Comparative genomic hybridization reveals novel chromosome deletions in 90 primary soft tissue tumors

Comparative genomic hybridization (CGH) was used to detect chromosomal gains and losses in a series of 90 frozen soft tissue primary tumors (STTs), all untreated. The material consisted of 69 malignant sarcomas, including 20 malignant fibrous histiocytomas (MFH), 23 liposarcomas (LPS), 6 leiomyosarcomas (LMS), 4 synovial sarcomas, 4 primitive neuroectodermal tumors (PNETs), and various others subtypes, in addition to 21 benign tumors. Within the benign tumors, only 2 of the 3 schwannomas showed genetic changes. In malignant sarcomas, genetic changes were detected in 64 of the 69 samples analyzed (92%), with a mean of 4.5 per sample (range 0-10). Gains and losses on chromosome 13 were observed in 32% of the sarcomas with genomic imbalance. Recurring low-level copy number increases were found at new sites on chromosomes 7 (6 MFH samples, 30%) and 8 (10 LPS samples, 43%), the minimal common regions being 7p15-pter and 8q24. No new recurring high-level amplifications were found. Surprisingly, losses of DNA sequences were more frequent than gains; particularly, losses were the main feature in LMS, with highly recurrent common minimal losses at 11q14-qter and 13q21-q22 (4 samples, 66%, and 5 samples, 83%, respectively). Losses of chromosome 2 sequences (minimal common regions at 2p24-pter and 2q32-qter) were observed in 50% of the MFH analyzed. New recurrent losses of whole or part of chromosome 14 were found in 57% of the pleomorphic LPS (PLPS) analyzed. This study uncovers new clues for the diagnosis of malignant STTs and shows the importance of deletions as events in the early steps involved in the tumorigenesis of STTs.