GWASdb v2: An update database for human genetic variants identified by genome-wide association studies

Mulin Jun Li, Zipeng Liu, Panwen Wang, Maria P. Wong, Matthew R. Nelson, Jean-Pierre Kocher, Meredith Yeager, Pak Chung Sham, Stephen J. Chanock, Zhengyuan Xia, Junwen Wang

Research output: Contribution to journalArticle

68 Citations (Scopus)

Abstract

Genome-wide association studies (GWASs), now as a routine approach to study single-nucleotide polymorphism (SNP)-trait association, have uncovered over ten thousand significant trait/disease associated SNPs (TASs). Here, we updated GWASdb (GWASdb v2, http://jjwanglab.org/gwasdb) which provides comprehensive data curation and knowledge integration for GWAS TASs. These updates include: (i) Up to August 2015, we collected 2479 unique publications from PubMed and other resources; (ii) We further curated moderate SNP-trait associations (P-value <1.0×10-3) from each original publication, and generated a total of 252 530 unique TASs in all GWASdb v2 collected studies; (iii) We manually mapped 1610 GWAS traits to 501 Human Phenotype Ontology (HPO) terms, 435 Disease Ontology (DO) terms and 228 Disease Ontology Lite (DOLite) terms. For each ontology term, we also predicted the putative causal genes; (iv) We curated the detailed sub-populations and related sample size for each study; (v) Importantly, we performed extensive function annotation for each TAS by incorporating gene-based information, ENCODE ChIP-seq assays, eQTL, population haplotype, functional prediction across multiple biological domains, evolutionary signals and disease-related annotation; (vi) Additionally, we compiled a SNP-drug response association dataset for 650 pharmacogenetic studies involving 257 drugs in this update; (vii) Last, we improved the user interface of website.

Original languageEnglish (US)
Pages (from-to)D869-D876
JournalNucleic Acids Research
Volume44
Issue numberD1
DOIs
StatePublished - 2016

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Genome-Wide Association Study
Medical Genetics
Single Nucleotide Polymorphism
Databases
Publications
PubMed
Pharmaceutical Preparations
Sample Size
Haplotypes
Population
Genes
Phenotype

ASJC Scopus subject areas

  • Genetics

Cite this

GWASdb v2 : An update database for human genetic variants identified by genome-wide association studies. / Li, Mulin Jun; Liu, Zipeng; Wang, Panwen; Wong, Maria P.; Nelson, Matthew R.; Kocher, Jean-Pierre; Yeager, Meredith; Sham, Pak Chung; Chanock, Stephen J.; Xia, Zhengyuan; Wang, Junwen.

In: Nucleic Acids Research, Vol. 44, No. D1, 2016, p. D869-D876.

Research output: Contribution to journalArticle

Li, MJ, Liu, Z, Wang, P, Wong, MP, Nelson, MR, Kocher, J-P, Yeager, M, Sham, PC, Chanock, SJ, Xia, Z & Wang, J 2016, 'GWASdb v2: An update database for human genetic variants identified by genome-wide association studies', Nucleic Acids Research, vol. 44, no. D1, pp. D869-D876. https://doi.org/10.1093/nar/gkv1317
Li, Mulin Jun ; Liu, Zipeng ; Wang, Panwen ; Wong, Maria P. ; Nelson, Matthew R. ; Kocher, Jean-Pierre ; Yeager, Meredith ; Sham, Pak Chung ; Chanock, Stephen J. ; Xia, Zhengyuan ; Wang, Junwen. / GWASdb v2 : An update database for human genetic variants identified by genome-wide association studies. In: Nucleic Acids Research. 2016 ; Vol. 44, No. D1. pp. D869-D876.
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