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Series GSE7255 Query DataSets for GSE7255
Status Public on May 01, 2007
Title Genomic profiling data of 40 childhood leukemia patients
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary In this study, we performed an inventory of copy number changes present in childhood acute lymphoblastic leukemias. The cohort contains a total of 40 diagnosis samples, including 7 T-lineage ALLs and 33 precursor B-cell ALLs. High resolution genomic profiling was perfomed using Affymetrix SNP arrays. We detected multiple de novo genetic lesions, including gross aneuploidies and segmental gains and losses, some of which were subtle and affected single genes. Many of these lesions involved recurrent (partially) overlapping deletions and duplications, containing various established leukemia-associated genes, such as ETV6, RUNX1, and MLL. Importantly, the most frequently affected genes were those controlling G1/S cell cycle progression (e.g. CDKN2A, CDKN1B, and RB1), followed by genes associated with B-cell development. The latter group includes microdeletions of the B-lineage transcription factors PAX5, EBF, E2-2, and IKZF1 (Ikaros), as well as genes with other established roles in B-cell development, i.e., RAG1 and RAG2, FYN, PBEF1, or CBP/PAG. The fact that we frequently encountered multiple lesions affecting genes involved in cell cycle regulation and B-cell differentiation, strongly suggests that both these processes need to be targeted independently and simultaneously in order to trigger ALL-development.
Keywords: comparative genome hybridization
 
Overall design Genomic DNA from 40 bone marrow or periphearal blood was hybridized on Affymetrix Nsp, Xba or Hind SNP-based arrays according to manufacturer's procedures. Copy number detection was performed using CNAG2.0 software, Reference genomes are included in this data set
 
Contributor(s) Kuiper RP, vanReijmersdal SV, Schoenmakers EF, GeurtsvanKessel A, Hoogerbrugge PM
Citation(s) 17443227
Submission date Mar 13, 2007
Last update date Dec 22, 2017
Contact name Roland P. Kuiper
E-mail(s) r.kuiper@antrg.umcn.nl, e.verwiel@antrg.umcn.nl
Phone +31243610868
Fax +31243668752
Organization name Radboud University Nijmegen Medical Centre
Department Human Genetics
Street address Geert Grooteplein 10
City Nijmegen
ZIP/Postal code 6525GA
Country Netherlands
 
Platforms (3)
GPL2004 [Mapping50K_Hind240] Affymetrix Human Mapping 50K Hind240 SNP Array
GPL2005 [Mapping50K_Xba240] Affymetrix Human Mapping 50K Xba240 SNP Array
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
Samples (45)
GSM174829 9314
GSM174830 9256
GSM174831 9442
Relations
BioProject PRJNA98009

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
GSE7255_RAW.tar 1.1 Gb (http)(custom) TAR (of CEL, CHP)
Processed data provided as supplementary file

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