Our group aims to understand the mechanisms of alternative RNA splicing regulation and splicing dysregulation in cancer. Short-read, high-throughput cDNA sequencing (RNA-Seq) has revolutionized our ability to profile RNA splicing; however, this approach cannot capture the full complexity of RNA transcripts. First, “RNA-Seq” should, more appropriately, be called cDNA-Seq—it is not sequencing RNA directly. Second, short-reads limit our ability to accurately identify and quantify full-length RNA isoforms. For a more comprehensive characterization of alternative transcript isoform expression, we have been developing computational approaches to analyze long-read nanopore sequencing data. I will present a study to identify differentially expressed isoforms from nanopore cDNA sequencing of isogenic cell lines with and without a mutation in U2AF1, which is a recurrently mutated splicing factor in cancer. I will also present our analysis of native RNA sequencing of the GM12878 cell line, as part of the Nanopore RNA Consortium. Utilizing the full benefit of directly sequencing full-length RNA transcripts, we identified alternative transcript isoforms and their association with allele expression, RNA modifications, and poly(A) tail length.
Ami Bhatt, Assistant Professor of Medicine (Hematology) and of Genetics, Stanford University
Pre-Seminar April 9th, 2018 at 4:00 PM in Clark S361