Investigation Title	Transcription profiling and comparative genomic hybridization (CGH) of human dermatofibrosarcoma protuberans (DFSP), an aggressive spindle cell neoplasm. Iassociated with the chromosomal translocation, t(17:22), which fuses the COL1A1 and PDGFbeta genes
Comment[Submitted Name]	DFSP
Experimental Design	transcription profiling by array	disease_state_design	transcription profiling by array
Experimental Design Term Source REF	EFO	mo	EFO
Comment[ArrayExpressReleaseDate]	2005-11-03
Comment[AEMIAMESCORE]	3
Comment[ArrayExpressAccession]	E-SMDB-2439
Comment[MAGETAB TimeStamp_Version]	2011-01-23 15:02:07 Last Changed Rev: 14857
Experimental Factor Name
Experimental Factor Type
Experimental Factor Term Source REF
Person Last Name	Demeter	Van De Rijn
Person First Name	Janos	Matt
Person Mid Initials
Person Email	jdemeter@genome.stanford.edu	mrijn@stanford.edu
Person Phone	726-0075	498-7154
Person Fax	723-7016	725-6902
Person Address	Dept. Genetics, CCSR 2255, Stanford, CA, USA, 94305
Person Affiliation	Stanford University	Stanford University
Person Roles	submitter	submitter
Person Roles Term Source REF	mo	mo
Quality Control Type
Quality Control Term Source REF
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Normalization Type
Normalization Term Source REF
Date of Experiment
Public Release Date	2005-11-03
PubMed ID
Publication DOI
Publication Author List	West RB, Harvell J, Linn SC, Lui CL, Prapong W, Hernandez-Boussard T, Montgomery K, Nielsen TO, Rubin BP, Patel R, Goldblum JR, Brown PO, Van De Rijn M
Publication Title	Apo D in Soft Tissue Tumors: A Novel Marker for Dermatofibrosarcoma Protuberans.
Publication Status
Publication Status Term Source REF
Experiment Description	Dermatofibrosarcoma protuberans (DFSP) is an aggressive spindle cell neoplasm. It is associated with the chromosomal translocation, t(17:22), which fuses the COL1A1 and PDGFbeta genes. We determined the characteristic gene expression profile of DFSP and characterized DNA copy number changes in DFSP by array-based comparative genomic hybridization (array CGH). Fresh frozen and formalin-fixed, paraffin-embedded samples of DFSP were analyzed by array CGH (four cases) and DNA microarray analysis of global gene expression (nine cases). The nine DFSPs were readily distinguished from 27 other diverse soft tissue tumors based on their gene expression patterns. Genes characteristically expressed in the DFSPs included PDGFbeta and its receptor, PDGFRB, APOD, MEOX1, PLA2R, and PRKCA. Array CGH of DNA extracted either from frozen tumor samples or from paraffin blocks yielded equivalent results. Large areas of chromosomes 17q and 22q, bounded by COL1A1 and PDGFbeta, respectively, were amplified in DFSP. Expression of genes in the amplified regions was significantly elevated. Our data shows that: 1) DFSP has a distinctive gene expression profile; 2) array CGH can be applied successfully to frozen or formalin-fixed, paraffin-embedded tumor samples; 3) a characteristic amplification of sequences from chromosomes 17q and 22q, demarcated by the COL1A1 and PDGFbeta genes, respectively, was associated with elevated expression of the amplified genes.
Protocol Name	URN:LSID:smd.stanford.edu:tagset.tagset\_no:25/MAGE.Protocol
Protocol Type	feature_extraction
Protocol Description	Title: Feature Extraction. Description: Software and parameters for feature extraction.
Protocol Parameters	Datafile type;Image Origin;
Protocol Hardware
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Protocol Term Source REF
SDRF File	E-SMDB-2439.sdrf.txt
Term Source Name	ncbitax	mo	ArrayExpress	EFO	mo
Term Source File	http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php
Term Source Version