Project description:This SuperSeries is composed of the following subset Series: GSE12439: Genomic profiling of chondrosarcoma: implications for the distinction between central and peripheral tumors GSE12475: Genomic profiling of chondrosarcoma: implications for the distinction between central and peripheral tumors Refer to individual Series
Project description:Gene expression profiling of 17 fresh frozen chondrosarcoma biopsies using the Human-6 v2 Expression BeadChip (Illumina Inc., San Diego, CA, USA). DNA copy number analyses was also performed in these tumors. Keywords: chondrosarcoma, gene expression profiling, Illumina
Project description:Ollier disease is a rare, non-hereditary disorder which is characterized by the presence of multiple enchondromas (EC), benign cartilaginous neoplasms arising within the medulla of the bone, with an asymmetric distribution. The risk of malignant transformation towards central chondrosarcoma (CS) is increased up to 35%. The etiology of Ollier disease is unknown. We therefore undertook genome-wide expression profiling using Illumina Beadarray v3.0 for 7 enchondromas of 6 patients and compared them with controls in order to find differentially expressed genes in these benign tumors.
Project description:Illumina Infinium 450k Human DNA Methylation BeadChip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in 51 central chondrosarcoma.
Project description: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
Project description:Genome wide DNA methylation profiling of dedifferentiated chondrosarcoma samples. Genomic DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue after manual macrodissection to ensure at least 10% tumor content, followed by bisulfite converstion. All samples were processed on the Infinium 850k array and scanned using the Illumina iScan, according to the manufacturer's recommended protocol.
Project description:Illumina Infinium 450k Human DNA Methylation BeadChip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in 51 central chondrosarcoma. Bisulphite converted DNA from each sample was hybridised to the Illumina Infinium 450k Human Methylation BeadChip.
