Gene fusion and variant-aware isoform detection with functional prediction from long-read RNA sequencing

Presenter: Colette Felton

Description: Although most cancer variant profiling is done with short-read-based methods, many cancers are driven by structural variants that are difficult to detect with these methods. Our current approach to understanding driver mutations is also limited to single variants and rarely considers the context in which they are expressed. Alterations in the expression and splicing of genes containing variants can both impact their tumorigenicity and allow them to develop resistance to therapies. We present FLAIR3, which generates a custom transcriptome from long-read RNA sequencing and identifies SNVs, insertions, deletions, and gene fusions from alignment to this transcriptome. We show that this improves accuracy above alignment to the genome or annotated transcripts. FLAIR3 then integrates these variants with the transcripts to predict functional changes to the amino acid sequence. We apply this approach to patient-derived osteosarcoma cell lines, a cancer whose pathology is driven by complex structural variation. In these samples, we identify more complex changes to previously identified amplified drivers such as alternative splicing of MYC and alternative splicing of a gene fusion in CCNE1. We also identify a novel set of actionable cancer gene alterations not previously detected by short-read methods. This includes a large deletion in KEAP1 and a number of novel gene fusions, including TP53 and other genes fused with intergenic regions and a complex 4-locus fusion in NOTCH1 not detected by any preexisting tools. This analysis shows that long-read RNA sequencing can detect novel variants in actionable cancer genes and that integrating splicing and variant alterations provides the most complete picture of gene alterations in cancer.
Bio: Colette Felton is a Postdoctoral Scholar at the University of California, Santa Cruz in the Angela Brooks lab. She primarily develops tools to work with long-read sequencing data. This includes a tool for using long read sequencing to integrate variant and isoform detection for the functional prediction of cancer-related alterations from long-read RNA sequencing and work accurately detecting chromatin structure on the single-molecule level from long-read DNA sequencing. She is particularly interested in implementing these tools to identify mechanisms of resistance to treatment in cancer.

Enhancing Physiology: How transcriptional enhancers are regulated in development and adaptation

Presenter: Matt Romero
Description:Skeletal muscle is the largest organ by mass and constitutes ~40% of our body weight. It has an amazing ability to regenerate and adapt to almost any imposed demand. Much has been revealed about the genes that are responsible for the development and regeneration of muscle. More recently the genes responsible for adaptation have begun to be uncovered, but a large gap remains regarding how these genes are transcriptionally controlled by their enhancers and how these enhancers communicate to their cognate promoters in three-dimensions. The Romero lab focuses on describing chromatin dynamics and enhancer usage in human skeletal muscle development and introduce how enhancers are involved in skeletal muscle adaptation.
Bio: Matt Romero was born and raised in southeastern New Mexico where he attended New Mexico State University and studied exercise physiology. The majority of Matt’s graduate research has focused on the molecular mechanisms of exercise signaling in skeletal muscle. Matt’s postdoctoral work focused on chromatin folding during human skeletal muscle development. Outside of the lab you can find Matt spending time with his wife and daughter, attempting to lift heavy weights in the gym and/or overanalyzing basketball schemes and movies.

Hosted by: Nader Pourmand / BME