Current Bioinformatics Seminar
Time: 11AM Tuesdays.
Venue: Davis Auditorium and Online
24 June 2025
Back to the future! Using custom probes to detect cancer fusion transcripts in 10X Flex single-cell
Jovana MaksimovicPeter MacCallum Cancer Centre
Gene fusions are caused by chromosomal rearrangements such as translocations and can drive tumor initiation, progression, and resistance to therapy. It is estimated that they drive approximately 16.5% of all cancers, and are particularly prevalent in haematological malignancies. Bulk RNA sequencing (RNA-seq) is a powerful tool for identifying fusion transcripts that can be used clinically to guide diagnosis and treatment. However, it cannot determine which cell types express gene fusions or how their expression profiles differ from other cells. Detecting fusions at the single-cell level is of growing interest, but high noise, technical artifacts, cost and throughput are limiting factors in current fusion detection approaches that require full-length transcript protocols, such as Smart-seq or long-reads. Here, we develop an approach using the 10X Flex single-cell RNA-seq protocol to detect fusion expression at single-cell resolution. 10X Flex uses a probes to detect the expression of >18,000 protein-coding genes and allows for the design of custom probes to detect expression of features of interest. Our fusion detection approach leverages the sensitivity of bulk RNA-seq for the design of custom probes that target the fusion transcript breakpoint allowing their detection along with the transcriptome. We show detection of fusion transcripts in MCF7 cells and 11 B-ALL bone marrow samples and demonstrate biological insights that can be gained using the fusion data.