Genome-wide copy number variation in human metastatic melanoma cell lines
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE24890 | GEO | 2010/11/26
SECONDARY ACCESSION(S): PRJNA132185
REPOSITORIES: GEO
Similar Datasets
Project description:Illumina HumanExon510S-DUO bead arrays (Illumina Inc) were performed according to the manufacturer's protocol. Genome-wide copy number variation analysis was performed on the genomic DNA of two pairs of cell lines comprising of parental melanoma cell lines and corresponding resistant sub-lines.
2010-11-26 | E-GEOD-24890 | biostudies-arrayexpress
Project description:The exploration of copy number variation (CNV), notably of somatic cells, is an understudied aspect of genome biology. Any differences in the genetic make-up between twins derived from the same zygote represent an extreme example of somatic variation. We studied 19 pairs of monozygotic twins with either concordant or discordant phenotype using two platforms for genome-wide CNV analyses and show that CNVs exist within pairs in both groups. These findings impact our views of genotypic and phenotypic diversity in monozygotic twins, and suggest that CNV analysis in phenotypically discordant monozygotic twins may provide a powerful tool in identifying disease predisposition loci. Our results also imply that caution should be exercised with the interpretation of disease causality of de novo CNVs found in patients based on analysis of a single tissue in routine disease-related DNA diagnostics Analysis of copy number variability in concordant healthy monozygotic twin pairs as well as three monozygostic twin pairs discordant a Parkinsons disease (PD) phenotype using the Illumina HumanHap 300 dead chips. Genotyping using the HumanHap300-duo bead chip from Illumina, GEO accession GPL5711
2010-06-25 | E-GEOD-9608 | biostudies-arrayexpress
Project description:The PEO/PEA series of ovarian cancer cell lines was established in 1988 from samples in this dataset. Copy number profiling of ascitic effusion of PE cell lines on Illumina Infinium Human1M-Duo v3 BeadChips
2011-09-29 | E-GEOD-29398 | biostudies-arrayexpress
Project description: Not available
| S-EPMC4880759 | biostudies-other
Project description:The PEO/PEA series of ovarian cancer cell lines was established in 1988 from progressive samples from three separate cases of ovarian cancer (Langdon et al., 1988). Copy number profiling of PE lines on Illumina Infinium Human1M-Duo v3 BeadChips
2010-06-28 | E-GEOD-18461 | biostudies-arrayexpress
Project description:Melanoma is the least common form of skin cancer, but accounts for the most deaths. Dermatopathologists face difficult diganostic determinations with a subset of ambiguous melanoma cases. Copy number variation in melanoma can serve as an additional biomarker to distinguish melanoma from benign melanocytic lesions.
2016-04-22 | GSE68476 | GEO
Project description:In this study, we sought to indentify stable individual traits in developing metastatic melanoma, assess their stability in time, and analyze typical dynamics and common trends of genomic changes in individual cases of late stage metastatic cancer. To this end, we compared consecutive recurrent metastases developed by a special group of eight individuals with advanced metastatic melanoma, all developing several recurrent metastases over several months to years of natural disease evolution.
2013-12-31 | GSE38137 | GEO
Project description:In this study, we sought to indentify stable individual traits in developing metastatic melanoma, assess their stability in time, and analyze typical dynamics and common trends of genomic changes in individual cases of late stage metastatic cancer. To this end, we compared consecutive recurrent metastases developed by a special group of eight individuals with advanced metastatic melanoma, all developing several recurrent metastases over several months to years of natural disease evolution. Twenty-six recurrent melanoma metastases were surgically isolated from 8 patients experiencing relapse after one or more successful treatment intervention(s) with no signs of residual disease. Patients experiencing recurrent metastases were labeled with capital letters; M-bM-^@M-^\AM-bM-^@M-^], M-bM-^@M-^\BM-bM-^@M-^], M-bM-^@M-^\CM-bM-^@M-^], etc., their subsequent metastases as M-bM-^@M-^\A/1M-bM-^@M-^], M-bM-^@M-^\A/2M-bM-^@M-^], M-bM-^@M-^\B/1M-bM-^@M-^], M-bM-^@M-^\B/2M-bM-^@M-^], etc., while synchronous metastases in a given patient were labeled as M-bM-^@M-^\A/1aM-bM-^@M-^], M-bM-^@M-^\A/1bM-bM-^@M-^] etc. Another 22 melanoma cell lines isolated and maintained as above were expanded from melanoma patients with rapid disease curse, for whom only one metastasis was available. As no extended follow up was possible in these cases, the cell lines are considered representative of random time points in the natural course of metastatic melanoma. These cell lines were labeled with Arabic numbers, as M-bM-^@M-^\1M-bM-^@M-^], M-bM-^@M-^\2M-bM-^@M-^], M-bM-^@M-^]3M-bM-^@M-^], etc.
2013-12-31 | E-GEOD-38137 | biostudies-arrayexpress
Project description: Not available
| S-ECPF-GEOD-23056 | biostudies-other
Project description:Neuroblastoma is a tumour of the sympathetic nervous system, with a clinical phenotype resulting from complex patterns of genetic abnormalities, accounting for the most common extracranial neoplasia in childhood. Here we report 44 copy number variations, validated by qPCR, in paired tumour and blood samples of seven patients with neuroblastoma. Thirty four genes were included in altered regions while 11 altered regions did not apparently contain known genes. Five changes were present both in tumour and blood DNA samples in four patients, suggesting presence of germline and/or somatic changes maintained throughout tumorigenesis. Furthermore, some similar or identical changes were observed in different patients. The X chromosome showed the largest number of alterations. DNA from peripheral blood and tumour samples was isolated following using Qiagen DNA Blood Mini Kit. Microarray assays were performed in an Affymetrix platform with Cytogenetics Whole-Genome 2.7 M Array® (Affymetrix, Inc., Santa Clara, CA) for detecting copy number variation across coverage of the whole genome with the highest density of markers for superior resolution. Assays were performed following the procedure of Cytogenetics Copy Number Assay User Guide (Affymetrix®) and analysed with the Affymetrix® Chromosome Analysis Suite (ChAS) software. Gains and losses in tumour and blood samples from each patient were estimated with 95% confidence intervals.
2014-01-01 | E-GEOD-43454 | biostudies-arrayexpress