NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE24881 Query DataSets for GSE24881
Status Public on Feb 01, 2011
Title Affymetrix SNP array data for Marginal Zone Lymphoma samples
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Marginal zone B-cell lymphomas (MZL) have been divided into three distinct subtypes (extranodal MZL of MALT type, nodal MZL; splenic MZL). Nevertheless, the relationship between them is still unclear. We performed a comprehensive analysis of genomic DNA copy number changes in a very large series of MZL cases with the aim of addressing this question. Samples from 218 MZL patients (25 nodal, 57 MALT, 134 splenic and two not better specified MZL) were analyzed with the Affymetrix Human Mapping 250K SNP arrays, and the data combined with matched gene expression in 33/218 cases. MALT lymphoma presented significantly more frequently gains at 3p, 6p, 18p and del(6q23) (TNFAIP3/A20), whilst splenic MZL was associated with del(7q31), del(8p). Nodal MZL did not show statistically significant differences when compared with MALT lymphoma while lacked the splenic MZL-related 7q losses. Gains of 3q and 18q gains were common to all three subtypes. Del(8p) was often present together with del(17p) (TP53). While del(17p) did not determine a worse outcome and del(8p) was only of borderline significance, the presence of both deletions had a highly significant negative impact on the outcome of splenic MZL.
 
Overall design Copy number analysis of Affymetrix 250K Nsp SNP arrays was performed for a total of 218 MZL samples were analyzed by high resolution genome wide-DNA profiling: 57 MALT lymphoma, 134 splenic MZL, 25 nodal MZL and two MZL where allocation to a specific category was not possible.
 
Contributor(s) Bertoni F, Rinaldi A, Kwee I
Citation(s) 21115979, 22891273
Submission date Oct 21, 2010
Last update date May 17, 2017
Contact name Francesco Bertoni
E-mail(s) francesco.bertoni@ior.usi.ch
Phone +41 91 820 0367
Organization name IOR
Department Lymphoma & Genomics Research Program
Street address Via V. Vela 6
City Bellinzona
State/province Ticino
ZIP/Postal code 6500
Country Switzerland
 
Platforms (1)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
Samples (218)
GSM611734 Marginal zone B-cell lymphoma patient sample 06-R-389
GSM611735 Marginal zone B-cell lymphoma patient sample 06-R-391
GSM611736 Marginal zone B-cell lymphoma patient sample 07-005
Relations
BioProject PRJNA132023

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
GSE24881_RAW.tar 4.1 Gb (http)(custom) TAR (of CEL)
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap