Plenary speaker Nancy Murphy from Princess Marget in Ontario #NanoporeConf. Tells a story around a specific patient with leukemia where she got the result within 48 hours (I think - could not quite follow the timeline, but it was fast) and changed the path for this patient.
Takes us throw the leukemia pathway - complexity of bringing patients in and treatment, and in particular residual disease; some patients are not chemo-responsive. Mixed Linneage Leukemia is complex due to the translocation which is key to track.
Nanopore allows tracking patients throughout the treatment course. Diagnositic samples + Remission + Relapse. 40 samples; Sequence on PromethION to get both methylation and structural biology
An example: Samples on a Thursday, by Tuesday sequencing and analysis done and this confirmed likely residual disease. Shows that the full workflow can fit inside a diagnostic time course.
They do targeted local reassembly across the breakpoint. Described RACON has COVID lockdown haircut to post lockdown. (not quite sure about this analogy!).
Looked at methylation around the breakpoint. This is more exploratory but Nancy shows a striking change in methylation between samples - some big regions have big swings in methylation (again, not surprising from research - it is more that one can do this inside cancer care)
They can show that the nanopore based methylation calls map to the TCGA data for AML.
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