• Cell Lines
• Xenografts
• Tissue Microarrays
• Notochord
• Gene Expression Data
• Comparative Genomic Hybridization Data
• Sequence Variation Data

Cell Lines

U-CH1 and U-CH2

U-CH1 and U-CH2 are sacral-chordoma derived cell lines created by the lab of Dr. Peter Moeller at the University of Ulm, Germany. The Chordoma Foundation maintains a repository of these cell lines and makes them available to academic and industry investigators. To request U-CH1 or U-CH2 please sign this Material Transfer Agreement and return it to the Chordoma Foundation at PO Box 2127, Durham, NC 27702 or via email to mta@chordoma.org

References:

• Genome-wide analysis of sixteen chordomas by comparative genomic hybridization and cytogenetics of the first human chordoma cell line, U-CH1
• Molecular characterization of putative chordoma cell lines
• U-CH1 and U-CH2 Cell Culture Procedures

Xenografts

U-CH1

The U-CH1 cell line forms tumors that resemble chordomas in NSG mice. A protocol for creating a xenograft using U-CH1 was developed by Dr. Adrienne Flanagan.

• Protocol for developing xenografts using U-CH1 in NSG mice

Tissue Microarrays

Vanderbilt University

Creator: Justin Cates, MD, PhD (justin.m.cates@vanderbilt.edu)
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
• Methylthioadenosine phosphorylase and activated insulin-like growth factor-1 receptor/insulin receptor: potential therapeutic targets in chordoma

University of Pittsburgh

Creator: Raja Seethala, MD (seethalarr@upmc.edu)
Contents: 79 skull base
References:

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

University College London

Creator: Adrienne Flanagan, MD, PhD (a.flanagan@ucl.ac.uk)
Contents: 41 sacral, 6 lumbar, 3 cervical
References:

• Potential therapeutic targets for chordoma: PI3K/AKT/TSC1/TSC2/mTOR pathway

Massachusetts General Hospital

Creator: Zhenfeng Duan, MD, PhD (zduan@partners.org)
Contents: 44 sacral, 26 mobile spine
References:

• A novel target for treatment of chordoma: signal transducers and activators of transcription-3

University Hospital of Essen

Creator: Florian Grabellus (florian.grabellus@uk-essen.de)
Contents: 31 skull base, 15 spinal, 14 sacral, 6 other
References:

• MET overexpressing chordomas frequently exhibit polysomy of chromosome 7 but no MET activation through sarcoma-specific gene fusions

Notochord

Notochordal tissue is available from the Congenital Defects Lab at the University of Washington. Contact us for more information.

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.

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

Sequence Variation Data

COSMIC