Combining Panel-based and Whole Transcriptome-based Gene Fusion Detection by Long-Read Sequencing

Gene Fusions (GFs), resulting from chromosomal rearrangements, contribute to cancer development and progression. These GFs serve as diagnostic biomarkers and potential therapeutic targets. However, short-read sequencing has limitations including, alignment information often lacks power and specificity to detect GFs and pooling multiple samples can take days in practice. This presents challenges in time-sensitive scenarios where GFs inform cancer diagnosis, treatment, and prognosis. The Children's Hospital of Philadelphia (CHOP) developed a custom short-read RNA sequencing panel, CHOP Cancer Fusion panel, which uses one-sided anchored PCR to interrogate 119 oncogenes with diagnostic GFs. We evaluated adapting this panel through Oxford Nanopore Technologies' (ONT) long-read sequencing for fast-turnaround point-of-care applications. We developed a long-read GF detection pipeline and successfully identified expected fusions from most samples. By adapting a short-read fusion panel to the ONT long-read sequencing platform, we present a workflow for rapid detection of GFs with potential clinical significance.