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Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia

Krali, Olga ; Marincevic-Zuniga, Yanara ; Arvidsson, Gustav ; Enblad, Anna Pia ; Lundmark, Anders ; Sayyab, Shumaila ; Zachariadis, Vasilios ; Heinäniemi, Merja ; Suhonen, Janne and Oksa, Laura , et al. (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.

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organization
publishing date
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
2024-04-24 07:14:33
@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}},
}