Reagents & data
This page contains a compilation of published reagents and data relevant to chordoma research. If you would like help accessing any of the resources listed on this page, please contact our Director of Research, Joan Levy, PhD, at firstname.lastname@example.org.
- Tissue Microarrays
- Gene Expression Data
- Comparative Genomic Hybridization Data
- Sequence Variation Data
- 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
- Brachyury, SOX-9, and podoplanin, new markers in the skull base chordoma vs chondrosarcoma differential
University College London
Massachusetts General Hospital
University Hospital of Essen
Creator: Florian Grabellus (email@example.com)
Contents: 31 skull base, 15 spinal, 14 sacral, 6 other
- MET overexpressing chordomas frequently exhibit polysomy of chromosome 7 but no MET activation through sarcoma-specific gene fusions
Gene Expression Data
EBI Array Express Experiment E-MEXP-353: transcription profiling of human mesenchymal and some possibly neural crest derived neoplasms using the Affymetrix GeneChip® HG-U133A. This data set was generated by the University College London Cancer Institute and contains 96 tissue samples including 4 chordomas.
- Brachyury, a crucial regulator of notochordal development, is a novel biomarker for chordomas
- A molecular map of mesenchymal tumors
Chordoma and Notochord Project, Xavier Lab
Gene expression profiling of chordoma tumors as well as notochord specimens using both RNA-seq and microarrays (Affymetrix GeneChip® HG-U133A and HG-U133 Plus 2.0). This dataset was generated by Slim Sassi (Massachusetts General Hospital and Harvard Medical School), in collaboration with Yair Benita (Merck Research Labs; formerly affiliated with the Xavier Lab at Massachusetts General Hospital). The project used a panel of normal cells and cancer cells that encompassed 126 tissue types including the notochord. The data indicate that chordoma and notochord are similar on a molecular level and were used to generate a chordoma-specific gene set that distinguishes chordoma from most normal tissues and tumors.
Comparative Genomic Hybridization Data
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
- Frequent deletion of the CDKN2A locus in chordoma: analysis of chromosomal imbalances using array comparative genomic hybridization
CGH data from Kitamura et. al., 2013
This supplementary table presents the results of DNA copy number analysis of 37 skull base chordomas by aCGH and includes IHC and FISH data as well as patient characteristics. Kitamura et. al. performed tissue microdissection on formalin-fixed paraffin-embedded tissue followed by DNA extraction and amplification by DOP-PCR. They next analyzed the samples by array CGH using normal male or female DNA labeled with biotin-dUTP (Roche) as a reference. 24/37 cases showed copy number alterations. The most frequent alterations were chromosome 7 gain (in 10 cases) and chromosome 1q gain (in 9 cases). Log-rank test evaluating the relationship of copy number alterations to progression-free survival (PFS) found 1p loss, 1q gain, and 2p gain significantly associated with PFS.
- Download data: Summary of Clinical and Genetic Profiles of 37 Chordomas
- Molecular and Clinical Risk Factors for Recurrence of Skull Base Chordomas: Gain on Chromosome 2p, Expression of Brachyury, and Lack of Irradiation Negatively Correlate With Patient Prognosis
SNP microarray data from Diaz et. al., 2012
This whole-genome SNP analysis of 22 skull base chordomas using Affymetrix GeneChip® Human Mapping 500K Arrays revealed that losses are more frequent than gains. Significant deletions involved 3p, 3q, 9p, 9q, 10p, 10q, 13q, 14q, and 22q. Significant chromosomal gains involved 7p, 7q, 19p and 19q. Among the alterations noted were a previously reported deletion at 9p involving CDKN2A, CDKN2B, and MTAP in 22% of samples and aneuploidy of a chromosome 3 region including the FHIT gene in 21% of samples.
- Download supplementary material: Table W1
- High-resolution whole-genome analysis of skull base chordomas implicates FHIT loss in chordoma pathogenesis
Sequence Variation Data
European Genome-phenome Archive data set EGAS00001000188: Exome sequencing of 24 chordoma tumors and matched germ-line DNA using Agilent whole exome hybridisation capture and sequencing with Illumina HiSeq 2000 and Illumina Genome Analyzer II.