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Series GSE34005 Query DataSets for GSE34005
Status Public on Dec 23, 2013
Title Affymetrix SNP array data for recurrent deletion in 19p in DLBCLs and BLs
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary A single nucleotide polymorphism (SNP)-chip analysis of 98 cases of aggressive B-cell lymphomas revealed a recurrent deletion at 19p13 in 9 of the cases. Six further cases with deletions encompassing this region were found in array-comparative genomic hybridization data of 295 aggressive B-cell lymphomas from a previous study. Three cases even showed a homozygous deletion, suggesting a tumor suppressor gene in the deleted region. Two genes encoding members of the tumor necrosis factor superfamily were located in the minimally deleted region, i.e. TNFSF7 and TNFSF9. As no mutations were found within the coding exons of the remaining alleles in the lymphomas with heterozygous deletions, we speculate that the deletions may mostly function through a haploinsufficiency mechanism. The cases with deletions encompassed both diffuse large B-cell lymphomas and Burkitt lymphomas, and a deletion was also found in a Hodgkin lymphoma cell line. Thus, TNFSF7 and TNFSF9 deletions are recurrent genetic lesions in multiple types of human lymphomas.
Overall design Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from whole tissue. Copy number and LOH analysis of 500K SNP/250K SNP arrays was performed on 9 cases of aggressive B-cell lymphoma harboring the described deletion. Genotyping was performed using the BRLMM-algorithm. 20 normal references (10 of those hybridized to nsp-chips) extracted from healthy blood donors, used as normals in the analysis in addition to the HapMap references provided by Affymetrix, are included in the set.
Contributor(s) Scholtysik R
Citation(s) 22213068
Submission date Nov 29, 2011
Last update date May 17, 2017
Contact name Rene Scholtysik
Organization name University Hospital Essen
Department IFZ
Street address Virchowstrasse 173
City Essen
ZIP/Postal code 45127
Country Germany
Platforms (2)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
Samples (42)
GSM840290 Tumor MPI-031 nsp
GSM840291 Tumor MPI-032 nsp
GSM840292 Tumor MPI-528 nsp
BioProject PRJNA150583

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
GSE34005_RAW.tar 1.2 Gb (http)(custom) TAR (of CEL, CHP)
Processed data provided as supplementary file
Processed data included within Sample table

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