Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors (BAC/CGH)

DNA copy number analysis of 67 fresh frozen chondrosarcoma biopsies using 32k BAC and 244k oligo array CGH. Genomic imbalances, in most tumors affecting large regions of the genome, were found in 90% of the cases. Although rare, recurrent amplifications were found at 8q24.21-q24.22 and 11q22.1-q22.3, and homozygous deletions of loci previously implicated in chondrosarcoma development affected the CDKN2A, EXT1 and EXT2 genes. Keywords: chondrosarcoma, array comparative genomic hybridization DNA copy number analysis was performed using tiling microarrays containing more than 32,000 partly overlapping BAC clones, generating complete coverage of the Homo sapiens genome. The arrays were produced at the Swegene DNA Microarray Resource Center, Department of Oncology, Lund University (http://swegene.onk.lu.se), using BAC clones mapped to the hg17 genome build. Male genomic DNA (Promega) was used as reference. In five cases (cases 2, 4, 34, 36, and 67) the DNA copy number status was assessed by oligo microarrays containing ~236,000 oligonucleotide probes (Agilent, Palo Alto, CA, USA). These samples were hybridized against gender-matched reference DNA.