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[Cancer Research 62, 2993-2998, June 1, 2002]
© 2002 American Association for Cancer Research

Advances in Brief

Microarray-based Copy Number and Expression Profiling in Dedifferentiated and Pleomorphic Liposarcoma1

Björn Fritz, Falk Schubert, Gunnar Wrobel, Carsten Schwaenen, Swen Wessendorf, Michelle Nessling, Christian Korz, Ralf J. Rieker, Kate Montgomery, Raju Kucherlapati, Gunhild Mechtersheimer, Roland Eils, Stefan Joos and Peter Lichter2

Deutsches Krebsforschungszentrum, Abteilung Molekulare Genetik (H0700), D-69120 Heidelberg, Germany [B. F., G. W., C. S., M. N., C. K., S. J., P. L.]; Deutsches Krebsforschungszentrum, Arbeitsgruppe Intelligente Bioinformatiksysteme (H0900), D-69120 Heidelberg, Germany [F. S., R. E.]; Pathologisches Institut, Universität Heidelberg, D-69120 Heidelberg, Germany [R. J. R., G. M.]; Harvard-Partners Center for Genetics and Genomics and Harvard Medical School, Boston, Massachusetts 02115 [K. M., R. K.]; and Abteilung Innere Medizin III, D-89081 Ulm, Germany [S. W.]

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.




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Copyright © 2002 by the American Association for Cancer Research.