Using RNA-Seq Data to Study the Genetic Basis of Cancer Development

• Activity Number: 527
• Type: Topic Contributed
• Date/Time: Wednesday, August 7, 2013 : 10:30 AM to 12:20 PM
• Sponsor: Biometrics Section
• Author(s): Wei Sun*+ and Yun Li and Charles Perou
• Companies: UNC Chapel Hill and The University of North Carolina and UNC Chapel Hill
• Keywords: RNA-seq ; ASE ; TCGA ; eQTL ; association ; Cancer

Abstract

In a diploid individual, each gene has two alleles, the paternal allele and the maternal allele. The transcript abundance of each allele is referred to as Allele-Specific Expression (ASE). ASE cannot be measured by gene expression microarrays, but they are available from RNA-seq data. Using RNA-seq data from The Cancer Genome Atlas (TCGA) project, we seek to identify genes whose total expression and ASE are altered in tumor tissue, and associate such allelic imbalanced expression with DNA variations in either germline and tumor tissues.