Abstract

In this project we propose to develop statistical methods for the analysis of microarray and RNA-sequencing data for expression QTL mapping. Our project is designed to address a number of important methodological issues, with particular relevance to the forthcoming GTEx study. We propose to extend a Bayesian hierarchical model for cis-eQTL mapping to enable simultaneous mapping in multiple tissues, and to improve the use of external biological information. We also propose to develop methods to allow more sensitive detection of trans-acting eQTLs that are correlated with networks or modules of co-regulated genes. Finally, we aim to develop methods for estimating transcript abundances from RNA sequencing data, for use in QTL mapping.

Public Health Relevance

The purpose of this project is to develop new tools for analyzing and interpreting eQTL (expression quantitative trait loci) studies. We will develop analytical tools for both microarray-based and RNA-sequence-based measurements of gene expression.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of Mental Health (NIMH)
Type
Research Project (R01)
Project #
5R01MH090951-02
Application #
8144812
Study Section
Special Emphasis Panel (ZRG1-GGG-A (52))
Program Officer
Bender, Patrick
Project Start
2010-09-17
Project End
2013-07-31
Budget Start
2011-08-01
Budget End
2013-07-31
Support Year
2
Fiscal Year
2011
Total Cost
$334,704
Indirect Cost

  Institution

Name
University of Chicago
Department
Genetics
Type
Schools of Medicine
DUNS #
005421136
City
Chicago
State
IL
Country
United States
Zip Code
60637

  Publications

Zhang, Mingfeng; Lykke-Andersen, Soren; Zhu, Bin et al. (2018) Characterising cis-regulatory variation in the transcriptome of histologically normal and tumour-derived pancreatic tissues. Gut 67:521-533
Agrawal, A; Chou, Y-L; Carey, C E et al. (2018) Genome-wide association study identifies a novel locus for cannabis dependence. Mol Psychiatry 23:1293-1302
Gudmundsson, Julius; Thorleifsson, Gudmar; Sigurdsson, Jon K et al. (2017) A genome-wide association study yields five novel thyroid cancer risk loci. Nat Commun 8:14517
Dolan, M Eileen; El Charif, Omar; Wheeler, Heather E et al. (2017) Clinical and Genome-Wide Analysis of Cisplatin-Induced Peripheral Neuropathy in Survivors of Adult-Onset Cancer. Clin Cancer Res 23:5757-5768
Varma, V R; Varma, S; An, Y et al. (2017) Alpha-2 macroglobulin in Alzheimer's disease: a marker of neuronal injury through the RCAN1 pathway. Mol Psychiatry 22:13-23
Mohammadi, Pejman; Castel, Stephane E; Brown, Andrew A et al. (2017) Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change. Genome Res 27:1872-1884
Peckham-Gregory, Erin C; Chakraborty, Rikhia; Scheurer, Michael E et al. (2017) A genome-wide association study of LCH identifies a variant in SMAD6 associated with susceptibility. Blood 130:2229-2232
Saha, Ashis; Kim, Yungil; Gewirtz, Ariel D H et al. (2017) Co-expression networks reveal the tissue-specific regulation of transcription and splicing. Genome Res 27:1843-1858
Mercader, Josep M; Liao, Rachel G; Bell, Avery D et al. (2017) A Loss-of-Function Splice Acceptor Variant in IGF2 Is Protective for Type 2 Diabetes. Diabetes 66:2903-2914
Bai, Xue; Mangum, Kevin D; Dee, Rachel A et al. (2017) Blood pressure-associated polymorphism controls ARHGAP42 expression via serum response factor DNA binding. J Clin Invest 127:670-680

Showing the most recent 10 out of 58 publications