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Series GSE36908 Query DataSets for GSE36908
Status Public on Oct 11, 2012
Title High-Resolution Genomic Profiling of Chronic Lymphocytic Leukemia Reveals New Recurrent Genomic Alterations
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism (SNP)-array analysis on 353 samples from previously untreated patients entered on the CLL8 treatment trial. Based on paired-sample analysis (n=147), a mean of 1.8 copy number alterations (CNAs) per case were identified; about 60% of cases carried no CNAs other than those detected by routine fluorescence in-situ hybridization analysis. Copy-neutral loss-of- heterozygosity was detected in 6% of cases, and most frequently found on 13q, 17p and 11q. Minimal deleted regions (MDRs) were refined on 13q14 (deleted in 61% of cases) to the DLEU1 and DLEU2 genes, on 11q22.3 (27%) to ATM, on 2p (gained in 7% of cases) to a 1.9 Mb fragment containing 9 genes, and on 8q24 (5%) to a segment 486 Kb proximal of the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4%), with the smallest deletion (70.5 Kb) found in the MGA locus; sequence analysis of MGA in 59 samples revealed a truncating mutation in one case lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also found recurrently deleted.
 
Overall design Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic peripheral blood samples. Copy number analysis of Affymetrix® performed for 353 CLL samples. There are also 147 samples from mononuclear cells negative for CD19, which were used as references for copy number inference.
 
Contributor(s) Edelmann J, Holzmann K
Citation(s) 23047824
Submission date Mar 28, 2012
Last update date Nov 27, 2018
Contact name Karlheinz Holzmann
E-mail(s) karlheinz.holzmann@uni-ulm.de
Organization name Ulm University
Department Medical Faculty
Lab Genomics Core Facility
Street address Helmholtzstreet 8/1
City Ulm
ZIP/Postal code D-89081
Country Germany
 
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (500)
GSM911200 Chronic lymphocytic leukemia 1
GSM911201 Chronic lymphocytic leukemia 1 paired normal
GSM911202 Chronic lymphocytic leukemia 2
Relations
BioProject PRJNA158401

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
GSE36908_RAW.tar 19.7 Gb (http)(custom) TAR (of CEL, CHP)
Processed data provided as supplementary file
Processed data included within Sample table
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