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PancanQTLv2.0：一个全面的人类癌症表达数量性状基因座资源。

PancanQTLv2.0: a comprehensive resource for expression quantitative trait loci across human cancers.

机构信息

Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN 46202, USA.

Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN 46202, USA.

出版信息

Nucleic Acids Res. 2024 Jan 5;52(D1):D1400-D1406. doi: 10.1093/nar/gkad916.

DOI:10.1093/nar/gkad916
PMID:37870463
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10767806/
Abstract

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.

摘要

表达数量性状基因座 (eQTL) 分析是一种用于研究复杂疾病（包括癌症）遗传变异的强大工具。我们之前开发了一个综合数据库 PancanQTL，该数据库使用癌症基因组图谱 (TCGA) 数据集来描述癌症 eQTL，并将 eQTL 与患者生存和 GWAS 风险变异相关联。在这里，我们展示了一个更新的版本 PancanQTLv2.0（https://hanlaboratory.com/PancanQTLv2/），该版本在 eQTL 因果变异的精细映射方面取得了进展，更新了与 GWAS 连锁不平衡区域重叠的 eQTL，并鉴定了与药物反应和免疫浸润相关的 eQTL。通过精细映射分析，我们确定了 58747 个精细映射 eQTL 可信集，为癌症基因调控提供了机制见解。我们进一步整合了最新的 GWAS 目录，并确定了 eQTL 与现有 GWAS 基因座之间总共 84592135 个连锁关联，与上一版本相比，这代表了显著的约 50 倍增加。此外，PancanQTLv2.0 揭示了 eQTL 与药物反应之间的 659516 个关联，并确定了 eQTL 与免疫细胞丰度之间的 146948 个关联，为癌症治疗中的 eQTL 提供了潜在的临床应用价值。PancanQTLv2.0 扩展了用于研究人类癌症中基因表达调控的资源，推动了癌症研究和精准肿瘤学的发展。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5e8/10767806/887a3646c064/gkad916fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5e8/10767806/6b77ef2223bf/gkad916figgra1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5e8/10767806/67eb11ddeaa3/gkad916fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5e8/10767806/887a3646c064/gkad916fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5e8/10767806/6b77ef2223bf/gkad916figgra1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5e8/10767806/67eb11ddeaa3/gkad916fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5e8/10767806/887a3646c064/gkad916fig2.jpg

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