Julie Geyer from The University of North Carolina at Chapel Hill presented at London Calling 2024 on “Real-time genomic characterization of pediatric acute leukemia using adaptive sampling. They explained that leukemia can be acute myeloid leukemia or acute lymphoblastic leukemia. The presence of immature cells is typically performed with karyotype analysis, fluorescence in-situ hybridization (FISH), or targeted sequencing, PCR, or microarrays. Geyer and the team wanted to recapitulate these results using sequencing. For this, they obtained samples from their biobank, extracted DNA, prepared for sequencing, and loaded onto their PromethION cells. Adaptive sampling was used to enrich for ~60 genes involved with leukemia. The number of reads obtained for different chromosomes can be used to infer that there are extra copies. Gene fusions can be detected. The team ran thirty eight samples and 95% consistency with classifications. The retrospective sampling produced only two cases that needed more analysis. Next, real-time classification from blood samples was performed. The results from sequencing were obtained faster than typical karyotyping. Fourteen real-time samples were analyzed, and ~93% were consistent in gross karyotype abnormalities and fusion detection. Only one sample, due to low Blast cell count, was inconclusive. Geyer noted that this system offers rapid, cost-effective, and reliable analyses. The team is working on automating karyotyping and downsampling to reduce costs and methylation data. It was good to learn how nanopore sequencing is used at UNC!
