Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia

  • Olga Krali (Uppsala University) (Creator)
  • Yanara Marincevic-Zuniga (Creator)
  • Gustav Arvidsson (Uppsala University) (Creator)
  • Anna Pia Enblad (Uppsala University) (Creator)
  • Anders Lundmark (Uppsala University) (Creator)
  • Shumaila Sayyab (Uppsala University) (Creator)
  • Vasilios Zachariadis (Creator)
  • Merja Heinäniemi (Creator)
  • Janne Suhonen (University of Eastern Finland) (Creator)
  • Laura Oksa (Creator)
  • Kaisa Vepsäläinen (Creator)
  • Ingegerd Öfverholm (Karolinska University Hospital, Karolinska Institutet) (Creator)
  • Gisela Barbany (Karolinska Institutet, Karolinska University Hospital) (Creator)
  • Ann Nordgren (Karolinska Institutet, Karolinska University Hospital) (Creator)
  • Henrik Lilljebjörn (Lund University) (Creator)
  • Thoas Fioretos (Lund University) (Creator)
  • Hans O. Madsen (Copenhagen University Hospital - Rigshospitalet) (Contributor)
  • Hanne Vibeke Marquart (Copenhagen University Hospital - Rigshospitalet, University of Copenhagen) (Creator)
  • Trond Flaegstad ( Tromsø University and University Hospital) (Creator)
  • Erik Forestier (Umeå University) (Creator)
  • Ólafur G. Jónsson (Landspitali - The National University Hospital of Iceland) (Creator)
  • Jukka Kanerva (Creator)
  • Olli Lohi (Creator)
  • Ulrika Norén-Nyström (Umeå University) (Creator)
  • Kjeld Schmiegelow (Creator)
  • Arja Harila (Uppsala University) (Creator)
  • Mats Heyman (Creator)
  • Gudmar Lönnerholm (Uppsala University) (Creator)
  • Ann-Christine Syvänen (Creator)
  • Jessica Nordlund (Creator)

Dataset

Description

This dataset contains genome-wide DNA methylation data generated from 384 pediatric acute lymphoblastic leukemia (ALL) samples originating from bone marrow or peripheral blood samples taken at ALL diagnosis (n = 384). Further details regarding the samples are available in Supplementary Table S2 from Krali et al., 2023 (https://doi.org/10.1038/s41698-023-00479-5).Genome-wide DNA methylation was analyzed at the SNP&SEQ Technology Platform, SciLifeLab, National Genomics Infrastructure Uppsala, Sweden. 250 ng of bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using the standard protocol from Illumina (iScan SQ instrument).This metadata record contains information about the raw idat files generated from the Infinium DNA methylation arrays. The raw idat files were processed with Methylation Module (1.8.5) software in Genome Studio (V2010.3). Peak-based correction was used to normalize the beta-value matrix.The raw idat files along with a samplesheet, processed beta-value matrix, annotation file for CpG annotation will be made available upon request. Limited phenotype information is available in the Supplemental Table S2 of the manuscript. All scripts that give a walk-through to our project, including the modelling process with Machine Learning can be found in our GitHub repository.Terms for accessThe DNA methylation dataset is only to be used for research that is seeking to advance the understanding of the influence of epigenetic factors on leukemia etiology and biology.The data should not be used for other purposes, i.e. investigating the epigenetic signatures that may lead to identification of a person. For retrieving the data used for the scope of this publication, please contact datacentre@scilifelab.se.
Date made available23 Mar 2023

Field of science, Statistics Finland

  • 3111 Biomedicine
  • 3123 Gynaecology and paediatrics
  • 3122 Cancers
  • Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia

    Krali, O., Marincevic-Zuniga, Y., Arvidsson, G., Enblad, A. P., 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, H. O., Marquart, H. V., Flaegstad, T., Forestier, E., & 10 othersJónsson, Ó. G., Kanerva, J., Lohi, O., Norén-Nyström, U., Schmiegelow, K., Harila, A., Heyman, M., Lönnerholm, G., Syvänen, A. C. & Nordlund, J., Dec 2023, In: NPJ precision oncology. 7, 1, 131.

    Research output: Contribution to journalArticleScientificpeer-review

    Open Access
    File

Cite this