Sparse regression models for unraveling group and individual associations in eQTL mapping

Wei Cheng, Xiang Zhang, Wei Wang

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

As a promising tool for dissecting the genetic basis of common diseases, expression quantitative trait loci (eQTL) study has attracted increasing research interest. Traditional eQTL methods focus on testing the associations between individual single-nucleotide polymorphisms (SNPs) and gene expression traits. A major drawback of this approach is that it cannot model the joint effect of a set of SNPs on a set of genes, which may correspond to biological pathways. To alleviate this limitation, in this chapter, we propose geQTL, a sparse regression method that can detect both group-wise and individual associations between SNPs and expression traits. geQTL can also correct the effects of potential confounders. Our method employs computationally efficient technique, thus it is able to fulfill large scale studies. Moreover, our method can automatically infer the proper number of group-wise associations. We perform extensive experiments on both simulated datasets and yeast datasets to demonstrate the effectiveness and efficiency of the proposed method. The results show that geQTL can effectively detect both individual and group-wise signals and outperform the state-of-the-arts by a large margin. This book chapter well illustrates that decoupling individual and group-wise associations for association mapping is able to improve eQTL mapping accuracy, and inferring individual and group-wise associations.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages105-121
Number of pages17
DOIs
StatePublished - Jan 1 2020

Publication series

NameMethods in Molecular Biology
Volume2082
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

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    Cheng, W., Zhang, X., & Wang, W. (2020). Sparse regression models for unraveling group and individual associations in eQTL mapping. In Methods in Molecular Biology (pp. 105-121). (Methods in Molecular Biology; Vol. 2082). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-0026-9_8