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Title: Affymetrix copy number data for melanoma cell line mapping      
dateReleased:
04-07-2011
description:
We searched for putative phenotypic and genotypic differences between primary lesions and melanoma metastasis. Therefore, we investigated melanoma cells derived either from the primary tumor or from lymph node metastasis of the same individual patient. In vitro studies revealed high migratory and anchorage-independent growth of metastasis-derived cells. Unexpectedly, whole genome DNA analysis displayed a total of 10 homozygous losses in the primum-derived cell line, whereas the metastasis–derived cell line only shared 5 of those losses. We further tested these cells in a mouse model for intradermal melanoma growth and detected fast growth of the metastasis-derived cell line and delayed growth of primum-derived cells. However, after re-grafting of primum-derived cells, tumor growth kinetic was accelerated and therefore comparable to metastasis-derived cells. Moreover, re-grafted primum-derived cells now also harboured the same reduced DNA deletion pattern, identical to human metastasis-derived cells. We conclude that our xenotransplantation model mimics clonal selection from a heterogeneous starting population, and we suggest that tumor cell progression at the metastatic niche can occur parallel and independently from the primary tumor. Therefore, we propose that for mutation-targeted therapy approaches, the genotyping procedure should include primary as well as metastatic melanoma biopsies. DNA was extracted from in vitro grown cell lines, and Affymetrix SNP6.0 arrays were performed according to the manufacturer's instructions. Intensity Log2 ratios were used to manually search for homozygous deletions via the genotyping console.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-22461
refinement:
raw
alternateIdentifiers:
22461
keywords:
functional genomics
dateModified:
01-27-2013
availability:
available
types:
gene expression
name:
Homo sapiens
ID:
A-AFFY-142
name:
Affymetrix GeneChip Genome-Wide Human SNP 6.0 [GenomeWideSNP_6]
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-22461/E-GEOD-22461.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-22461/E-GEOD-22461.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22461
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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