London Calling 2023: Potential clinical utility of long-read sequencing in myeloid neoplasms

Recurrent gene fusions are known drivers of disease pathophysiology in acute and chronic myeloid leukemia. Rapid identification of these fusion genes helps stratify disease by risk and assists with therapy choice. Precise molecular diagnosis in low-and-middle-income countries is challenging given the complexity of assays, need for trained technical support, and availability of reliable electricity. Even in developed countries, fusion detection requires a 7–10-day turnaround. We developed a long-read sequencing DNA assay designed using CRISPR guides to enrich for single molecules of long genomic DNA for nanopore sequencing and successfully detected fusion genes in cell lines and primary research specimens (e.g. BCR–ABL1, PML–RARA, CBFB–MYH11, KMT2A–AF4). We also successfully developed a  cloud-based bioinformatics workflow with novel custom fusion finder software, Biodepot Fusion Finder. We detected fusion genes or confirmed the absence of fusions in 95% of cell lines and primary patient samples with the expected breakpoints. With optimized wet bench chemistry, sequencing workflow, and cloud-based bioinformatics data analytics, fusion detection in patient samples could be performed in under eight hours from sample draw to fusion confirmation.