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Series GSE49031 Query DataSets for GSE49031
Status Public on Sep 18, 2013
Title Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary We surveyed the DNA methylation levels of 435,941 CpG sites in samples from 764 children at diagnosis of ALL and from 27 children at relapse. This survey uncovered four characteristic methylation signatures. First, compared with control blood cells, the methylomes of ALL cells shared 9,406 predominantly hypermethylated CpG sites, independent of cytogenetic background. Second, each cytogenetic subtype of ALL displayed a unique set of hyper- and hypomethylated CpG sites. The CpG sites that constituted these two signatures differed in their functional genomic enrichment to regions with marks of active or repressed chromatin. Third, we identified subtype-specific differential methylation in promoter and enhancer regions that were strongly correlated with gene expression. Fourth, a set of 6,612 CpG sites was predominantly hypermethylated in ALL cells at relapse, compared with matched samples at diagnosis. Analysis of relapse-free survival identified CpG sites with subtype-specific differential methylation that divided the patients into different risk groups, depending on their methylation status.
Overall design The DNA methylation levels of primary pediatric ALL samples taken at diagnosis (n= 764), remission(n=86), first relapse (n=27), second relapse (n=5), fractionated blood cells from healthy blood donors (n=51), and methylation +/- controls (n=11) were analyzed with the Illumina Infinium HumanMethylation 450k BeadChips. One ALL sample was run in duplicate (technical replicate).
Contributor(s) Nordlund J, Bäcklin CL, Lönnerholm G, Syvänen AC
Citation(s) 24063430, 25729447, 26494837, 29515676
Submission date Jul 18, 2013
Last update date May 23, 2019
Contact name Jessica Nordlund
Phone +46186114912
Organization name Uppsala University
Department Medical Sciences
Lab Molecular Medicine
Street address Academic Hospital, Entrance 70, 3rd floor
City Uppsala
ZIP/Postal code 75185
Country Sweden
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (945)
GSM1203372 genomic DNA at diagnosis from BCP-ALL patient ALL_1
GSM1203373 genomic DNA at diagnosis from BCP-ALL patient ALL_2
GSM1203374 genomic DNA at diagnosis from BCP-ALL patient ALL_3
This SubSeries is part of SuperSeries:
GSE49032 Genome-wide signatures of differential DNA methylation and gene expression in pediatric ALL
BioProject PRJNA214597

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE49031_RAW.tar 7.8 Gb (http)(custom) TAR (of IDAT)
GSE49031_methylated_unmethylated_signal_intensities.txt.gz 3.8 Gb (ftp)(http) TXT
GSE49031_processed.txt.gz 1.8 Gb (ftp)(http) TXT
Processed data are available on Series record

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