Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia
(2023) In NPJ precision oncology 7(1).- Abstract
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... (More)
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.
(Less)
- author
- organization
- publishing date
- 2023-12
- type
- Contribution to journal
- publication status
- published
- subject
- in
- NPJ precision oncology
- volume
- 7
- issue
- 1
- article number
- 131
- publisher
- Springer Nature
- external identifiers
-
- pmid:38066241
- scopus:85179355296
- ISSN
- 2397-768X
- DOI
- 10.1038/s41698-023-00479-5
- language
- English
- LU publication?
- yes
- id
- 98c6efff-535e-43fc-a5a7-dfd3e89816d8
- date added to LUP
- 2024-01-09 11:17:55
- date last changed
- 2024-08-01 16:57:21
@article{98c6efff-535e-43fc-a5a7-dfd3e89816d8, abstract = {{<p>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.</p>}}, author = {{Krali, Olga and Marincevic-Zuniga, Yanara and Arvidsson, Gustav and Enblad, Anna Pia and Lundmark, Anders and Sayyab, Shumaila and Zachariadis, Vasilios and Heinäniemi, Merja and Suhonen, Janne and Oksa, Laura and Vepsäläinen, Kaisa and Öfverholm, Ingegerd and Barbany, Gisela and Nordgren, Ann and Lilljebjörn, Henrik and Fioretos, Thoas and Madsen, Hans O. and Marquart, Hanne Vibeke and Flaegstad, Trond and Forestier, Erik and Jónsson, Ólafur G. and Kanerva, Jukka and Lohi, Olli and Norén-Nyström, Ulrika and Schmiegelow, Kjeld and Harila, Arja and Heyman, Mats and Lönnerholm, Gudmar and Syvänen, Ann Christine and Nordlund, Jessica}}, issn = {{2397-768X}}, language = {{eng}}, number = {{1}}, publisher = {{Springer Nature}}, series = {{NPJ precision oncology}}, title = {{Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia}}, url = {{http://dx.doi.org/10.1038/s41698-023-00479-5}}, doi = {{10.1038/s41698-023-00479-5}}, volume = {{7}}, year = {{2023}}, }