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.
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.
|Chiang, Colby; Scott, Alexandra J; Davis, Joe R et al. (2017) The impact of structural variation on human gene expression. Nat Genet 49:692-699|
|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|
|Tan, Meng How; Li, Qin; Shanmugam, Raghuvaran et al. (2017) Dynamic landscape and regulation of RNA editing in mammals. Nature 550:249-254|
|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|
|Yang, Fan; Wang, Jiebiao; GTEx Consortium et al. (2017) Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis. Genome Res 27:1859-1871|
|Agrawal, A; Chou, Y-L; Carey, C E et al. (2017) Genome-wide association study identifies a novel locus for cannabis dependence. Mol Psychiatry :|
|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|
|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|
|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|
|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|
Showing the most recent 10 out of 55 publications