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Transcription profiling of human retinoblastoma samples to compare the transcriptomes of retinoblastoma with LOH on 16q to tumors without alterations on 16q

ABSTRACT: Genomic losses on chromosome 16q are among the most frequent alterations found in retinoblastoma. In this study, Affymetrix GeneChip analyses along with LOH analysis of microsatellie markers was used to identify candidate tumor suppressor loci in a set of retinoblastoma. We used microarrays to identify genes differentially expressed in retinoblastoma with LOH on 16q (M19484, M22590, M22641, M22860) compared to retinoblastoma without alterations in this region (M20517, M22067, M22233, M23209, M23449, M23818, M23896, M23978) Experiment Overall Design: To compare the transcriptosomes of retinoblastoma with and without LOH on 16q, total RNA was isolated from a 30 mg block of each tumor and subjected to Affymetrix microarray analysis on HG-U133A arrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Ludger Klein-Hitpass

PROVIDER: E-GEOD-5222 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Allelic loss in a minimal region on chromosome 16q24 is associated with vitreous seeding of retinoblastoma.

Gratias Sandrine S Rieder Harald H Ullmann Reinhard R Klein-Hitpass Ludger L Schneider Stephanie S Bölöni Réka R Kappler Martin M Lohmann Dietmar R DR

Cancer research 20070101 1

In addition to RB1 gene mutations, retinoblastomas frequently show gains of 1q and 6p and losses of 16q. To identify suppressor genes on 16q, we analyzed 22 short tandem repeat loci in 58 patients with known RB1 mutations. A subset of tumors was also investigated by conventional and matrix comparative genomic hybridization. In 40 of 58 (69%) tumors, we found no loss of heterozygosity (LOH) at any 16q marker. LOH was detected in 18 of 58 (31%) tumors, including five with allelic imbalance at some ...[more]

PMID: 17210724

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Expression data from retinoblastoma

Project description:Genomic losses on chromosome 16q are among the most frequent alterations found in retinoblastoma. In this study, Affymetrix GeneChip analyses along with LOH analysis of microsatellie markers was used to identify candidate tumor suppressor loci in a set of retinoblastoma. We used microarrays to identify genes differentially expressed in retinoblastoma with LOH on 16q (M19484, M22590, M22641, M22860) compared to retinoblastoma without alterations in this region (M20517, M22067, M22233, M23209, M23449, M23818, M23896, M23978) Keywords: Disease progression

2007-01-29 | GSE5222 | GEO

Gene expression profiles of retinoblastoma cell lines

Project description:In order to identify the gene targets of frequently altered chromosomal regions in retinoblastoma, a meta-analysis of genome-wide copy number alterations studies on primary retinoblastoma tissue and retinoblastoma cell lines was performed. Published studies were complemented by copy number and gene expression analysis on primary and cell line samples of retinoblastoma. This dataset includes the gene expression data of the retinoblastoma cell lines This data set contains the gene expression (Affymetrix human genome u133 plus 2.0 PM) results for 7 unique retinoblastoma cell lines. For one of the 7 unique cell lines, 3 RNA isolations were performed and were profiled on seperate arrays, adding up to 9 unique array files. Copy number data for primary retinoblastoma (tumor and blood DNA) and retinoblastoma cell lines are available (controlled-access) at the European Genomics Archive. Gene expression data of primary retinoblastoma is available under GSE59983. The GSE59983 records represent the primary tissue gene expression data and the CN data will be deposited into a controlled-access database, probably EGA.

2016-03-31 | E-GEOD-77094 | biostudies-arrayexpress

Affymetrix SNP array data for cone precursor derived retinoblastoma like samples

Project description:Retinoblastoma is a childhood retinal tumor that initiates in response to biallelic RB1 inactivation. We show that post-mitotic human cone precursors are uniquely sensitive to the oncogenic effects of Rb depletion. Rb knockdown induced cone precursor proliferation in prospectively isolated populations. SNP-array analysis of two Rb/p130-depleted cone precursor cell lines, revealing no megabase-size loss of heterozygosity (LOH) or copy number alterations (CNAs). SNP-array analysis of one Rb/p130-depleted (tumor 1) or one Rb-depleted (tumor 2) cone precursor-derived tumors, revealing no megabase-size LOH or CNAs, consistent with the lack of DNA copy number alterations in some retinoblastomas. Thus, the cone precursor tumors resembled human retinoblastomas at the molecular cytogenetic level. High resolution SNP-array DNA copy number analyses were performed using CytoScan® HD (Affymetrix, 901835) according to the manufacturer's directions. Data were analyzed using Chromosome Analysis Suite 2.0 (Affymetrix). DNA was extracted from two Rb/p130 depleted cone precursor cell lines and two cryopreserved mouse retinoblastoma samples from eyes xenograted with Rb/p130 or Rb depleted cone precursors. Affymetrix SNP analysis on retinoblastoma cell lines Y79, RB176, and WERI were used as control. Normal human genome 19 was used as reference.

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Affymetrix SNP array data for cone precursor derived retinoblastoma like samples

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Germline Variant in Ctcf Links Mental Retardation to Wilms Tumor Predisposition

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QUANTITATIVE PHOSPHOPROTEOMIC PROFILING OF PRIMARY RETINOBLASTOMA TUMORS

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