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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Comparative genomic hybridization of 100 favourable histology Wilms tumour samples taken at immediate nephrectomy in order to identify changes in DNA copy number associated with clinical outcome

ABSTRACT: We have carried out microarray-based comparative genomic hybridisation (arrayCGH) on 100 favourable histology Wilms tumour samples taken at immediate nephrectomy in order to identify changes in DNA copy number associated with clinical outcome. Tumour DNA was co-hybridised with normal female genomic DNA onto microarrays consisting of 4263 BAC clones with an approximate 1Mb spacing throughout the genome. Data was normalised and quality-filtered, an adapted weights smoothing algorithm fitted, and changes in DNA copy number assessed for each clone.

ORGANISM(S): Homo sapiens

DISEASE(S): normal

SUBMITTER: Anita Grigoriadis

PROVIDER: E-TABM-10 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Amplification and overexpression of CACNA1E correlates with relapse in favorable histology Wilms' tumors.

Natrajan Rachael R Little Suzanne E SE Reis-Filho Jorge S JS Hing Lara L Messahel Boo B Grundy Paul E PE Dome Jeffrey S JS Schneider Toni T Vujanic Gordan M GM Pritchard-Jones Kathy K Jones Chris C

Clinical cancer research : an official journal of the American Association for Cancer Research 20061201 24

<h4>Purpose</h4>The most well established molecular markers of poor outcome in Wilms' tumor are loss of heterozygosity at chromosomes 1p and/or 16q, although to date no specific genes at these loci have been identified. We have previously shown a link between genomic gain of chromosome 1q and tumor relapse and sought to further elucidate the role of genes on 1q in treatment failure.<h4>Experimental design</h4>Microarray-based comparative genomic hybridization identified a microamplification harb ...[more]

PMID: 17189400

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Comparative genomic hybridization of 17 favourable histology Wilms tumour samples taken at immediate nephrectomy in order to identify changes in DNA copy number associated with clinical outcome

Project description:We have carried out microarray-based comparative genomic hybridisation (arrayCGH) on 17 Favourable histology Wilms tumour samples taken at immediate nephrectomy in order to identify changes in DNA copy number associated with clinical outcome. Tumour DNA was co-hybridised with normal female genomic DNA onto microarrays consisting of 2118 BAC clones with tiling-path coverage of chromosome 1. Data was normalised and quality-filtered, an adapted weights smoothing algorithm fitted, and changes in DNA copy number assessed for each clone.

2006-05-11 | E-TABM-13 | biostudies-arrayexpress

Comparative genomic hybridization of human perilobar nephrogenic rest and matching Wilms tumours to identify changes in DNA copy number associated with IGF-driven Wilms tumorigenesis

Project description:We have carried out microarray-based comparative genomic hybridisation (arrayCGH) on 50 perilobar nephrogenic rest and 25 matching Wilms tumours in order to identify changes in DNA copy number associated with IGF-driven Wilms tumorigenesis. All patient samples were formalin fixed-paraffin embedded archival material. Tumour DNA was co-hybridised with normal female genomic DNA onto 5.8K, 0.9Mb-spaced (E-MEXP-213) and/or a 16K, 100kb-spaced BAC array. Data was normalised and quality-filtered, an adapted weights smoothing algorithm fitted, and changes in DNA copy number assessed for each clone.

2009-02-25 | E-TABM-436 | biostudies-arrayexpress

Comparative genomic hybridization of high grade gliomas arising in children and young people

Project description:As genome-scale technologies begin to unravel the complexity of the equivalent tumours in adults, detailed characterisation of high grade gliomas in children have until recently been lacking. In order to validate and extend investigations of the differences between paediatric and adult tumours, we carried out copy number profiling by array CGH using a 32K BAC platform on 63 formalin-fixed paraffin-embedded (FFPE) cases of high grade glioma arising in children and young people (<23 yrs).

2010-07-01 | E-TABM-857 | biostudies-arrayexpress

Comparative genomic hybridization of kidney samples from Wilms tumor patients to accurately map 1p13 breakpoints

Project description:Wilms tumour karyotypes frequently exhibit recurrent, large-scale chromosomal imbalances, among the most common of which are concurrent loss of 1p and gain of 1q. We have previously identified a novel breakpoint at 1p13 by 1Mb-spaced array CGH, and undertook a fine-tiling oligonucleotide array approach to accurately map the region in four tumours exhibiting rearrangements at this locus. The use of a 10 bpspaced platform revealed that all four tumours in fact harboured different breakpoints, which were mapped to target four distinct genes PHTF1, DCLRE1B, TRIM33 and NRAS. The precise breakpoint interval was confirmed for one case to lie within intron 3 of DCLRE1B by quantitative copy number PCR and RT-PCR. In addition, expression profiling revealed a pattern of down- and up-regulation of genes either side of the breakpoint in all cases. Although it appears that no single gene is the driver of this rearrangement, this study highlights the power of fine-tiling oligonucleotide arrays to delineate breakpoint regions identified by other genome-wide screens. Processed data is provided as one archive per processed data file obtained via clicking on the ftp link. Related experiment E-TABM-164.

2007-03-21 | E-TABM-155 | biostudies-arrayexpress

Transcription profiling, comparative genomic hybridization, genotyping and methylation profiling by array of human breast cancer cell lines

Project description:Integrative analysis of breast cancer cell lines, using expression, comparative genomics, SNP and methylation profiling

2012-11-09 | E-TABM-928 | biostudies-arrayexpress

TP53 mutational status is a potential marker for risk stratification in Wilms tumour with diffuse anaplasia

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-08-30 | E-GEOD-60940 | biostudies-arrayexpress

TP53 mutational status is a potential marker for risk stratification in Wilms tumour with diffuse anaplasia [aCGH]

Project description:The presence of diffuse anaplasia in Wilms tumours (DAWT) is associated with TP53 mutations and poor outcome. As patients receive intensified treatment, we sought to identify whether TP53 mutational status confers additional prognostic information. We studied 40 patients with DAWT with anaplasia in the tissue from which DNA was extracted and analysed for TP53 mutations and 17p loss. The majority of cases were profiled by copy number (n=32) and gene expression (n=36) arrays. TP53 mutational status was correlated with patient event-free and overall survival, genomic copy number instability and gene expression profiling. From the 40 cases, 22 (55%) had TP53 mutations (2 detected only after deep-sequencing), 20 of which also had 17p loss (91%); 18 (45%) cases had no detectable mutation but three had 17p loss. Tumours with TP53 mutations and/or 17p loss (n=25) had an increased risk of recurrence as a first event (p=0.03, hazard ratio (HR), 3.89; 95% confidence interval (CI), 1.26-16.0) and death (p=0.04, HR, 4.95; 95% CI, 1.36-31.7) compared to tumours lacking TP53 abnormalities. DAWT carrying TP53 mutations showed increased copy number alterations compared to those with wild-type, suggesting a more unstable genome (p=0.03). These tumours showed deregulation of genes associated with cell cycle and DNA repair biological processes. This study provides evidence that TP53 mutational analysis improves risk stratification in DAWT. This requires validation in an independent cohort before clinical use as a biomarker. 32 tumour samples were profiled by aCGH, in 2-colour hybridisations with common pooled unrelated normal genomic DNA in the reference channel. There were no replicates.

2014-08-30 | E-GEOD-60852 | biostudies-arrayexpress

Comparative genomic hybridization by array of human lymphoma samples

Project description:Profiling of DNA copy number alterations by array CGH in 100 sequential samples from 44 patients diagnosed with follicular lymphoma using a inhouse 1 Mb BAC/PAC array CGH

2010-11-03 | E-TABM-930 | biostudies-arrayexpress

Diverse routes to oral cancer differing in genome instability and risk for cervical node metastasis

Project description:Clinically evident oral lesions, oral epithelial dysplasia, precede development of oral squamous cell carcinomas (SCC) and are considered to transform to cancer by acquisition of genetic or epigenetic alterations. Here, we show that, +3q24-qter, -8pter-p23.1, +8q12-q24.2 and +20 are early events identifying two pathways to oral cancers that differ in clinical behavior. One or more of these copy number aberrations is present in the major subgroup (3q8pq20 subtype, 75-80% of lesions) that develops with chromosomal instability and risk for metastasis, while they are absent from the smaller and chromosomally stable non-3q8pq20 subgroup (20-25% of lesions) associated with low risk for metastasis. Thus, +3q, -8p, +8q and +20 is a biomarker for oral SCC metastasis. On the other hand, while increased numbers of genomic alterations can be harbingers of progression to cancer, dysplastic lesions lacking copy number changes cannot be considered benign as they are potential precursors to non-3q8pq20 oral SCC. 63 oral SCCs and adjacent regions of normal tissue, 44 oral dysplasias

2011-11-18 | E-GEOD-28407 | biostudies-arrayexpress

Transcriptomic responses to high water temperature in Pacific salmon [2007]

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2013-11-01 | E-GEOD-42555 | biostudies-arrayexpress

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