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Krali O, Marincevic-Zuniga Y, Arvidsson G, Enblad AP, Lundmark A, Sayyab S, Zachariadis V, Heinäniemi M, Suhonen J, Oksa L, Vepsäläinen K, Öfverholm I, Barbany G, Nordgren A, Lilljebjörn H, Fioretos T, Madsen HO, Marquart HV, Flaegstad T, Forestier E, Jónsson ÓG, Kanerva J, Lohi O, Norén-Nyström U, Schmiegelow K, Harila A, Heyman M, Lönnerholm G, Syvänen AC, Nordlund J
NPJ Precis Oncol 7 (1) 131 [2023-12-08; online 2023-12-08]
Genomic analyses have redefined the molecular subgrouping of pediatric acute lymphoblastic leukemia (ALL). Molecular subgroups guide risk-stratification and targeted therapies, but outcomes of recently identified subtypes are often unclear, owing to limited cases with comprehensive profiling and cross-protocol studies. We developed a machine learning tool (ALLIUM) for the molecular subclassification of ALL in retrospective cohorts as well as for up-front diagnostics. ALLIUM uses DNA methylation and gene expression data from 1131 Nordic ALL patients to predict 17 ALL subtypes with high accuracy. ALLIUM was used to revise and verify the molecular subtype of 281 B-cell precursor ALL (BCP-ALL) cases with previously undefined molecular phenotype, resulting in a single revised subtype for 81.5% of these cases. Our study shows the power of combining DNA methylation and gene expression data for resolving ALL subtypes and provides a comprehensive population-based retrospective cohort study of molecular subtype frequencies in the Nordic countries.
Clinical Genomics Stockholm [Service]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
National Genomics Infrastructure [Service]
PubMed 38066241
DOI 10.1038/s41698-023-00479-5
Crossref 10.1038/s41698-023-00479-5
pmc: PMC10709574
pii: 10.1038/s41698-023-00479-5