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Series GSE9113 Query DataSets for GSE9113
Status Public on Sep 02, 2009
Title Affymetrix SNP array data for acute lymphoblastic leukemia samples
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary BCR-ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros. The Philadelphia chromosome, encoding BCR-ABL1, is the defining lesion of chronic myelogenous leukemia (CML) and a subset of acute lymphoblastic leukemia (ALL) cases. To define oncogenic lesions that cooperate with BCR-ABL1 to induce ALL, we performed genome-wide analysis of leukemic samples from 23 CML cases and 304 ALL cases, including 43 BCR-ABL1 B-ALL cases. IKZF1 (encoding the transcription factor Ikaros) was deleted in 83.7% of BCR-ABL1 B-ALL cases, but not in chronic phase CML. Deletion of IKZF1 was also identified as an acquired lesion in lymphoid blast crisis of CML. The IKZF1 deletions resulted in haploinsufficiency, expression of a dominant negative Ikaros isoform or the complete loss of Ikaros expression. Sequencing of IKZF1 deletion breakpoints suggested that aberrant V(D)J recombination is responsible for the deletions. These findings suggest that genetic lesions resulting in the loss of Ikaros function are a key event in the development of BCR-ABL1 ALL.

*** Due to privacy concerns, the primary SNP array data is no longer available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access using the Web links below. ***

This SuperSeries is composed of the SubSeries listed below.
 
Overall design Affymetrix SNP arrays were performed according to the maufacturers directions on DNA extracted from cryopreserved diagnostic bone marrow or peripheral blood samples.
Copy number analysis of Affymetrix 100K and 500K SNP arrays was performed for 304 pediatric and adult ALL samples, 23 chronic myeloid leukemia samples, and 36 ALL cell lines. There are also 50 samples from leukemia in remission, which were used as references for copy number inference.
 
Contributor(s) Mullighan CG, Downing JR
Citation(s) 18408710
Submission date Sep 20, 2007
Last update date Dec 22, 2017
Contact name Charles G Mullighan
E-mail(s) charles.mullighan@stjude.org
Phone 1-901-595-3387
Organization name St Jude Children's Research Hospital
Department Pathology
Street address 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38105
Country USA
 
Platforms (4)
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 (1496)
GSM235081 Diagnostic_acute_leukemia Other-SNP-#21-250ksty
GSM235082 Diagnostic_acute_leukemia Pseudodip-SNP-#1-250ksty
GSM235083 Diagnostic_acute_leukemia Hyperdip47-50-SNP-#1-250ksty
This SuperSeries is composed of the following SubSeries:
GSE9109 SNP array data for 304 pediatric and adult acute lymphoblastic leukemia cases
GSE9110 SNP array data for 56 chronic myeloid leukemia samples.
GSE9111 SNP array data for 50 leukemia remission samples
Relations
BioProject PRJNA102641

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