Workshop in Biostatistics


M112 Alway Building, Medical Center

(next to the Dean's courtyard)

DATE: January 19, 2017
TIME: 1:30 - 2:50 pm
TITLE: High-throughput and full-length characterization of transcript isoforms and their function
SPEAKER: Angela Brooks, Assistant Professor of Biomolecular Engineering
Faculty of the UCSC Genomics Institute
University of California, Santa Cruz


Although over 95% of human genes are alternatively processed into multiple transcript isoforms, our current short-read sequencing methods are limited in their ability to identify and quantify full-length transcripts due to the complexity of alternative isoforms. Moreover, even if we were able to accurately quantify full-length transcripts, there is limited functional evidence of how isoform changes result in changes in function for the vast majority of genes. Our lab is developing computational methods for full-length isoform-level expression analysis using nanopore sequencing technology and developing high-throughput experimental characterization of the functional impact of isoform changes on gene function. A complete characterization of transcript isoforms is critical to the biomedical field as splicing has been shown to be a major source of expression differences linked to genetic differences between individuals and splicing is known to be altered in human disease, such as cancer.

Suggested readings:

Oikonomopoulos, et al. 2016, “Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations”:

Berger, Brooks, Wu, et al. 2016, “High-throughput Phenotyping of Lung Cancer Somatic Mutations”.