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Regions of acquired UPD at diagnosis of FL are associated with both overall survival and risk of transformation

ABSTRACT: 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). Keywords: Genomic analysis of FL samples

ORGANISM(S): Homo sapiens

PROVIDER: GSE14582 | GEO | 2009/01/30

SECONDARY ACCESSION(S): PRJNA111699

REPOSITORIES: GEO

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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

SNP chip data of MCL

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2009-11-13 | GSE18820 | GEO

RNA Sequencing Quantitative Analysis of cell lines derived from tumours from two mouse models of human osteosarcoma that recapitulate clinically distinct human osteosarcoma subtypes.

Project description:Purpose: Osteosarcoma (OS) is the most common primary bone malignancy. OS consists of several subtypes including fibroblastic, osteoblastic and chondroblastic OS. We have developed genetically engineered mouse models of human OS that recapitulate two distinct subtypes, fibroblastic (Osx-CreLox p53-/- Rb-/-) and osteoblastic (Osx-Cre shRNA p53-/-) OS. The goal of this study was to identify transcriptional differences that distinguish the two subtypes. Methods: mRNA profiles of cell lines derived from tumours from Osx-Cre p53fl/fl Rbfl/fl (fibroblastic OS) and Osx-Cre shRNA TRE-p53.1224 pRbfl/fl (osteoblastic OS) mouse models were generated by RNA sequencing, in triplicate, using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript level with TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 12,436 transcripts in the tumours of Osx-Cre p53fl/fl Rbfl/fl and 12,074 Osx-Cre shRNA TRE-p53.1224 pRbfl/fl with the TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes. Conclusions: Our study represents a detailed analysis of OS subtype transcriptomes generated by RNA-seq technology.

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RNA Sequencing Quantitative Analysis of cell lines derived from tumours from two mouse models of human osteosarcoma that recapitulate clinically distinct human osteosarcoma subtypes.

2015-07-06 | E-GEOD-58916 | biostudies-arrayexpress

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Project description:Most treatment failures of glioblastoma (GBM) occur within high-dose radiation fields, in part due to increased capacity for DNA damage repair. We retrospectively quantified the expression levels of key repair genes GBM tissue samples and correlated those expression levels with overall survival (OS). Differential expression analysis identified 7 repair genes that were significantly upregulated in GBM tissues relative to the controls (> 4-fold difference and all adjusted p values < 0.001). Of these 7 genes, Cox proportional hazards models identified RAD51 as being associated with an increased risk of death (HR = 3.49; p = 0.03). Kaplan-Meier (KM) analysis also demonstrated that patients with high levels of RAD51 had significantly shorter OS compared to patients with low levels (median OS of 10.6 months vs 20.1 months, log-rank p = 0.03). These findings were then validated in a larger external dataset of 162 patients using publicly available gene expression data quantified by the same NanoString technology (median OS of 13.8 months vs. 17.4 months; log-rank p = 0.006)

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Analysis of the coding exome of follicular lymphoma

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2014-01-17 | GSE50973 | GEO

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2013-01-05 | E-GEOD-43290 | biostudies-arrayexpress

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Project description:Identify shear and side-specific miRNAs in Human Aortic Valvular Endothelial Cells using the following conditions: 1) fHAVEC exposed to OS (FO), 2) vHAVEC exposed to OS (VO), 3) fHAVEC exposed to LS (FL), and 4) vHAVEC exposed to LS (VL). 24 samples; n=6 for the following 4 groups: FO, VO, FL, and VL. 48 samples total (24 miRNA, 24mRNA)

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Discovery of Shear- and Side-specific mRNAs and miRNAs in Human Aortic Valvular Endothelial Cells

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