Real-time genomic characterisation of paediatric acute leukaemia using adaptive sampling
Most cancer treatment centres globally are in low and middle-income countries (LMICs), often without access to reliable cytogenetic testing approaches. Geyer et al. trialled targeted nanopore sequencing as an accessible, scalable approach to improve genomic classification of acute leukaemia.
Key points:
- Peripheral blood or bone marrow from 54 paediatric acute leukaemia cases with diverse genomic subtypes were analysed.
- Adaptive sampling was used to enrich 59 genes commonly involved in translocations/fusions in B-cell acute lymphoblastic leukaemia (B-ALL) and acute myeloid leukaemia (AML).
- Oxford Nanopore sequencing provided all genomic information currently offered by traditional diagnostic testing (karyotype, FISH, and occasional microarray) for paediatric acute leukaemia, but was also able to characterise aneuploidy and structural variants in challenging repetitive regions.
- There was no loss in sensitivity or throughput between freshly collected and cryopreserved samples, whereas karyotype and FISH are reliant on high-quality viable cells.
- The researchers suggested that nanopore sequencing could be a low-cost future alternative to current diagnostic tools, increasing accessibility to LMICs.
Watch Julie Geyer's talk at London Calling 2024
Sample type: human peripheral blood mononuclear cells, bone marrow mononuclear cells, and whole blood