Applying meta-analysis to genotype-tissue expression data from multiple tissues to identify eQTLs and increase the number of eGenes

Dat Duong, a graduate student in our lab, developed a novel method that will help find more eQTLs and eGenes in gene expression data from many tissues. A paper presenting his method is published in an upcoming issue of Bioinformatics.

Genome-wide association studies (GWAS) seek links between single-nucleotide polymorphisms (SNPs) and traits or diseases. SNPs are the most commonly occurring sources of variation in the human genome. Many SNPs identified by GWAS are located in intergenic regions, stretches of DNA sequences located between genes. SNPs identified in these primarily noncoding regions often do not have an obvious relationship to the disease phenotype. Other lines of evidence, such as gene expression, are required to explore this relationship and learn about disease function.

Gene expression, an intermediate phenotype between a causal SNP and a disease, can be used to interpret positive results produced by a GWAS. Common data types include expression quantitative trait loci (eQTLs), genetic variants associated with gene expression in particular tissue types, and eGenes, genes whose expression levels are associated with genetic variants. Both eQTL studies and GWAS focus on SNPs, but eQTL studies may provide biological insights into the disease development mechanism. For this reason, we pay special attention to the variants that are eQTLs or eGenes and have strong association signals identified by GWAS.

Multi-tissue gene expression datasets like the Gene Tissue Expression (GTEx) data are used to find eQTLs and eGenes. However, these datasets have small sample sizes in some tissues. Many meta-analysis methods have been designed to increase power for finding eQTLs and eGenes by combining gene expression data across many tissues However, these techniques cannot scale to datasets containing many tissue types, like the GTEx data. Such methods also ignore a biological principle that the same variant may be associated with the same gene across similar tissues.


Venn diagram of the numbers of eGenes found by existing methods and RECOV, along with correlation matrices comparing methods. For more information, read our full paper.

To leverage the analytical power of eQTLs and eGenes in association studies, Duong and his team developed a new meta-analysis method named RECOV. Based on the principle that a SNP may have similar effect on the same gene in related tissues, RECOV can be applied to large gene expression datasets and can analyze all 44 tissues present in the GTEx data.

In our Bioinformatics paper, we use simulated datasets to show that RECOV has a correct false positive rate. When applied to real multi-tissue expression data from the GTEx dataset, RECOV detects 3% more eGenes than previous methods. RECOV is a general framework for meta-analysis that can be used with any COV matrix. We hope this software will be used by other researchers in the scientific community!

RECOV was developed by Dat Duong. The source code for RECOV is freely available at:

Our paper can be downloaded at Bioinformatics:


The full reference for our paper is:
Duong, D., Gai, L., Snir, S., Kang, E.Y., Han, B., Sul, J.H. and Eskin, E., 2017. Applying meta-analysis to Genotype-Tissue Expression data from multiple tissues to identify eQTLs and increase the number of eGenes. Bioinformatics, 33(14), pp.i67-i74.

Incorporating prior information into association studies

Genome-wide association studies (GWAS) seek to identify genetic variants involved in specific traits. GWAS are advantageous for linking variants with traits, because they interrogate the genome in a uniform way. In other words, they examine the whole genome without a preconceived notion of where the associations may lie.

However, we now know a lot about the putative function of genetic variants due to tremendous progress in functional genomics. In many cases, we even know which variants are more likely to be involved in disease when compared to others. Advancements in our understanding of functional genomics motivate the strategic incorporation of prior information in GWAS.

Our group has been interested in this problem for many years. One challenge to addressing this problem is that the widely utilized approach for GWAS involves evaluating an association statistic at each single nucleotide polymorphism (SNP), and these methods take into account only one SNP at a time. The results are then adjusted for multiple testing, and an association is identified if a statistic exceeds a certain threshold. This approach can be described as a frequentist approach. On the other hand, one can incorporate prior information on which SNPs are likely to be the causal variants affecting the trait. This approach is inherently a Bayesian concept. Reconciling these two approaches is not straightforward.

Average power under varying relative risks. For more information, see our paper.

In a 2008 paper published in Genome Research, our group proposed a modification of the multiple testing framework to address this problem. Instead of using the same specific threshold for all of the association statistics, we use a different threshold for each association statistic, where the thresholds are adjusted based on the prior information. Our method takes advantage of the correlation structure by considering multiple markers within a region. In our paper, we demonstrate how to set the thresholds in order to optimally utilize prior information and maximize statistical power.

Using prior information in genetic association studies increases power over traditional association studies while maintaining the same overall false-positive rate. Compared to standard methods, our approach is equally simple to apply to association studies, produces interpretable results as p-values, and is optimal in its use of prior information in regards to statistical power.

In 2012, we extended this work to use only tag SNPs for the putative causal variant. This project was developed by Gregory Darnell (then UCLA undergraduate, now PhD student at Princeton University), Dat Duong (then UCLA undergraduate, now UCLA PhD student), and Buhm Han.

More recently, we have applied this framework to incorporate functional information in analysis of eQTL data. In this case, incorporating genomic annotation of variants significantly increases the statistical power of existing eQTL methods and detects more eGenes in comparison to standard approaches. Read the blog post on this paper, and download the full article.

For more information on our general approach, see our paper, which is available for download through Bioinformatics:
In addition, the open source implementation of our 2012 paper, MASA, which was developed by Greg Darnell and Dat Duong, is freely available for download at

The full citations to our papers on this topic are:

Darnell, Gregory; Duong, Dat ; Han, Buhm ; Eskin, Eleazar

Incorporating prior information into association studies. Journal Article

In: Bioinformatics, 28 (12), pp. i147-i153, 2012, ISSN: 1367-4811.

Abstract | Links | BibTeX

Eleazar Eskin. “Increasing Power in Association Studies by using Linkage Disequilibrium
Structure and Molecular Function as Prior Information.” Genome Research.
18(4):653-60 Special Issue Proceedings of the 12th Annual Conference on Research
in Computational Biology (RECOMB-2008), 2008.

ZarLab goes to Vancouver for ASHG!


Last week many members of our group traveled to Vancouver, British Columbia, for the annual meeting of the American Society of Human Genetics. The 66th Annual Meeting, which took place October 18-22, 2016, featured over 3000 talks, workshops, and poster presentations on topics such as bioinformatics and computational methods, developmental genetics and gene function, cancer and cardiovascular diseases, evolutionary and population genetics, and genetic counseling.

ZarLab contributed 8 poster presentations and one research talk. Serghei Mangul discussed his recent work on dumpster-diving techniques in a talk titled, “Comprehensive analysis of RNA-sequencing to find the source of every last read across 544 individuals from 53 tissues,” as part of the Interpreting the Transcriptome in Health and Disease symposium. You can view his slides here:

ZarLab in Vancouver!

ZarLab in Vancouver!

Recent alumni Farhad Hormozdiari received a Reviewers’ Choice ribbon for his poster titled, “Joint fine mapping of GWAS and eQTL detects target gene and relevant tissue.” Only the top 10% of posters by topic receive this honor, as determined by the reviewers’ scores of the submitted abstracts. Congratulations, Farhad!

Other posters presented by members of our group:

  • Prevalence of allelic heterogeneity in complex traits. Eleazar Eskin
  • Modeling the covariance of effect sizes in a meta-analysis. Dat Duong
  • Estimating regional heritability in the presence of linkage disequilibrium. Lisa Gai
  • linear mixed models for quantitative traits in health-system scale data. Michael Bilow
  • Utilizing allele specific expression to identify cis-regulatory variants. Jennifer Zou
  • Haplotype-based predictors for complex trait association. Rob Brown
  • Repeat elements expression profile across different tissues in GTEx samples. Harry Yang