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Series GSE9611 Query DataSets for GSE9611
Status Public on Apr 10, 2008
Title Adult and adolescent acute lymphoblastic leukemia
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary We present here a genome-wide map of abnormalities found in diagnostic samples from 45 adults and adolescents with acute lymphoblastic leukemia (ALL). 500K single nucleotide polymorphism (SNP) array analysis uncovered frequent genetic abnormalities, with cryptic deletions constituting half of the detected changes, implying that microdeletions are a characteristic feature of this malignancy. Importantly, the pattern of deletions resembled that recently reported in pediatric ALL, suggesting that adult, adolescent, and childhood cases may be more similar on the genetic level than previously thought. Thus, 70% of the cases displayed deletion of one or more of the CDKN2A, PAX5, IKZF1, ETV6, RB1, and EBF1 genes. Furthermore, several genes not previously implicated in the pathogenesis of ALL were identified as possible recurrent targets of deletion. In total, the SNP array analysis identified 367 genetic abnormalities not corresponding to known copy number polymorphisms, with all but two cases (96%) displaying at least one cryptic change. This SNP array study is the first to specifically address adult and adolescent ALL, and the resolution level is the highest used to date to investigate a malignant hematologic disorder. Our findings provide insights into the leukemogenic process and may be clinically important in adult and adolescent ALL. Most importantly, we report that microdeletions of key genes appear to be a common, characteristic feature of ALL that is shared between different clinical, morphological, and cytogenetic subgroups.
Keywords: Genomic analysis of acute lymphoblastic leukemia samples
Overall design Diagnostic samples from 45 adult or adolescent acute lymphoblastic leukemia samples were analyzed with the Affymetrix 250K Nsp, 250K Sty, and 10K 2.0 SNP arrays. Ten samples from leukemia patients in remission were used as normal controls. Copy number changes were analyzed with the NSP and STY arrays, and regions of uniparental disomies with the 10K arrays.
Contributor(s) Paulsson K, Cazier J, MacDougall F, Stevens J, Stasevich I, Vrcelj N, Chaplin T, Lillington DM, Lister TA, Young BD
Citation(s) 18458336
Submission date Nov 14, 2007
Last update date May 17, 2017
Contact name Kajsa Paulsson
Organization name Cancer Research UK
Department Medical Oncology Centre
Street address John Vane Science Centre, Charterhouse Square
City London
ZIP/Postal code EC1M 6BQ
Country United Kingdom
Platforms (3)
GPL2641 [Mapping10K_Xba142] Affymetrix Human Mapping 10K 2.0 Array
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
Samples (165)
GSM243017 ALL_10kXba_#1
GSM243018 ALL_10kXba_#2
GSM243019 ALL_10kXba_#3
BioProject PRJNA103463

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
GSE9611_RAW.tar 3.3 Gb (http)(custom) TAR (of CEL, TXT)
Processed data included within Sample table

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