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Series GSE38235 Query DataSets for GSE38235
Status Public on Jun 04, 2013
Title Integration of high-resolution methylome and transcriptome analyses to dissect epigenomic changes in childhood acute lymphoblastic leukemia
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary B-cell precursor acute lymphoblastic leukemia (pre-B ALL) is the most common pediatric cancer. Although the genetic origin of the disease remains unclear, epigenetic modifications including DNA methylation are suggested to contribute significantly to leukemogenesis. We assessed the DNA methylation status of 402,842 CpG-sites across the genome (Illumina 450k array) in tumor and remission samples of 46 pre-B ALL patients, thus generating the most comprehensive single CpG-site resolution pre-B ALL methylomes so far. Unsupervised hierarchical clustering of CpG-site neighborhood, protein-coding gene, or miRNA gene associated methylation levels separated the tumor cohort according to major pre-B ALL subtypes, and methylation in CpG islands, shores, and in regions around the transcription start site of protein-coding genes strongly correlated with transcript expression. Focusing on samples carrying the t(12;21)(p13;q22) translocation (ETV6-RUNX1 fusion gene) we identified subtype-specific methylation of 430 CpG-sites. Pathway analyses implied the associated genes in hematopoiesis and cancer. Further intersection with transcriptome data identified methylation to impact expression of 18 genes. In summary, our data illustrate the power of methylation profiling to classify leukemic subtypes and to identify subtype-specific methylation markers. Further, we demonstrate that integration of methylome and transcriptome alterations allows the study of downstream effects of individual genomic rearrangements in cancer.
 
Overall design Bisulfite converted DNA of tumor (isolated on day of diagnosis) and remission (isolated after disease remission) samples derived from 46 patients of French-Canadian origin diagnosed with pre-B ALL were analyzed on the Illumina Infinium HumanMethylation 450k BeadChips.
 
Contributor(s) Busche S, Ge B, Vidal R, Spinella J, Saillour V, Richer C, Healy J, Chen S, Droit A, Sinnett D, Pastinen T
Citation(s) 23722552
Submission date May 24, 2012
Last update date Mar 22, 2019
Contact name Stephan Busche
Organization name McGill University
Department Human Genetics
Street address 740 Dr. Penfield Avenue
City Montreal
State/province Quebec
ZIP/Postal code H3A 0G1
Country Canada
 
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (92)
GSM937109 genomic DNA (tumor sample) from pre-B ALL patient 356
GSM937110 genomic DNA (tumor sample) from pre-B ALL patient 372
GSM937111 genomic DNA (tumor sample) from pre-B ALL patient 373
Relations
BioProject PRJNA167462

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
GSE38235_RAW.tar 183.1 Mb (http)(custom) TAR
GSE38235_non-normalized.txt.gz 217.5 Mb (ftp)(http) TXT
Processed data included within Sample table
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