Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA114213 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors (BAC/CGH)
| PRJNA114223 | ENA
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
2009-04-01 | E-GEOD-12532 | biostudies-arrayexpress
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
2009-04-01 | GSE12475 | GEO
Project description:DNA methylation and copy number variation (CNV) profiling has emerged as a promising tool for the classification of bone and soft tissue tumors. We evaluated its utility in cartilage tumors, where distinguishing low-grade from high-grade conventional central chondrosarcoma (CS) as well as atypical cartilaginous tumors (ACT) from enchondromas are frequent diagnostic challenges, particularly on biopsy material. We analyzed 214 chondrogenic tumors, including enchondromas, ACT, conventional central, dedifferentiated, and clear cell chondrosarcomas, and determined their IDH1/2 mutation status. Unsupervised dimensionality reduction of genome-wide DNA methylation patterns revealed four clusters among IDH-mutant tumors (IDH-MUT-1: mostly enchondromas and ACT and some high-grade CS; IDH-MUT-2: predominantly high-grade CS; IDH-MUT-3: largely dedifferentiated CS; IDH-MUT-HN: distinct head and neck group with markedly different methylation pattern) and two clusters among IDH-wildtype tumors (IDH-WT-1 and IDH-WT-2: both primarily high-grade CS, with IDH-WT-2 showing higher tumor grade and more extensive CNVs). Clear cell chondrosarcomas formed a separate cluster (CC). The amount of CNVs, including loss of CDKN2A, increased with tumor grade, reflecting increased genomic instability during chondrosarcoma progression. Supervised classifiers trained separately, both on methylation and CNV data, distinguished low- and high-grade cartilaginous tumors with AUC values of 0.87–0.97 and 85–90% accuracy. Furthermore, we tested whether dedifferentiated chondrosarcoma (DDCS) can be distinguished from metastatic carcinomas and other high-grade sarcomas of bone. Across 246 reference samples, a supervised classifier achieved 97.2% accuracy (AUC 99.8%) and correctly identified 30/32 (93.8%) DDCS. These results indicate that DNA methylation and CNV data analysis provide a valuable tool for distinguishing most low- and high-grade chondrosarcomas, with additional utility also in differentiating DDCS from morphologic mimics.
2026-08-14 | GSE320217 | GEO
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.
2011-08-26 | GSE22855 | GEO
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.
2013-07-15 | GSE40853 | GEO
Project description:Peripheral regions and central regions from HT-29 tumors
| PRJNA272132 | ENA
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
2009-04-01 | GSE12439 | GEO
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.
2023-01-01 | GSE214180 | GEO