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 #
1R01MH090951-01
Application #
7935141
Study Section
Special Emphasis Panel (ZRG1-GGG-A (52))
Program Officer
Bender, Patrick
Project Start
2010-09-17
Project End
2012-07-31
Budget Start
2010-09-17
Budget End
2011-07-31
Support Year
1
Fiscal Year
2010
Total Cost
$338,085
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
Calabrese, Gina M; Mesner, Larry D; Stains, Joseph P et al. (2017) Integrating GWAS and Co-expression Network Data Identifies Bone Mineral Density Genes SPTBN1 and MARK3 and an Osteoblast Functional Module. Cell Syst 4:46-59.e4
Picardi, Ernesto; D'Erchia, Anna Maria; Lo Giudice, Claudio et al. (2017) REDIportal: a comprehensive database of A-to-I RNA editing events in humans. Nucleic Acids Res 45:D750-D757
Liu, C; Bousman, C A; Pantelis, C et al. (2017) Pathway-wide association study identifies five shared pathways associated with schizophrenia in three ancestral distinct populations. Transl Psychiatry 7:e1037
McCoy, Rajiv C; Wakefield, Jon; Akey, Joshua M (2017) Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression. Cell 168:916-927.e12
Tsai, Teresa; Veitinger, Sophie; Peek, Irina et al. (2017) Two olfactory receptors-OR2A4/7 and OR51B5-differentially affect epidermal proliferation and differentiation. Exp Dermatol 26:58-65
Collado-Torres, Leonardo; Nellore, Abhinav; Kammers, Kai et al. (2017) Reproducible RNA-seq analysis using recount2. Nat Biotechnol 35:319-321
Benítez-Buelga, Carlos; Baquero, Juan Miguel; Vaclova, Tereza et al. (2017) Genetic variation in the NEIL2 DNA glycosylase gene is associated with oxidative DNA damage in BRCA2 mutation carriers. Oncotarget 8:114626-114636
Tukiainen, Taru; Villani, Alexandra-Chloé; Yen, Angela et al. (2017) Landscape of X chromosome inactivation across human tissues. Nature 550:244-248

Showing the most recent 10 out of 58 publications