PancanQTLv2.0: a comprehensive resource for expression quantitative trait loci across human cancers-Reference-Cited by-同舟云学术

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

Published:2023-10-23 Issue:D1 Volume:52 Page:D1400-D1406
ISSN:0305-1048
Container-title:Nucleic Acids Research
language:en
Short-container-title:

Author:

Chen Chengxuan¹²³^ORCID,Liu Yuan¹²³,Luo Mei¹²,Yang Jingwen¹²,Chen Yamei¹²,Wang Runhao¹²,Zhou Joseph³,Zang Yong²,Diao Lixia⁴,Han Leng¹²³^ORCID

Affiliation:

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

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

3. Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University , Houston , TX 77030 , USA

4. Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center , Houston , TX 77030 , USA

Abstract

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.

Funder

National Institutes of Health

Publisher

Oxford University Press (OUP)

Subject

Genetics

Link

https://academic.oup.com/nar/article-pdf/52/D1/D1400/55040731/gkad916.pdf

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