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Full-length alternative transcript isoform analysis using long-read nanopore sequencing

April 11, 2019 4:00 PM to 5:00 PM
Clark Center Seminar Room S360
James H. Clark Center 318 Campus Drive West, Stanford, CA 94305
Event Type: 

"Full-length alternative transcript isoform analysis using long-read nanopore sequencing"

Stanford Bio-X Frontiers in Interdisciplinary Biosciences Seminar
ANGELA BROOKS, UNIVERSITY OF CALIFORNIA, SANTA CRUZ


Abstract:

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.

April 11th, 2019 at 4:00 PM in Clark Center Seminar Room S360


Hosted by:

Ami Bhatt, Assistant Professor of Medicine (Hematology) and of Genetics, Stanford University

Pre-Seminar April 9th, 2018 at 4:00 PM in Clark S361