Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA133103 | ENA |
REPOSITORIES: ENA
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Project description:All cancers are diseases of the genome. A combination of somatic point mutations, focal amplifications and deletions, and chromosome level aberrations conspire to disrupt gene expression and the interplay between signaling pathways that control normal growth and tissue homeostasis. Here we investigate somatic copy number abberations in metastatic melanomas. A metastatic melanoma was assayed on Affymetrix SNP arrays to detect copy number abberations. 7 cutaneous melanomas as well as their matched control ( peripheral blood lymphocytes (PBL) or Epstein-Barr virus transformed lymphoblastoid cell lines ) and 2 control melanocytes were assayed on Illumina SNP arrays. 7 metastatic melanomas were hybridized on Agilent CGH arrays using donor matched control as reference.
2011-04-07 | E-GEOD-22928 | biostudies-arrayexpress
Project description:Melanoma cell lines were genotyped to evaluate copy number differences between nodular melanoma (NM) and superficial spreading melanoma (SSM). Cell lines were also evaluated for copy number alterations in the SKP2/p27 axis. Affymetrix SNP arrays were performed according to manufacturer's instructions using DNA extracted from 18 melanoma cell lines and 4 melanocyte controls. Affymetrix SNP6.0 Array data for melanoma cell lines Copy number analysis of Affymetrix SNP 6.0 arrays was performed on 18 melanoma cell lines including 2 primary superficial spreading melanoma, 2 primary nodular melanoma, 2 metastatic nodular melanoma, and 12 metastatic cell lines. Four melanocyte control lines were also evaluated including 2 immortalized melanocyte cell lines (Hermes 1 and 2B) and 2 normal melanocyte lines cultured from neonatal foreskin (HEM-N and HEM-LP) that were used to construct the baseline for copy number analysis.
2010-10-21 | E-GEOD-22305 | biostudies-arrayexpress
Project description:BACKGROUND: Cervical carcinoma develops as a result of multiple genetic alterations. Different studies investigated genomic alterations in cervical cancer mainly by means of metaphase comparative genomic hybridization (mCGH) and microsatellite marker analysis for the detection of loss of heterozygosity (LOH). Currently, high throughput methods such as array comparative genomic hybridization (array CGH), single nucleotide polymorphism array (SNP array) and gene expression arrays are available to study genome-wide alterations. Integration of these 3 platforms allows detection of genomic alterations at high resolution and investigation of an association between copy number changes and expression. RESULTS: Genome-wide copy number and genotype analysis of 10 cervical cancer cell lines by array CGH and SNP array showed highly complex large-scale alterations. A comparison between array CGH and SNP array revealed that the overall concordance in detection of the same areas with copy number alterations (CNA) was above 90%. The use of SNP arrays demonstrated that about 75% of LOH events would not have been found by methods which screen for copy number changes, such as array CGH, since these were LOH events without CNA. Regions frequently targeted by CNA, as determined by array CGH, such as amplification of 5p and 20q, and loss of 8p were confirmed by fluorescent in situ hybridization (FISH). Genome-wide, we did not find a correlation between copy-number and gene expression. At chromosome arm 5p however, 22% of the genes were significantly upregulated in cell lines with amplifications as compared to cell lines without amplifications, as measured by gene expression arrays. For 3 genes, SKP2, ANKH and TRIO, expression differences were confirmed by quantitative real-time PCR (qRT-PCR). CONCLUSION: This study showed that copy number data retrieved from either array CGH or SNP array are comparable and that the integration of genome-wide LOH, copy number and gene expression is useful for the identification of gene specific targets that could be relevant for the development and progression in cervical cancer. Keywords: DNA copynumber RNA expression correlation
2007-07-31 | GSE8605 | GEO
Project description:Genome-Wide Analysis of Somatic Copy Number Alterations and Gene Expression in Metastatic Melanoma: RNA-Seq
| PRJNA133097 | ENA
Project description:BACKGROUND: Cervical carcinoma develops as a result of multiple genetic alterations. Different studies investigated genomic alterations in cervical cancer mainly by means of metaphase comparative genomic hybridization (mCGH) and microsatellite marker analysis for the detection of loss of heterozygosity (LOH). Currently, high throughput methods such as array comparative genomic hybridization (array CGH), single nucleotide polymorphism array (SNP array) and gene expression arrays are available to study genome-wide alterations. Integration of these 3 platforms allows detection of genomic alterations at high resolution and investigation of an association between copy number changes and expression. RESULTS: Genome-wide copy number and genotype analysis of 10 cervical cancer cell lines by array CGH and SNP array showed highly complex large-scale alterations. A comparison between array CGH and SNP array revealed that the overall concordance in detection of the same areas with copy number alterations (CNA) was above 90%. The use of SNP arrays demonstrated that about 75% of LOH events would not have been found by methods which screen for copy number changes, such as array CGH, since these were LOH events without CNA. Regions frequently targeted by CNA, as determined by array CGH, such as amplification of 5p and 20q, and loss of 8p were confirmed by fluorescent in situ hybridization (FISH). Genome-wide, we did not find a correlation between copy-number and gene expression. At chromosome arm 5p however, 22% of the genes were significantly upregulated in cell lines with amplifications as compared to cell lines without amplifications, as measured by gene expression arrays. For 3 genes, SKP2, ANKH and TRIO, expression differences were confirmed by quantitative real-time PCR (qRT-PCR). CONCLUSION: This study showed that copy number data retrieved from either array CGH or SNP array are comparable and that the integration of genome-wide LOH, copy number and gene expression is useful for the identification of gene specific targets that could be relevant for the development and progression in cervical cancer. Keywords: DNA copynumber RNA expression correlation Cervival cancer cell lines were hybridized to Affymetrix Focus arrays in duplicate. Correlations were made with copynumber profiles from arrayCGH and SNP arrays.
2010-06-05 | E-GEOD-8605 | biostudies-arrayexpress
Project description:Background: Metastases result in 90% of all cancer deaths. Prostate cancer primary tumors evolve to become metastatic through selective alterations, such as amplification and deletion of genomic DNA. Methods: Genomic DNA copy number alterations were used to develop a gene signature that measured the metastatic potential of a prostate cancer primary tumor. We studied the genomic landscape of these alterations in 294 primary tumors and 49 metastases from 5 independent cohorts. Receiver-operating characteristic cross-validation and Kaplan-Meier survival analysis were performed to assess the accuracy of our predictive model. The signature was measured in a panel of 337 cancer cell lines from 29 different tissue origins. Results: We identified 399 copy number alterations around genes that were over-represented in metastases and predictive of whether a primary tumor will metastasize. Cross-validation analysis resulted in a predictive accuracy of 80.5% and log rank analysis of the metastatic potential score was significantly related to the endpoint of metastasis-free survival (p=0.014). The metastatic signature was observed in cell lines originating from lung, breast, colon, thyroid, rectum, pancreas and melanoma. The signature was comprised in part of genes of known or putative metastatic role — 8 solute carrier genes, 6 Cadherin family genes and 5 potassium channel genes — that function in metabolism, cell-to-cell adhesion and escape from anoikis/apoptosis. Conclusions: Somatic Copy number alterations are an independent predictor of metastatic potential. The data indicate a prognostic utility for using primary tumor genomics to assist in clinical decision making and developing therapeutics for prostate and likely other cancers. genomic DNA from 29 prostate cancer tumors with matched normals run on Affymetrix 6.0 SNP arrays.
2013-12-01 | E-GEOD-27105 | biostudies-arrayexpress
Project description:Comparison between the copy number of differentially methylated sites between lymph node metastasis from melanoma patients with good prognosis and melanoma brain metastasis. All samples are taken from different patients, and were established as cell lines in the John Wayne Cancer Institute. Sixteen metastatic melanomas were run on Affymetrix Genome-Wide Human SNP Array 6.0. Lymph node metastases and brain metastases genetic copy number variations were compared.
2013-09-19 | E-GEOD-44019 | biostudies-arrayexpress
Project description:Melanoma cell lines were genotyped to evaluate copy number differences between nodular melanoma (NM) and superficial spreading melanoma (SSM). Cell lines were also evaluated for copy number alterations in the SKP2/p27 axis. Affymetrix SNP arrays were performed according to manufacturer's instructions using DNA extracted from 18 melanoma cell lines and 4 melanocyte controls.
2010-10-21 | GSE22305 | GEO
Project description:Copy number analysis of recurrent metastatic melanoma lesions
| PRJNA167382 | ENA