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Series GSE12439 Query DataSets for GSE12439
Status Public on Apr 01, 2009
Title Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors (BAC/CGH)
Organism Homo sapiens
Experiment type Genome variation profiling by array
Summary 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
Overall design 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 (, 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.
Contributor(s) Hallor K, Staaf J, Bovée J, Hogendoorn P, Cleton-Jansen A, Knuutila S, Savola S, Brosjö O, Bauer H, VultvonSteyern F, Jonsson K, Skorpil M, Mandahl N, Mertens F
Citation(s) 19336518
Submission date Aug 13, 2008
Last update date Jan 17, 2013
Contact name Karolin H Nord
Organization name Lund University
Department Dept of Clinical Genetics
Street address BMC C13
City Lund
ZIP/Postal code SE-22184
Country Sweden
Platforms (2)
GPL7203 LUH Human Genome CGH Microarray 244A
Samples (67)
GSM312343 Chondrosarcoma_case_1
GSM312344 Chondrosarcoma_case_3
GSM312345 Chondrosarcoma_case_5
This SubSeries is part of SuperSeries:
GSE12532 Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors
BioProject PRJNA114223

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE12439_RAW.tar 490.7 Mb (http)(custom) TAR (of GPR, TXT)
Processed data included within Sample table

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