Extensive co-regulation of neighboring genes complicates the use of eQTLs in target gene prioritization

被引:0
作者
Tambets, Ralf [1 ]
Kolde, Anastassia [2 ,3 ]
Kolberg, Peep [1 ]
Love, Michael I. [4 ,5 ]
Alasoo, Kaur [1 ]
机构
[1] Univ Tartu, Inst Comp Sci, Tartu, Estonia
[2] Univ Tartu, Inst Genom, Tartu, Estonia
[3] Univ Tartu, Inst Math & Stat, Tartu, Estonia
[4] Univ N Carolina, Dept Biostat, Chapel Hill, NC USA
[5] Univ N Carolina, Dept Genet, Chapel Hill, NC USA
来源
HUMAN GENETICS AND GENOMICS ADVANCES | 2024年 / 5卷 / 04期
关键词
MENDELIAN RANDOMIZATION; FUNCTIONAL VARIATION; R PACKAGE; TRANSCRIPTOME; COLOCALIZATION; EXPRESSION; ASSOCIATION; DRIVERS; GWAS;
D O I
10.1016/j.xhgg.2024.100348
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Identifying causal genes underlying genome-wide association studies (GWASs) is a fundamental problem in human genetics. Although colocalization with gene expression quantitative trait loci (eQTLs) is often used to prioritize GWAS target genes, systematic benchmarking has been limited due to unavailability of large ground truth datasets. Here, we re-analyzed plasma protein QTL data from 3,301 individuals of the INTERVAL cohort together with 131 eQTL Catalog datasets. Focusing on variants located within or close to the affected protein identified 793 proteins with at least one cis-pQTL where we could assume that the most likely causal gene was the gene coding for the protein. We then benchmarked the ability of cis-eQTLs to recover these causal genes by comparing three Bayesian colocalization methods (coloc.susie, coloc.abf, and CLPP) and five Mendelian randomization (MR) approaches (three varieties of inversevariance weighted MR, MR-RAPS, and MRLocus). We found that assigning fine-mapped pQTLs to their closest protein coding genes outperformed all colocalization methods regarding both precision (71.9%) and recall (76.9%). Furthermore, the colocalization method with the highest recall (coloc.susie - 46.3%) also had the lowest precision (45.1%). Combining evidence from multiple conditionally distinct colocalizing QTLs with MR increased precision to 81%, but this was accompanied by a large reduction in recall to 7.1%. Furthermore, the choice of the MR method greatly affected performance, with the standard inverse-variance-weighted MR often producing many false positives. Our results highlight that linking GWAS variants to target genes remains challenging with eQTL evidence alone, and prioritizing novel targets requires triangulation of evidence from multiple sources.
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页数:12
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