Cecilia C.S. Yeung & Olga Sala-Torra from the Fred Hutchinson Cancer Center presented the session “Potential clinical utility of long-read sequencing in myeloid neoplasms.” They are both clinicians and saw the potential of long-read sequencing for detection of myeloid neoplasms. The assay has the potential to rapid detect cytogenetic aberrations. Sala-Torra spoke about how fusions could be detected. The approach they used was targeted enrichment with CRISPR-Cas9. The team designed targets involved in translocations in myeloid leukemia. Sala-Torra and colleagues partnered with BioDepot-workflow-builder to package a GPU-enabled workflow. There is a cloud portal and Docker package. Sala-Torra shared a screen capture of the workflow and how it uses drag-and-drop workflow elements and a play button to run several packages linked together. The team implemented the BwB pipeline with blood specimens. The time spent basecalling and sequencing was described for several cell lines and primary specimens… some samples were processed in hours! Yeung spoke about their work in the Fred Hutchinson Cancer Center work in Uganda. There is a need to screen for heme malignancy for patients in regions in Africa. Yeung noted barriers include access to pathology and rapid diagnosis. Yeung and team wanted to detect myeloid leukemia with some of the updated guidelines. The team used long-read sequencing in several patient cases. In one case, they were able to detect a precise breakpoint. A second patient benefited from long-read sequencing for diagnosis and treatment. Case 3 was a mystery that was solved with long-read sequencing: an intronic insertion was detected! A TTMV virus was detected! This virus infects many and this case revealed that the viral product in this case led to disease. Yeung concluded that only three unique reads at a good quality passing QC parameters can confirm a fusion. I am impressed by the speed of the targeted enrichment and bioinformatics workflow the group designed.
