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. 2018 Jan 4;46(D1):D971-D976.
doi: 10.1093/nar/gkx861.

PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types

Jing Gong  1   2 , Shufang Mei  1 , Chunjie Liu  2   3 , Yu Xiang  2 , Youqiong Ye  2 , Zhao Zhang  2 , Jing Feng  2 , Renyan Liu  4 , Lixia Diao  5 , An-Yuan Guo  3 , Xiaoping Miao  1 , Leng Han  2
Affiliations

PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types

Jing Gong et al. Nucleic Acids Res. .

Abstract

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.

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Figures

Figure 1.
Figure 1.
Identification of eQTLs in PancanQTL database. (A) Genotyping data collection and processing. (B) Covariates analyzed in eQTL mapping. (C) Gene expression data collection and processing. (D) eQTL analyses of cis-eQTLs, trans-eQTLs, survival-associated eQTLs and GWAS-related eQTLs.
Figure 2.
Figure 2.
Overview of PancanQTL database. (A) Four modules in PancanQTL, including cis-eQTLs, trans-eQTLs, survival-associated eQTLs and GWAS-related eQTLs. (B) Advanced search box in PancanQTL. (C) Example of an eQTL boxplot in cis-eQTL page. (D) Example of a KM plot in survival-eQTL page.
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