Imputing the Transcriptome in Inaccessible Tissues in and Beyond the GTEx Project

• Activity Number: 428
• Type: Contributed
• Date/Time: Tuesday, August 11, 2015 : 2:00 PM to 3:50 PM
• Sponsor: Biometrics Section
• Author(s): Jiebiao Wang* and Eric Gamazon and Barbara Stranger and Hae Kyung Im and Nancy Cox and Dan L. Nicolae and Lin S. Chen
• Companies: The University of Chicago and Vanderbilt University and The University of Chicago and The University of Chicago and Vanderbilt University and The University of Chicago and The University of Chicago
• Keywords: imputation ; transcriptome ; robust ; eQTL

Abstract

Gene expression and its regulation can vary substantially across tissues. The accessibility of certain human tissues limits the feasibility of large-scale expression studies on those tissues. In order to generate new knowledge about gene expression across human tissues, the Genotype-Tissue Expression (GTEx) project collected transcriptome data in a wide variety of tissues from a large number of donors. In this work, we analyze data from nine selected model tissues in the GTEx pilot project, and we show that transcriptome data from inaccessible/uncollected tissues can be imputed by harnessing the rich information in GTEx. We propose a multi-tissue imputation approach "Robust Imputation of Multi-tissue Expression incorporating EQTLs" (RIMEE), and evaluate its performance. We suggest that using GTEx data as a reference, it is feasible to impute expression in inaccessible/uncollected tissues in future multi-tissue gene expression studies.