Current Bioinformatics Seminar
Time: 11AM Tuesdays.
Venue: Davis Auditorium and Online
20 October 2026
This is a WEHI only event.Navigating Transcriptomic Complexity in Cancer with Long-Read RNA Sequencing
Jia Wei TanWEHI
Cancer transcriptomes contain substantial hidden complexity, including gene fusions, structural variants and aberrant splicing events that can shape tumour behaviour and treatment response. Long-read RNA sequencing (RNA-seq) captures full-length transcripts and so offers a more complete view of this complexity, but turning long-read data into biological insight requires robust computational methods. In this seminar, I will first present a benchmarking study of fusion detection across eight lung cancer cell lines, each sequenced with four bulk protocols: Illumina, Oxford Nanopore Technologies (ONT) cDNA, ONT direct RNA and PacBio. I will show how protocol choice affects sensitivity, and how PCR duplicates inflate fusion calls in ONT cDNA data. I will then introduce LINDTIE, a computational tool I developed to detect a broad range of aberrant transcripts from long-read RNA-seq, including fusions, non-canonical fusions, transcribed structural variants and novel splice variants. I will describe how it was validated using simulated data, healthy donor samples, cancer cell lines and patient samples. Together, these studies show the potential of long-read RNA-seq to characterise transcriptomic complexity, while highlighting the challenges of extracting biologically meaningful signals from long-read data.