title: Molecular characterisation of soft tissue tumours: a gene expression study.
abstract: BACKGROUND
  Soft-tissue tumours are derived from mesenchymal cells such as fibroblasts, muscle cells, or adipocytes, but for many such tumours the histogenesis is controversial. We aimed to start molecular characterisation of these rare neoplasms and to do a genome-wide search for new diagnostic markers.
  
  
  METHODS
  We analysed gene-expression patterns of 41 soft-tissue tumours with spotted cDNA microarrays. After removal of errors introduced by use of different microarray batches, the expression patterns of 5520 genes that were well defined were used to separate tumours into discrete groups by hierarchical clustering and singular value decomposition.
  
  
  RESULTS
  Synovial sarcomas, gastrointestinal stromal tumours, neural tumours, and a subset of the leiomyosarcomas, showed strikingly distinct gene-expression patterns. Other tumour categories--malignant fibrous histiocytoma, liposarcoma, and the remaining leiomyosarcomas--shared molecular profiles that were not predicted by histological features or immunohistochemistry. Strong expression of known genes, such as KIT in gastrointestinal stromal tumours, was noted within gene sets that distinguished the different sarcomas. However, many uncharacterised genes also contributed to the distinction between tumour types.
  
  
  CONCLUSIONS
  These results suggest a new method for classification of soft-tissue tumours, which could improve on the method based on histological findings. Large numbers of uncharacterised genes contributed to distinctions between the tumours, and some of these could be useful markers for diagnosis, have prognostic significance, or prove possible targets for treatment.
authors.affiliation: Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Torsten O
authors.initials: TO
authors.lastname: Nielsen
authors.forename: Rob B
authors.initials: RB
authors.lastname: West
authors.forename: Sabine C
authors.initials: SC
authors.lastname: Linn
authors.forename: Orly
authors.initials: O
authors.lastname: Alter
authors.forename: Margaret A
authors.initials: MA
authors.lastname: Knowling
authors.forename: John X
authors.initials: JX
authors.lastname: O'Connell
authors.forename: Shirley
authors.initials: S
authors.lastname: Zhu
authors.forename: Mike
authors.initials: M
authors.lastname: Fero
authors.forename: Gavin
authors.initials: G
authors.lastname: Sherlock
authors.forename: Jonathan R
authors.initials: JR
authors.lastname: Pollack
authors.forename: Patrick O
authors.initials: PO
authors.lastname: Brown
authors.forename: David
authors.initials: D
authors.lastname: Botstein
authors.forename: Matt
authors.initials: M
authors.lastname: van de Rijn
mesh_terms: D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012509:Sarcoma / Q000145:classification / Q000235:genetics* / Q000473:pathology; D012983:Soft Tissue Neoplasms / Q000145:classification / Q000235:genetics* / Q000473:pathology