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Affymetrix OncoScan SNP arrays for profiling copy-number alterations (CNAs) and loss-of-heterozygosity (LOH) in colon cancer

ABSTRACT: Affymetrix OncoScan SNP arrays for profiling copy-number alterations (CNAs) and loss-of-heterozygosity (LOH) in colon cancer

PROVIDER: PRJNA720909 | ENA |

REPOSITORIES: ENA

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Affymetrix OncoScan SNP arrays for profiling somatic copy-number alterations in blastic plasmacytoid dendritic cell neoplasm

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Paired copy number analysis of Diffuse Large B Cell Lymphoma [OncoScan]

Project description: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.

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Rawcopy: Improved copy number analysis with Affymetrix arrays.

Project description: Not available

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