title: Microarray-based copy number and expression profiling in dedifferentiated and pleomorphic liposarcoma.
abstract: Sixteen dedifferentiated and pleomorphic liposarcomas were analyzed by comparative genomic hybridization (CGH) to genomic microarrays (matrix-CGH), cDNA-derived microarrays for expression profiling, and by quantitative PCR. Matrix-CGH revealed copy number gains of numerous oncogenes, i.e., CCND1, MDM2, GLI, CDK4, MYB, ESR1, and AIB1, several of which correlate with a high level of transcripts from the respective gene. In addition, a number of genes were found differentially expressed in dedifferentiated and pleomorphic liposarcomas. Application of dedicated clustering algorithms revealed that both tumor subtypes are clearly separated by the genomic profiles but only with a lesser power by the expression profiles. Using a support vector machine, a subset of five clones was identified as "class discriminators." Thus, for the distinction of these types of liposarcomas, genomic profiling appears to be more advantageous than RNA expression analysis.
authors.affiliation: Deutsches Krebsforschungszentrum, Abteilung Molekulare Genetik (H0700), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.
authors.forename: Björn
authors.initials: B
authors.lastname: Fritz
authors.forename: Falk
authors.initials: F
authors.lastname: Schubert
authors.forename: Gunnar
authors.initials: G
authors.lastname: Wrobel
authors.forename: Carsten
authors.initials: C
authors.lastname: Schwaenen
authors.forename: Swen
authors.initials: S
authors.lastname: Wessendorf
authors.forename: Michelle
authors.initials: M
authors.lastname: Nessling
authors.forename: Christian
authors.initials: C
authors.lastname: Korz
authors.forename: Ralf J
authors.initials: RJ
authors.lastname: Rieker
authors.forename: Kate
authors.initials: K
authors.lastname: Montgomery
authors.forename: Raju
authors.initials: R
authors.lastname: Kucherlapati
authors.forename: Gunhild
authors.initials: G
authors.lastname: Mechtersheimer
authors.forename: Roland
authors.initials: R
authors.lastname: Eils
authors.forename: Stefan
authors.initials: S
authors.lastname: Joos
authors.forename: Peter
authors.initials: P
authors.lastname: Lichter
mesh_terms: D000465:Algorithms; D002869:Chromosome Aberrations; D018628:Gene Dosage; D020869:Gene Expression Profiling; D016147:Genes, Tumor Suppressor; D006801:Humans; D008080:Liposarcoma / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D005810:Multigene Family; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D009857:Oncogenes; D016133:Polymerase Chain Reaction; D012983:Soft Tissue Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology