File(s) not publicly available
Reason: IDAT files are sensitive data and are available only upon request
Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia
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 (DOI to publication when available).
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 firstname.lastname@example.org.
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 CouncilFind out more...
Capturing the cell state space from genomics data into models of treatment resistance in childhood leukemia
Academy of FinlandFind out more...