.0 contains >6.2 million SNP-phenotype association from among 1390 GWAS studies. We re-annotated GWAS results with 16 annotation sources including some rarely compared to GWAS results (e.g. RNAediting sites, lincRNAs, PTMs). To create a high-quality resource to facilitate further use and interpretation of human GWAS results in order to address important scientific questions. GWAS have grown exponentially, with increases in sample sizes and markers tested, and continuing bias toward European ancestry samples. GRASP contains >100 000 phenotypes, roughly: eQTLs (71.5%), metabolite QTLs (21.2%), methylation QTLs (4.4%) and diseases, biomarkers and other traits (2.8%). cis-eQTLs, meQTLs, mQTLs and MHC region SNPs are highly enriched among significant results. After removing these categories, GRASP still contains a greater proportion of studies and results than comparable GWAS catalogs. Cardiovascular disease and related risk factors pre-dominate remaining GWAS results, followed by immunological, neurological and cancer traits. Significant results in GWAS display a highly gene-centric tendency. Sex chromosome X (OR = 0.18[0.16-0.20]) and Y (OR = 0.003[0.001-0.01]) genes are depleted for GWAS results. Gene length is correlated with GWAS results at nominal significance (P ≤ 0.05) levels. We show this gene-length correlation decays at increasingly more stringent P-value thresholds. Potential pleotropic genes and SNPs enriched for multi-phenotype association in GWAS are identified. However, we note possible population stratification at some of these loci. Finally, via re-annotation we identify compelling functional hypotheses at GWAS loci, in some cases unrealized in studies to date. Pooling summary-level GWAS results and re-annotating with bioinformatics predictions and molecular features provides a good platform for new insights. The GRASP database is available at http://apps.nhlbi.nih.gov/grasp. Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.