| URL: | https://hanlaboratory.com/PancanQTLv2 |
| Full name: | PancanQT |
| Description: | PancanQTLv2.0 is the updated database of PancanQTL. In PancanQTLv2.0, we have made significant advancements by identifying credible sets of causal variants for eQTLs, updating numerous eQTLs that overlap with GWAS linkage disequilibrium (LD) regions, and identifying eQTLs that relate to pharmacogenomics and immune infiltration in human cancers |
| Year founded: | 2018 |
| Last update: | 2024 |
| Version: | v2.0 |
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Manual:
Accessible
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| Country/Region: | United States |
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| University/Institution: | University of Texas Health Science Center at Houston |
| Address: | Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA |
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| Province/State: | Indiana |
| Country/Region: | United States |
| Contact name (PI/Team): | Leng Han |
| Contact email (PI/Helpdesk): | leng.han@uth.tmc.edu |
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PancanQTLv2.0: a comprehensive resource for expression quantitative trait loci across human cancers. [PMID: 37870463]
Expression quantitative trait locus (eQTL) analysis is a powerful tool used to investigate genetic variations in complex diseases, including cancer. We previously developed a comprehensive database, PancanQTL, to characterize cancer eQTLs using The Cancer Genome Atlas (TCGA) dataset, and linked eQTLs with patient survival and GWAS risk variants. Here, we present an updated version, PancanQTLv2.0 (https://hanlaboratory.com/PancanQTLv2/), with advancements in fine-mapping causal variants for eQTLs, updating eQTLs overlapping with GWAS linkage disequilibrium regions and identifying eQTLs associated with drug response and immune infiltration. Through fine-mapping analysis, we identified 58 747 fine-mapped eQTLs credible sets, providing mechanic insights of gene regulation in cancer. We further integrated the latest GWAS Catalog and identified a total of 84 592 135 linkage associations between eQTLs and the existing GWAS loci, which represents a remarkable ∼50-fold increase compared to the previous version. Additionally, PancanQTLv2.0 uncovered 659516 associations between eQTLs and drug response and identified 146948 associations between eQTLs and immune cell abundance, providing potentially clinical utility of eQTLs in cancer therapy. PancanQTLv2.0 expanded the resources available for investigating gene expression regulation in human cancers, leading to advancements in cancer research and precision oncology. |
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PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types. [PMID: 29036324]
Expression quantitative trait locus (eQTL) analysis, which links variations in gene expression to genotypes, is essential to understanding gene regulation and to interpreting disease-associated loci. Currently identified eQTLs are mainly in samples of blood and other normal tissues. However, no database comprehensively provides eQTLs in large number of cancer samples. Using the genotype and expression data of 9196 tumor samples in 33 cancer types from The Cancer Genome Atlas (TCGA), we identified 5 606 570 eQTL-gene pairs in the cis-eQTL analysis and 231 210 eQTL-gene pairs in the trans-eQTL analysis. We further performed survival analysis and identified 22 212 eQTLs associated with patient overall survival. Furthermore, we linked the eQTLs to genome-wide association studies (GWAS) data and identified 337 131 eQTLs that overlap with existing GWAS loci. We developed PancanQTL, a user-friendly database (http://bioinfo.life.hust.edu.cn/PancanQTL/), to store cis-eQTLs, trans-eQTLs, survival-associated eQTLs and GWAS-related eQTLs to enable searching, browsing and downloading. PancanQTL could help the research community understand the effects of inherited variants in tumorigenesis and development. |