Cell Lines

U-CH1
U-CH1 was created in the Lab of Dr. Peter Moeller in the Institute of Pathology at the University of Ulm, Germany. It was established in 1999 from a large recurrent sacral Chordoma and was the first published chordoma cell line.

References:

» Genome-wide analysis of sixteen chordomas by comparative genomic hybridization and cytogenetics of the first human chordoma cell line, U-CH1

Distribution
The Chordoma Foundation has an agreement to distribute this cell line to interested researchers  on behalf of it's creators. To request U-CH1 please download the MTA below and follow the attached instructions. After completing the MTA, please request U-CH1 by email. Completed MTA's can be returned by email or by fax at 866-367-3910.

Download MTA
U-CH1 Cell Culture Procedures

Tissue Microarrays

Vanderbilt University

Creator: Justin Cates, MD, PhD ()
Contents: 10 sacral, 3 spine, 8 skull base
References:

» Immunohistochemical analysis of receptor tyrosine kinase signal transduction activity in chordoma

» Steroid hormone receptor and COX-2 expression in chordoma 

University of Pittsburgh

Creator: Raja Seethala, MD ()
Contents: 79 skull base
References:

» Brachyury, SOX-9, and podoplanin, new markers in the skull base chordoma vs chondrosarcoma differential

Gene Expression Data

E-MEXP-353

EBI Array Express Experiment E-MEXP-353: transcription profiling of human mesenchymal and some possibly neural crest derived neoplasms using the Affymetrix GeneChip? Human Genome HG-U133A. This data set was generated by the University College London Cancer Institute and contains 96 tissue samples including 4 chordomas:

Download .CEL file 10744
Download .CEL file 10750
Download .CEL file 10756
Download .CEL file 10762

References:

» Brachyury, a crucial regulator of notochordal development, is a novel biomarker for chordomas

» A molecular map of mesenchymal tumors
 

Comparative Genomic Hybridization Data

GSE9023
Gene Expression Omnibus Series GSE9023: DNA copy number analysis of 21 fresh frozen chordoma biopsies, and the respective relapse in four of them, using 32k and 1Mb array CGH. Cases 1-11 were analyzed using 32k array CGH and male genomic DNA (Promega) was used as reference. Cases 17-26, and the respective relapse in four of these tumors, were analyzed with 1 Mb array CGH, using sex matched controls. All cases showed copy number alterations and primarily deletions of chromosomal regions were found. Particularly, the CDKN2A and CDKN2B loci in 9p21 were homo- or heterozygously lost in 70% of the tumors.

Download raw data: GSE9023_RAW.tar

References:

» Frequent deletion of the CDKN2A locus in chordoma: analysis of chromosomal imbalances using array comparative genomic hybridization