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Homo sapiens

ABSTRACT: Genome-wide copy number analyses reveal genomic abnormalities involved in transformation of follicular lymphoma [SNP arrays]

OTHER RELATED OMICS DATASETS IN: GSE81184

PROVIDER: PRJNA279786 | ENA |

REPOSITORIES: ENA

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Genome-wide copy number analyses reveal genomic abnormalities involved in transformation of follicular lymphoma

Project description:Genome-wide copy number analyses reveal genomic abnormalities involved in transformation of follicular lymphoma

| PRJNA320838 | ENA

Homo sapiens

Project description:Genome-wide copy number analyses reveal genomic abnormalities involved in transformation of follicular lymphoma [gene expression]

| PRJNA320842 | ENA

Transcription profiling of human follicular and transformed follicular lymphoma samples revals genome-wide detection of recurring sites of uniparental disomy

Project description:Follicular lymphoma (FL) is the second most common B-cell malignancy representing one quarter of Non-Hodgkin's Lymphomas. Although the disease has a relatively long median survival, the illness follows a fluctuating course of progression punctuated by remissions of variable duration. For as many as half of patients, transformation to a more aggressive lymphoma (t-FL) may occur; this event is often associated with a particularly poor response to treatment. SNP analysis has revealed the presence of large regions of homozygosity in the absence of copy number change. These events can result in the selection of of daughter cells made homozygous for a pre-existing mutation. We have used SNPs array technology to investigate regions of loss of hetrozygosity in the absence of copy number change in order to establish the contribution of these abnormalities to the evolution of FL and t-FL. Experiment Overall Design: DNA from 26 pairs of follicular and transformed follicular lymphoma samples and 3 cell lines were analysed using Affymetrix 10K SNP arrays. The genotype data of transformed follicular lymphoma samples were compared with the data from the corresponding follicular lymphoma sample.

2008-06-17 | E-GEOD-7425 | biostudies-arrayexpress

Affymetrix SNP array data for follicular lymphoma (FL) and transformed follicular lymphoma (tFL) samples

Project description:Follicular lymphoma is the most common indolent non-Hodgkin's lymphoma involving germinal centre B cells, with a subset of patients undergoing transformation to a diffuse large B-cell lymphoma (DLBCL) morphology for which the clinical outcomes are poor. To elucidate the differences in copy number profiles between FL and tFL groups, we performed Affymetrix SNP 6.0 Array analysis on 31 paired FL-tFL cases. We wanted to identify and compare recurrent somatic copy number alterations (CNAs) between the two groups (FL vs. tFL). In addition, the concordance and discordance in the copy neutral loss of heterozygosity (cnLOH) between the two groups were also investigated to identify recurrent target gene regions. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from follicular lymphoma (FL), transformed follicular lymphoma (tFL) and matching germline (GL) sample (if available). Copy number analysis of Affymetrix SNP 6.0 Array were performed on 91 DNA samples, consisting of 31 patients. Among the 31 patients, 19 had matching germline samples, while 12 had no germline samples. The Log R Ratio (LRR) values and the B Allele Frequency (BAF) values were subsequently calculated to search for copy number aberrations and copy neutral (CN)-LOH in the FL and tFL samples. Paired and unpaired analyses were performed accordingly.

2013-10-01 | E-GEOD-42525 | biostudies-arrayexpress

Genome-wide copy number analyses reveal genomic abnormalities involved in transformation of follicular lymphoma

Project description:We studied 277 lymphoma samples (198 FL and 79 transformed FL [tFL]) using a single-nucleotide polymorphism array to identify the secondary chromosomal abnormalities that drive the development of FL and its transformation to diffuse large B-cell lymphoma. Affymetrix 250K NspI SNP arrays were performed according to the manufacturer's directions on DNA extracted from frozen follicular lymphoma or transformed follicular lymphoma tumor specimens

2015-03-30 | E-GEOD-67385 | biostudies-arrayexpress

Cell resilience to folate deprivation boosts aberration tolerance [Illumina]

Project description:We detected numerous copy number aberrations in SNP arrays from follicular lymphoma patients. Additionally, we found an outstanding homozygous state involving folic acid-related genes. To study a hypothetical association between both traits, we cultured folate-depleted cell lines. After restoring normal medium to the cultures, we performed CGH arrays to examine the induced copy number aberrations.

2019-05-23 | GSE54916 | GEO

Cell resilience to folate deprivation boosts aberration tolerance [Agilent]

2019-05-23 | GSE54919 | GEO

Genome-wide detection of recurring sites of uniparental disomy in folicular and transformed follicular lymphoma

2007-04-02 | GSE7425 | GEO

Affymetrix SNP array data for follicular lymphoma (FL) and transformed follicular lymphoma (tFL) samples

2013-10-01 | GSE42525 | GEO

Genotyping of human diagnostic Follicular Lymphoma (FL) patients to assess the prognostic relevance of aUPD reveals regions of acquired UPD at diagnosis of FL are associated with both overall survival and risk of transformation

Project description:SNP array analysis was performed using the Affymetrix 10K 2.0 Gene-chip array on DNA from 181 diagnostic Follicular Lymphoma (FL) patients to assess the prognostic relevance of aUPD. Genetic abnormalities were detected in 118/181 (65%) patients. Number of abnormalities was predictive of outcome; > 3 abnormalities was associated with inferior overall survival (OS) (p<0.03). Sites of recurrent aUPD were detected on 6p (n=25), 16p (n=22), 12q (n=17), 1p36 (n=14), 10q (n=8) and 6q (n=8). On multivariate analysis aUPD 1p36 correlated with shorter OS (p=0.05). aUPD 16p was predictive of transformation (p=0.03) and correlated with poorer progression free survival (p=0.02). Experiment Overall Design: Genomic DNA from 181 diagnostic FL samples were analysed using Affymetrix 10K 2.0 SNP arrays. Genomic DNA from the blood of ten unrelated Hapmap controls was used as reference for all FL samples. Prevalence and regions of homozygosity were identified.

2009-02-09 | E-GEOD-14582 | biostudies-arrayexpress

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