Genomics

Dataset Information

42

Paired copy number analysis of DLBCL Diffuse Large B Cell Lymphoma [SNP 6.0 Array]


ABSTRACT: 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).

INSTRUMENT(S): Affymetrix Genome-Wide Human SNP 6.0 Array

SUBMITTER: Elena Sebastián 

PROVIDER: GSE71389 | GEO | 2016-01-22

SECONDARY ACCESSION(S): PRJNA291079

REPOSITORIES: GEO

altmetric image

Publications


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 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 c  ...[more]

Similar Datasets

| GSE71386 | GEO
2014-07-22 | E-GEOD-57277 | ArrayExpress
2014-07-22 | E-GEOD-57611 | ArrayExpress
| GSE8123 | GEO
2008-06-16 | E-GEOD-8123 | ArrayExpress
2010-04-03 | E-GEOD-14016 | ArrayExpress
2009-11-23 | GSE16406 | GEO
2015-08-12 | E-GEOD-28571 | ExpressionAtlas
2009-04-01 | GSE14016 | GEO
2011-04-01 | GSE21452 | GEO