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Methylation array profiling of small B-cell lymphomas

ABSTRACT: Methylation array profiling of small B-cell lymphomas

PROVIDER: PRJNA719541 | ENA |

REPOSITORIES: ENA

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Methylation array profiling of small B-cell lymphomas

Project description:This dataset includes chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), follicular lymphoma (FL), mantle cell lymphoma (MCL), and marginal zone lymphoma (MZL) cases reviewed for pathology consensus at the University Health Network. Also included are challenging cases of small B-cell lymphomas without pathology consensus. Methylation array profiling was performed using the Infinium MethylationEPIC array platform. Unprocessed IDAT files and matrix with beta values (beta_TGL51_illumina_annot_geo.txt) are provided.

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Array-based profiling of the lymphoma cell DNA methylome does not unequivocally distinguish primary lymphomas of the central nervous system from non-CNS diffuse large B-cell lymphomas

Project description:Genome wide DNA methylation profiling of 26 primary central nervous system lymphomas (PCNSL). The Illumina Infinium HumanMethylation 450 BeadChip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in PCNSL samples.

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High-resolution genomic profiling of marginal zone B-cell lymphomas and variants

Project description:We studied marginal zone B-cell lymphomas of the gastrointestinal tract including seven small cell MALT lymphomas, eight composite lymphomas and thirteen large cell variants using SNP-array profiling. We found an increase of genomic complexity with lymphoma progression, and could identify gains of prominent (proto)oncogenes REL, ETS1, PTPN1, PTEN and KRAS that were associated exclusively with the large cell presentation of MALT lymphoma. Losses of ADAM3A and SCAPER, as well as gains of SIRPB1 occur during progression from small cell to large cell lymphoma. In two case studies, we examined lymphoma progression comparing two different regions of the same tumor and material acquired at two different time points from another lymphoma. Our analyses reveal genomic heterogeneity in both cases, supporting the theory of an oligoclonal tumor evolution model for MALT lymphomas and its variants. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved tumor samples. Copy number and loss of heterozygosity analysis of Affymetrix GenomeWide SNP 6.0 arrays was performed for 7 small cell MALT lymphomas, 8 large cell areas of Composite lymphomas and 13 large cell variants. Two independant hybridizations of one of the small cell MALT lymphoma and one of the large cell areas of Composite lymphoma Samples were performed.

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DNA methylation profiles of SMARCB1-deficient T cell lymphomas

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Array-based DNA methylation profiling of primary lymphomas of the central nervous system.

Project description:BackgroundAlthough primary lymphomas of the central nervous system (PCNSL) and extracerebral diffuse large B-cell lymphoma (DLBCL) cannot be distinguished histologically, it is still a matter of debate whether PCNSL differ from systemic DLBCL with respect to their molecular features and pathogenesis. Analysis of the DNA methylation pattern might provide further data distinguishing these entities at a molecular level.MethodsUsing an array-based technology we have assessed the DNA methylation status of 1,505 individual CpG loci in five PCNSL and compared the results to DNA methylation profiles of 49 DLBCL and ten hematopoietic controls.ResultsWe identified 194 genes differentially methylated between PCNSL and normal controls. Interestingly, Polycomb target genes and genes with promoters showing a high CpG content were significantly enriched in the group of genes hypermethylated in PCNSL. However, PCNSL and systemic DLBCL did not differ in their methylation pattern.ConclusionsBased on the data presented here, PCNSL and DLBCL do not differ in their DNA methylation pattern. Thus, DNA methylation analysis does not support a separation of PCNSL and DLBCL into individual entities. However, PCNSL and DLBCL differ in their DNA methylation pattern from non- malignant controls.

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Methylation in mouse lymphomas

Project description:We want to determine if there is a difference in the DNA methylation status of liver and Bone marrow in Cbs-/- mice under + or - ZnH20.

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