JAFFAL: detection of fusion genes with Oxford Nanopore transcriptome sequencing

Nadia Davidson

Nadia Davidson, Peter MacCallum Cancer Centre, Australia

Abstract

Short-read transcriptome sequencing has expanded our knowledge of fusion genes that drive cancer. However, fusion-finding algorithms designed for short reads do not work on data from Oxford Nanopore Technologies. JAFFAL is a new method to identify fusions from long-read transcriptome sequencing. We validated JAFFAL using simulation, patient, and cell line data. By applying JAFFAL, we show that direct RNA sequencing is free from chimeric molecules generated during cDNA library preparation, long reads capture fusion transcript splicing, and fusions can be detected in single cells. JAFFAL is available at https://github.com/Oshlack/JAFFA/wiki

 

Bio

Dr. Nadia Davidson is a senior postdoctoral researcher in the bioinformatics group of Prof. Alicia Oshlack at the Peter MacCallum Cancer Centre in Melbourne, Australia. She develops methods for RNA sequencing data analysis. Naida has built novel methods for cancer research, such as fusion and transcribed structural variant finders and her research has informed practices for transcriptome analysis in non-model organisms. She received her Ph.D. in Physics from the University of Melbourne in 2011.