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Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia

Version 3 2024-01-10, 10:20
Version 2 2023-03-30, 05:29
Version 1 2023-03-23, 12:41
dataset
posted on 2024-01-10, 10:20 authored by Olga KraliOlga Krali, Yanara Marincevic-Zuniga, Gustav ArvidssonGustav Arvidsson, Anna Pia Enblad, Anders Lundmark, Shumaila SayyabShumaila Sayyab, Vasilios Zachariadis, Merja Heinäniemi, Janne Suhonen, Laura Oksa, Kaisa Vepsäläinen, Ingegerd Öfverholm, Gisela Barbany, Ann Nordgren, Henrik LilljebjörnHenrik Lilljebjörn, Thoas Fioretos, Hans O. Madsen, Hanne Vibeke Marquart, Trond Flaegstad, Erik Forestier, Ólafur G. Jónsson, Jukka Kanerva, Olli Lohi, Ulrika Norén-Nyström, Kjeld Schmiegelow, Arja Harila, Mats Heyman, Gudmar Lönnerholm, Ann-Christine Syvänen, Jessica NordlundJessica Nordlund

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 access

The 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.

Funding

The Swedish Cancer Society (#CAN2018-623, #CAN2022-2395)

The Swedish Childhood Cancer Foundation (#PR2017-0023, #PR2019-0046)

The Göran Gustafsons Foundation

Single-cell analysis for precision medicine in acute pediatric leukemia

Swedish Research Council

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Capturing the cell state space from genomics data into models of treatment resistance in childhood leukemia

Academy of Finland

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Jane and Aatos Erkko Foundation

History

Publisher

Uppsala University

Access request email

datacentre@scilifelab.se