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

doi:10.1093/nar/gkv1317

. 2016 Jan 4;44(D1):D869-76.

doi: 10.1093/nar/gkv1317. Epub 2015 Nov 28.

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

Affiliations

¹ Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
² Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China Department of Anaesthesiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
³ Department of Pathology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
⁴ Quantitative Sciences, GlaxoSmithKline, Research Triangle Park, NC, USA.
⁵ Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN, USA.
⁶ Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.
⁷ Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China State Key Laboratory of Brain and Cognitive Sciences and Department of Psychiatry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
⁸ Department of Anaesthesiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
⁹ Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China junwen@uw.edu.

PMID: 26615194
PMCID: PMC4702921
DOI: 10.1093/nar/gkv1317

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

Mulin Jun Li et al. Nucleic Acids Res. 2016.

. 2016 Jan 4;44(D1):D869-76.

doi: 10.1093/nar/gkv1317. Epub 2015 Nov 28.

Authors

Affiliations

¹ Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
² Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China Department of Anaesthesiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
³ Department of Pathology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
⁴ Quantitative Sciences, GlaxoSmithKline, Research Triangle Park, NC, USA.
⁵ Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN, USA.
⁶ Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.
⁷ Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China State Key Laboratory of Brain and Cognitive Sciences and Department of Psychiatry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
⁸ Department of Anaesthesiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
⁹ Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China junwen@uw.edu.

PMID: 26615194
PMCID: PMC4702921
DOI: 10.1093/nar/gkv1317

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.

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Figures

**Figure 1.**
Main functions of GWASdb v2. (A) Interactive Manhattan panel; (B) TAS summary information; (C) Genome browser to show important functional elements; (D) Interactive LD panel; (E) GWASdb v2 annotation tabs.

**Figure 2.**
Trait/disease mapping interface in GWASdb v2. (A) Ontology tree viewer; (B) Genomic overview of SNPs associated with a particular disease.

See this image and copyright information in PMC

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References

1. McCarthy M.I., Abecasis G.R., Cardon L.R., Goldstein D.B., Little J., Ioannidis J.P., Hirschhorn J.N. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat. Rev. Genet. 2008;9:356–369. - PubMed
1. Stranger B.E., Stahl E.A., Raj T. Progress and promise of genome-wide association studies for human complex trait genetics. Genetics. 2011;187:367–383. - PMC - PubMed
1. Rietveld C.A., Medland S.E., Derringer J., Yang J., Esko T., Martin N.W., Westra H.J., Shakhbazov K., Abdellaoui A., Agrawal A., et al. GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. Science. 2013;340:1467–1471. - PMC - PubMed
1. Spain S.L., Barrett J.C. Strategies for fine-mapping complex traits. Hum. Mol. Genet. 2015;24:R111–R119. - PMC - PubMed
1. Lambert J.C., Ibrahim-Verbaas C.A., Harold D., Naj A.C., Sims R., Bellenguez C., DeStafano A.L., Bis J.C., Beecham G.W., Grenier-Boley B., et al. Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. Nat. Genet. 2013;45:1452–1458. - PMC - PubMed

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[1] McCarthy M.I., Abecasis G.R., Cardon L.R., Goldstein D.B., Little J., Ioannidis J.P., Hirschhorn J.N. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat. Rev. Genet. 2008;9:356–369. - PubMed

[2] McCarthy M.I., Abecasis G.R., Cardon L.R., Goldstein D.B., Little J., Ioannidis J.P., Hirschhorn J.N. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat. Rev. Genet. 2008;9:356–369. - PubMed

[3] Stranger B.E., Stahl E.A., Raj T. Progress and promise of genome-wide association studies for human complex trait genetics. Genetics. 2011;187:367–383. - PMC - PubMed

[4] Stranger B.E., Stahl E.A., Raj T. Progress and promise of genome-wide association studies for human complex trait genetics. Genetics. 2011;187:367–383. - PMC - PubMed

[5] Rietveld C.A., Medland S.E., Derringer J., Yang J., Esko T., Martin N.W., Westra H.J., Shakhbazov K., Abdellaoui A., Agrawal A., et al. GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. Science. 2013;340:1467–1471. - PMC - PubMed

[6] Rietveld C.A., Medland S.E., Derringer J., Yang J., Esko T., Martin N.W., Westra H.J., Shakhbazov K., Abdellaoui A., Agrawal A., et al. GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. Science. 2013;340:1467–1471. - PMC - PubMed

[7] Spain S.L., Barrett J.C. Strategies for fine-mapping complex traits. Hum. Mol. Genet. 2015;24:R111–R119. - PMC - PubMed

[8] Spain S.L., Barrett J.C. Strategies for fine-mapping complex traits. Hum. Mol. Genet. 2015;24:R111–R119. - PMC - PubMed

[9] Lambert J.C., Ibrahim-Verbaas C.A., Harold D., Naj A.C., Sims R., Bellenguez C., DeStafano A.L., Bis J.C., Beecham G.W., Grenier-Boley B., et al. Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. Nat. Genet. 2013;45:1452–1458. - PMC - PubMed

[10] Lambert J.C., Ibrahim-Verbaas C.A., Harold D., Naj A.C., Sims R., Bellenguez C., DeStafano A.L., Bis J.C., Beecham G.W., Grenier-Boley B., et al. Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. Nat. Genet. 2013;45:1452–1458. - PMC - PubMed

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

Affiliations

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

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