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Methylation profiling categorizes HIV-associated lymphomas in two distinctive groups

ABSTRACT: HIV-positive patients have a higher risk of non-Hodgkin's lymphoma with poor prognostic features. To characterize features of HIV-associated lymphoma, we compared the DNA methylation profiles of 803 cancer-related genes in between 9 HIV-associated and 12 non-HIV lymphoma samples by Illumina GoldenGate Methylation Cancer Panel I microarray.

ORGANISM(S): Homo sapiens

PROVIDER: GSE42626 | GEO | 2014/01/30

SECONDARY ACCESSION(S): PRJNA182372

REPOSITORIES: GEO

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Methylation profiling categorizes HIV-associated lymphomas in two distinctive groups

Project description:HIV-positive patients have a higher risk of non-Hodgkin's lymphoma with poor prognostic features. To characterize features of HIV-associated lymphoma, we compared the DNA methylation profiles of 803 cancer-related genes in between 9 HIV-associated and 12 non-HIV lymphoma samples by Illumina GoldenGate Methylation Cancer Panel I microarray. Bisulfite-converted DNA from the 42 samples (duplicate analysis of 21 samples) were analyzed to obtain the methylation profiles of cancer-associated genes by using Illumina GoldenGate Methylation Cancer Panel I microarray.

2014-01-30 | E-GEOD-42626 | biostudies-arrayexpress

Methylation profiling classifies HIV-associated lymphoma

2014-01-30 | GSE42372 | GEO

Methylation profiling classifies HIV-associated lymphoma

Project description:HIV-positive patients have a higher risk of non-Hodgkin's lymphoma with poor prognostic features. To characterize features of HIV-associated lymphoma, we compared the genome-wide DNA methylation profiles in between 11 HIV-associated and 20 non-HIV lymphoma samples by Illumina Infinium HumanMethylation450 BeadChip v1.0. Bisulfite-converted DNA from the 31 samples were analyzed to obtain the genome-wide methylation profile by using Illumina Infinium HumanMethylation450 BeadChip microarray.

2014-01-30 | E-GEOD-42372 | biostudies-arrayexpress

Homo sapiens

Project description:DNA Methylation in Hodgkin's and non-Hodgkin's lymphoma

| PRJNA225479 | ENA

Molecular Classification of AIDS-Related Lymphomas

2010-03-07 | E-GEOD-17189 | biostudies-arrayexpress

Molecular Classification of AIDS-Related Lymphomas

2010-03-01 | GSE17189 | GEO

Molecular Classification of AIDS-Related Lymphomas [including third-party data]

Project description:Gene expression profiling (GEP) of ARL patient samples was done to determine whether gene expression signatures derived from HIV- lymphomas retained their ability to molecularly classify HIV+ lymphomas. The GEP-based predictors robustly classified ARL tumors, distinguishing molecular Burkitt lymphoma (BL) and diffuse large B-cell lymphoma (DLBCL), as well as activated B-cell-like (ABC) and germinal center B-cell-like (GCB) molecular subtypes of DLBCL. Gene expression profiles were used to identify coordinately regulated gene sets and pathways that differ between HIV+ and HIV- lymphomas of corresponding molecular subtype. Frozen tumor biopsies were obtained from 20 HIV-positive patients with an AIDS-defining lymphoma. Cases were ascertained at the University of Nebraska Medical Center and through the NCI AIDS and Cancer Specimen Resource tumor bank. Sufficient RNA for hybridization to Affymetrix U133 plus 2 arrays was obtained on 17 ARL cases. Details of all 20 HIV-positive patients can be found in the supplementary file below. Third party array data from HIV- lymphomas of corresponding molecular subtype were used for the comparison and molecular classification of the HIV+ cases in this study. The third party HIV- lymphoma samples include the following. [1] HIV- lymphoma, BL cases: 84 samples profiled on the Affymetrix HG U133 Plus 2 array. The data are publicly available on the website companion to Dave et al. NEJM 2006; Volume 354:13-24 (http://llmpp.nih.gov/BL/) and were used 'as is' (ie, not reanalyzed). [2] HIV- lymphoma, DLBCL cases: 200 of the 414 cases in Series GSE10846 (listed in the supplementary file below). These included all R-CHOP treated cases of either ABC or GCB subtype. These data were also used as is. These data were published in Lenz et al. NEJM 2008; Volume 359: 2313-2323.

2012-07-17 | E-GEOD-17372 | biostudies-arrayexpress

Molecular Classification of AIDS-Related Lymphomas [including third-party data]

2012-07-18 | GSE17372 | GEO

Genome-wide DNase-Seq and methylation profiles in Hodgkin's and non-Hodgkin's lymphoma

Project description:Genome-wide DNase-Seq and methylation profiles in Hodgkin's and non-Hodgkin's lymphoma

| PRJNA225476 | ENA

Gene expression profiles of Hodgkin’s lymphoma cells

Project description:By using high-density DNA microarrays, we analyzed the gene-expression profile of Hodgkin's lymphoma cell lines. RNA was extracted from established Hodgkin's lymphoma cell lines and analyzed with Affymetrix Human Exon 1.0ST microarrays.

2013-07-16 | E-GEOD-47686 | biostudies-arrayexpress

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