Academic Commons

Articles

HT-eQTL: integrative expression quantitative trait loci analysis in a large number of human tissues

Li, Gen; Jima, Dereje; Wright, Fred A.; Nobel, Andrew B.

Background
Expression quantitative trait loci (eQTL) analysis identifies genetic markers associated with the expression of a gene. Most existing eQTL analyses and methods investigate association in a single, readily available tissue, such as blood. Joint analysis of eQTL in multiple tissues has the potential to improve, and expand the scope of, single-tissue analyses. Large-scale collaborative efforts such as the Genotype-Tissue Expression (GTEx) program are currently generating high quality data in a large number of tissues. However, computational constraints limit genome-wide multi-tissue eQTL analysis.


Results
We develop an integrative method under a hierarchical Bayesian framework for eQTL analysis in a large number of tissues. The model fitting procedure is highly scalable, and the computing time is a polynomial function of the number of tissues. Multi-tissue eQTLs are identified through a local false discovery rate approach, which rigorously controls the false discovery rate. Using simulation and GTEx real data studies, we show that the proposed method has superior performance to existing methods in terms of computing time and the power of eQTL discovery.


Conclusions
We provide a scalable method for eQTL analysis in a large number of tissues. The method enables the identification of eQTL with different configurations and facilitates the characterization of tissue specificity.

Files

  • thumnail for 12859_2018_Article_2088.pdf 12859_2018_Article_2088.pdf application/pdf 1.08 MB Download File

Also Published In

Title
BMC Bioinformatics
DOI
https://doi.org/10.1186/s12859-018-2088-3

More About This Work

Published Here
March 16, 2018

Notes

Expression quantitative trait loci, Genotype-tissue expression project, Empirical Bayes, Tissue specific, Local false discovery rate

Academic Commons provides global access to research and scholarship produced at Columbia University, Barnard College, Teachers College, Union Theological Seminary and Jewish Theological Seminary. Academic Commons is managed by the Columbia University Libraries.