CAUSALdb: a database for disease/trait causal variants identified using summary statistics of genome-wide association studies.
paper
Cited
Public
- Authors
- Wang, Jianhua; Huang, Dandan; Zhou, Yao; Yao, Hongcheng; Liu, Huanhuan; Zhai, Sinan; Wu, Chengwei; Zheng, Zhanye; Zhao, Ke; Wang, Zhao; Yi, Xianfu; Zhang, Shijie; Liu, Xiaorong; Liu, Zipeng; Chen, Kexin; Yu, Ying; Sham, Pak Chung; Li, Mulin Jun
- Year
- 2020
- Journal
- Nucleic acids research
- PMID
- 31691819
- DOI
- 10.1093/nar/gkz1026
- PMCID
- PMC7145620
Genome-wide association studies (GWASs) have revolutionized the field of complex trait genetics over the past decade, yet for most of the significant genotype-phenotype associations the true causal variants remain unknown. Identifying and interpreting how causal genetic variants confer disease susceptibility is still a big challenge. Herein we introduce a new database, CAUSALdb, to integrate the most comprehensive GWAS summary statistics to date and identify credible sets of potential causal variants using uniformly processed fine-mapping. The database has six major features: it (i) curates 3052 high-quality, fine-mappable GWAS summary statistics across five human super-populations and 2629 unique traits; (ii) estimates causal probabilities of all genetic variants in GWAS significant loci using three state-of-the-art fine-mapping tools; (iii) maps the reported traits to a powerful ontology MeSH, making it simple for users to browse studies on the trait tree; (iv) incorporates highly interactive Manhattan and LocusZoom-like plots to allow visualization of credible sets in a single web page more efficiently; (v) enables online comparison of causal relations on variant-, gene-Β and trait-levels among studies with different sample sizes or populations and (vi) offers comprehensive variant annotations by integrating massive base-wise and allele-specific functional annotations. CAUSALdb is freely available at http://mulinlab.org/causaldb.
Data processing workflow and overall architecture of CAUSALdb.
Query results from CAUSALdb. (A) Scatter plot of βlog10(P-value) and posterior probability for rs12740374. (B) Heatmap plot of the number of potential causal variants in all causal blocks across CAD GWASs. (C) Scatter plot of βlog10(median P-value) and the number of potential causal variants for CDKN2B located causal block.
Causal block viewer in CAUSALdb. (A) QQ plot of selected GWAS. (B) Manhattan plot of selected GWAS, with highlighted blocks that are clickable. (C) LocusZoom-like plot of the selected causal block from Manhattan plot. (D) Functional annotation panel of a selected variant in LocusZoom-like plot.
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| SNPs in genes encoding for IL-10, TNF-Ξ±, and NFΞΊB p105/p50 are associated with clinical prognostic factors for patients with Hodgkin lymphoma. | Gaiolla RD et al. | β | 2021 | β |
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