The second talk in the session I started watching yesterday was by a postdoctoral fellow from UNC. Julie Geyer from the University of North Carolina Chapel Hill School of Medicine described their research. The title of the talk was “Real-time genomic characterization of pediatric acute leukemia using adaptive sampling.” Leukemia is cancer of the blood. Different subtypes of leukemia have specific hallmarks. These genomic signatures can be identified through sequencing. At the chromosome level, copy number variation can be assessed. Fluorescence in situ hybridization is a common way of identifying gene-level changes. For this research, the team started with DNA extraction from samples from the UNC Hospitals. Ligation-based library prep was used. Sequencing on a PromethION flow cell is performed using adaptive sampling. Karyotyping is performed using the number of reads to infer the number of copies. The team has run about thirty samples in a retrospective study. The results are 100% consistent with the gross karyotype results. The group is now optimizing the workflow to improve throughput. The process takes 6-9 hours from sample to results! Geyer summarized the advantages of this workflow in the clinic, including rapid turnaround, the ability to detect structural variations, and opportunities for automation and inclusion of methylation data.
