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Series GSE71386 Query DataSets for GSE71386
Status Public on Jan 22, 2016
Title Paired copy number analysis of Diffuse Large B Cell Lymphoma [OncoScan]
Organism Homo sapiens
Experiment type Genome variation profiling by array
Summary Copy number analysis can be useful for assessing prognosis in diffuse large B cell lymphoma (DLBCL). We analyzed copy number data from tumor samples of 60 patients diagnosed with DLBCL de novo and their matched normal samples. We detected a total of 63 recurrent copy number alterations (CNAs), including 33 gains, 30 losses, and nine recurrent acquired copy number neutral loss of heterozygosity (CNN-LOH). Interestingly, 20% of cases acquired CNN-LOH of 6p21 locus, which involves the HLA region. In normal cells there were no CNAs but we observed CNN-LOH involving some key lymphoma regions such as 6p21 and 9p24.1 (5%) and 17p13.1 (2.5%) in DLBCL patients. Furthermore, a model with some specific CNA was able to predict the subtype of DLBCL, 1p36.32 and 10q23.31 losses being restricted to germinal center B cell-like (GCB) DLBCL. In contrast, 8p23.3 losses and 11q24.3 gains were strongly associated with the non-GCB subtype. A poor prognosis was associated with biallelic inactivation of TP53 or 18p11.32 losses, while prognosis was better in cases carrying 11q24.3 gains, which includes ETS1 and FLI1 genes. In summary, CNA abnormalities identify specific DLBCL groups, and we describe CN-LOH in germline cells from DLBCL patients that are associated with genes that probably play a key role in DLBCL development.
 
Overall design A total of 60 DLBCL cases and paired constitutional DNA from 40 of these patients, were successfully analyzed using copy number arrays. Thirty-eight cases with FFPE DNA available were hybridized on the MIP-assay using Oncoscan FFPE Express custom service (Affymetrix, Santa Clara, CA, USA).Twenty-two cases with HMW DNA from frozen tissue and 40 normal DNAs were analyzed using SNP 6.0 array. Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, El Segundo, CA, USA).
 
Contributor(s) Sebastián E, Salaverria I, Martín-García D
Citation(s) 26573278
Submission date Jul 27, 2015
Last update date Jan 22, 2016
Contact name Elena Sebastián
Organization name Hospital Universitario de Salamnca
Department Hematology
Lab Molecular Biology
Street address Paseo de San Vicente
City Salamanca
ZIP/Postal code 38007
Country Spain
 
Platforms (1)
GPL18602 [OncoScan] Affymetrix OncoScan FFPE Assay
Samples (38)
GSM1833472 Diffuse Large B Cell Lymphoma tumor sample 01
GSM1833473 Diffuse Large B Cell Lymphoma tumor sample 02
GSM1833474 Diffuse Large B Cell Lymphoma tumor sample 03
This SubSeries is part of SuperSeries:
GSE71394 Paired copy number analysis of Diffuse Large B Cell Lymphoma
Relations
BioProject PRJNA291078

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
GSE71386_DLBCLCNO2_Copy_Number.txt.gz 222.9 Mb (ftp)(http) TXT
GSE71386_DLBCLCNO2_Genotypes.txt.gz 6.9 Mb (ftp)(http) TXT
GSE71386_RAW.tar 357.8 Mb (http)(custom) TAR (of CEL)
GSE71386_corresponding_samples_name.xls.gz 15.8 Kb (ftp)(http) XLS
Processed data are available on Series record
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