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


ABSTRACT: 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.

ORGANISM(S): Homo sapiens

SUBMITTER: Karolin Nord 

PROVIDER: E-GEOD-12439 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors.

Hallor Karolin H KH   Staaf Johan J   Bovée Judith V M G JV   Hogendoorn Pancras C W PC   Cleton-Jansen Anne-Marie AM   Knuutila Sakari S   Savola Suvi S   Niini Tarja T   Brosjö Otte O   Bauer Henrik C F HC   Vult von Steyern Fredrik F   Jonsson Kjell K   Skorpil Mikael M   Mandahl Nils N   Mertens Fredrik F  

Clinical cancer research : an official journal of the American Association for Cancer Research 20090331 8


<h4>Purpose</h4>Histologic grade is currently the best predictor of clinical course in chondrosarcoma patients. Grading suffers, however, from extensive interobserver variability and new objective markers are needed. Hence, we have investigated DNA copy numbers in chondrosarcomas with the purpose of identifying markers useful for prognosis and subclassification.<h4>Experimental design</h4>The overall pattern of genomic imbalances was assessed in a series of 67 chondrosarcomas using array compara  ...[more]

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