Microarray-based copy number and expression profiling in dedifferentiated and pleomorphic liposarcoma.
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.
Fritz
Björn
B
Deutsches Krebsforschungszentrum, Abteilung Molekulare Genetik (H0700), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.
Schubert
Falk
F
Wrobel
Gunnar
G
Schwaenen
Carsten
C
Wessendorf
Swen
S
Nessling
Michelle
M
Korz
Christian
C
Rieker
Ralf J
RJ
Montgomery
Kate
K
Kucherlapati
Raju
R
Mechtersheimer
Gunhild
G
Eils
Roland
R
Joos
Stefan
S
Lichter
Peter
P
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