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Series GSE19996 Query DataSets for GSE19996
Status Public on Jul 07, 2010
Title Affy SNP-array data for 23 ETV6/RUNX1-positive ALL patient samples and one cell line
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary The ETV6/RUNX1 fusion gene, present in 25% of B-lineage childhood acute lymphoblastic leukemia (ALL), is thought to represent an initiating event, which requires additional genetic changes for leukemia development. To identify additional genetic alterations, 24 ETV6/RUNX1-positive ALLs were analyzed using 500K single nucleotide polymorphism arrays. The results were combined with previously published data sets, allowing us to ascertain genomic copy number aberrations (CNAs) in 164 cases. In total, 45 recurrent CNAs were identified with an average number of 3.5 recurrent changes per case (range 0-13). Twenty-six percent of cases displayed a set of recurrent CNAs identical to that of other cases in the data set. The majority (74%), however, displayed a unique pattern of recurrent CNAs, indicating a large heterogeneity within this ALL subtype. As previously demonstrated, alterations targeting genes involved in B-cell development were common (present in 28% of cases). However, the combined analysis also identified alterations affecting nuclear hormone response (24%) to be a characteristic feature of ETV6/RUNX1-positive ALL. Studying the correlation pattern of the CNAs allowed us to highlight significant positive and negative correlations between specific aberrations. Furthermore, oncogenetic tree models identified ETV6, CDKN2A/B, PAX5, del(6q), and +16 as possible early events in the leukemogenic process.
 
Overall design Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from 23 leukemic bone marrow samples and one ETV6/RUNX1-positive cell line.
 
Contributor(s) Lilljebjörn H, Fioretos T
Citation(s) 20513752
Submission date Jan 21, 2010
Last update date May 17, 2017
Contact name Henrik Lilljebjörn
Organization name Lund University
Department Dept of Clinical Genetics
Street address Lund University Hospital
City Lund
ZIP/Postal code 22185
Country Sweden
 
Platforms (2)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
Samples (48)
GSM499491 ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 1 (Nsp)
GSM499492 ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 2 (Nsp)
GSM499493 ETV6/RUNX1-positive acute lymphoblastic leukemia, patient sample 3 (Nsp)
Relations
BioProject PRJNA120161

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
GSE19996_RAW.tar 1.5 Gb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file
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