GWASdb: a database for human genetic variants identified by genome-wide association studies

GWASdb: a database for human genetic variants identified by genome-wide association studiesMulin Jun Li1, Panwen Wang1, Xiaorong Liu1, Ee Lyn Lim1,2, Zhangyong Wang1,3, Meredith Yeager4,5, Maria P. Wong6, Pak Chung Sham7, Stephen J. Chanock5 and Junwen Wang1,*

+ Author Affiliations
1Department of Biochemistry, The University of Hong Kong, Hong Kong SAR, China, 2Trinity College, University of Oxford, Oxford, UK, 3Department of Computer Science, UCLA, Los Angeles, CA, 4Core Genotyping Facility, SAIC-Frederick Inc., Frederick, MD, USA, 5Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA, 6Department of Pathology and 7Department of Psychiatry, The University of Hong Kong, Hong Kong SAR, China
↵*To whom correspondence should be addressed. Tel: +852 2819 2809; Fax: +852 2855 1254; Email: junwen@uw.edu
Received August 11, 2011.
Revision received October 11, 2011.
Accepted November 14, 2011.

Abstract
Recent advances in genome-wide association studies (GWAS) have enabled us to identify thousands of genetic variants (GVs) that are associated with human diseases. As next-generation sequencing technologies become less expensive, more GVs will be discovered in the near future. Existing databases, such as NHGRI GWAS Catalog, collect GVs with only genome-wide level significance. However, many true disease susceptibility loci have relatively moderate P values and are not included in these databases. We have developed GWASdb that contains 20 times more data than the GWAS Catalog and includes less significant GVs (P < 1.0 × 10−3) manually curated from the literature. In addition, GWASdb provides comprehensive functional annotations for each GV, including genomic mapping information, regulatory effects (transcription factor binding sites, microRNA target sites and splicing sites), amino acid substitutions, evolution, gene expression and disease associations. Furthermore, GWASdb classifies these GVs according to diseases using Disease-Ontology Lite and Human Phenotype Ontology. It can conduct pathway enrichment and PPI network association analysis for these diseases. GWASdb provides an intuitive, multifunctional database for biologists and clinicians to explore GVs and their functional inferences. It is freely available at http://jjwanglab.org/gwasdb and will be updated frequently.
full-text:
GWASdb: a database for human genetic variants identified by genome-wide association studies