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Methylation profiling classifies HIV-associated lymphoma

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 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.

ORGANISM(S): Homo sapiens

SUBMITTER: Akihiro Matsunaga

PROVIDER: E-GEOD-42372 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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DNA methylation profiling can classify HIV-associated lymphomas.

Matsunaga Akihiro A Hishima Tsunekazu T Tanaka Noriko N Yamasaki Maria M Yoshida Lui L Mochizuki Makoto M Tanuma Junko J Oka Shinichi S Ishizaka Yukihito Y Shimura Mari M Hagiwara Shotaro S

AIDS (London, England) 20140201 4

<h4>Background</h4>HIV-positive patients have a 60-fold to 200-fold increased incidence of non-Hodgkin lymphomas, including Burkitt lymphoma, diffuse large B-cell lymphoma, and primary central nervous system lymphoma. HIV-associated lymphomas frequently have features such as extranodal involvement, decreased responses to standard chemotherapy, and high relapse rates, which indicate a poor prognosis. General pathological features do not clearly differentiate HIV-associated lymphomas from non-HIV ...[more]

PMID: 24335480

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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.

2014-01-30 | GSE42372 | GEO

Cerebellum Illumina Inf 450 DNA methylation samples from HIV+ and HIV- human subjects

Project description:Genome wide DNA methylation profiles of cerebellum from HIV positive and HIV negative human subjects. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 486,000 CpGs. Dataset included 20 subjects from the USA. The epigenetic clock software (Horvath 2013) was used to measure epigenetic age acceleration effects and to relate them to HIV status. Bisulphite converted DNA from the 20 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. 8 HIV+ subjects were compared to 12 HIV- subjects.

2015-06-09 | E-GEOD-67748 | biostudies-arrayexpress

Frontal lobe (brain) Illumina Inf 450 DNA methylation samples from HIV+ and HIV- human subjects

Project description:Genome wide DNA methylation profiles of Frontal Lobe from HIV positive and HIV negative human subjects. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 486,000 CpGs. Dataset included 33 subjects from the USA. The epigenetic clock software (Horvath 2013) was used to measure epigenetic age acceleration effects and to relate them to HIV status. Bisulphite converted DNA from the 33 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. 8 HIV+ subjects were compared to 25 HIV- subjects.

2015-06-09 | E-GEOD-67749 | biostudies-arrayexpress

Array-based determination of DNA methylation in children born small for gestational age

Project description:Genome wide DNA methylation profiling of peripheral blood samples obtained from normal controls and children born SGA. Illumina's HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across approximately 450.000 CpGs. Bisulphite converted DNA from the 110 samples were hybridised to the Illumina HumanMethylation450 Beadchip.

2016-07-03 | E-GEOD-47880 | biostudies-arrayexpress

DNA methylation in colon mucosa samples from individuals with Crohns' disease or ulcerative colitis and normal controls

Project description:Genome wide DNA methylation profiling of Crohn's disease, ulcerative colitis, and normal colon mucosa samples. The Illumina Infinium HumanMethylation450 BeadChip v1.1 was used to obtain DNA methylation profiles across 482,421 CpGs in colon mucosa samples. Samples came from 9 Crohn's disease affected, 5 ulcerative colitis affected, and 10 normal individuals. Bisulfite converted DNA from the 24 samples were hybridized to the Illumina Infinium HumanMethylation450 BeadChip v1.1

2013-06-01 | E-GEOD-32146 | biostudies-arrayexpress

Molecular alterations in bone marrow mesenchymal stromal cells (BM-MSC) derived from acute myeloid leukemia patients (AML)

Project description:Genome wide methylation profiling of BM-MSC derived from AML patients in comparison to healthy donor controls using Illumina Infinium HumanMethylation450 Beadchip bisulfit converted genomic DNA extracted from BM-MSC samples (AML n=32) and healthy donor controls (n=12) were hybridized onto an Illumina Infinium HumanMethylation450 Beadchip

2016-03-30 | E-GEOD-79695 | biostudies-arrayexpress

The tissue is the issue: Improved methylome analysis from paraffin-embedded tissues by application of the HOPE-technique

Project description:Genome wide DNA methylation profiling of DNA samples obtained from normal lung tissue and lung carcinoma, either fixed by formalin (FFPE), HOPE (paraffin embedded) or cryo-preserved. Illumina's HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across approximately 450.000 CpGs. Bisulphite converted DNA from the 36 samples were hybridized to the Illumina HumanMethylation450 Beadchip.

2016-08-22 | E-GEOD-51077 | biostudies-arrayexpress

Genome wide methylation array analysis in T-ALL

Project description:In short: Genome wide promoter DNA methylation profiling of 43 T-ALL samples and 5 T-cell controls (normal bone marrow and stimulated T-cells) . The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Manuscript abstract: Background: Treatment of pediatric T-cell acute lymphoblastic leukemia (T-ALL) has improved, but there is a considerable fraction of patients experiencing a poor outcome. There is a need for better prognostic markers and aberrant DNA methylation is a candidate in other malignancies, but its potential prognostic significance in T-ALL is hitherto undecided. Design and Methods: Genome wide promoter DNA methylation analysis was performed in pediatric T-ALL samples (n=43) using arrays covering >27000 CpG sites. Clinical outcome was evaluated in relation to methylation status and compared with a contemporary T-ALL group not tested for methylation (n= 32). Results: Based on CpG island methylator phenotype (CIMP), T-ALL samples were subgrouped as CIMP+ (high methylation) and CIMP- (low methylation). CIMP- T-ALL patients had significantly worse overall and event free survival (p=0.02 and p=0.001, respectively) compared to CIMP+ cases. CIMP status was an independent factor for survival in multivariate analysis including age, gender and white blood cell count. Analysis of differently methylated genes in the CIMP subgroups showed an overrepresentation of transcription factors, ligands and polycomb target genes. Conclusions: We identified global promoter methylation profiling as being of relevance for subgrouping and prognostication of pediatric T-ALL. Bisulphite converted DNA from the 48 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

2013-07-01 | E-GEOD-42079 | biostudies-arrayexpress

Epigenome analysis of female identical twins

Project description:Genome wide DNA methylation profiling of blood samples from eight female identical twins of Han Chinese for forensic age prediction, age 21 to 32. The Illumina Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across approximately 485,000 CpGs at a single-nucleotide resolution. Samples included 8 pairs of identical female twins of Han Chinese. Bisulphite converted DNA isolated from blood of identical twin pairs were hybridised to the Illumina Infinium HumanMethylation450 BeadChip.

2015-12-08 | E-GEOD-65638 | biostudies-arrayexpress

Illumina Infinium HumanMethylation450 data for human whole blood samples and for mixtures of purified white blood cells reconstructing human blood

Project description:The objective of the study was to utilize DNA methylation to quantify human leukocyte subsets in human blood. This file contains data from an Illumina Infinium HumanMethlation450 for human whole blood samples as well as complex mixtures of DNA from purified human leukocyte subtypes in quantities that mimick human blood under different clinical conditions. Bisulphite converted DNA from the samples were hybridized to an Illumina Infinium HumanMethylation450 beadchip

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