Chordoma Foundation

Chordoma -omics data

This page contains a compilation of published data relevant to chordoma research. If you would like help accessing any of the resources listed on this page, please contact



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.

Tissue Microarrays

Vanderbilt University

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

University of Pittsburgh

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

University College London

Creator: Adrienne Flanagan, MD, PhD (
Contents: 41 sacral, 6 lumbar, 3 cervical

Massachusetts General Hospital

Creator: Zhenfeng Duan, MD, PhD (
Contents: 44 sacral, 26 mobile spine

University Hospital of Essen

Creator: Florian Grabellus (
Contents: 31 skull base, 15 spinal, 14 sacral, 6 other

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.


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.


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.


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


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.


The Catalogue of Somatic Mutations in Cancer (COSMIC) database contains a compilation of all published cancer-associated mutations. A list of published mutations in chordoma is available here.

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