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

Br J Cancer. 2008 Jan 29;98(2):434-42. doi: 10.1038/sj.bjc.6604130. Epub 2007 Dec 11.


The initiating somatic genetic events in chordoma development have not yet been identified. Most cytogenetically investigated chordomas have displayed near-diploid or moderately hypodiploid karyotypes, with several numerical and structural rearrangements. However, no consistent structural chromosome aberration has been reported. This is the first array-based study characterising DNA copy number changes in chordoma. Array comparative genomic hybridisation (aCGH) identified copy number alterations in all samples and imbalances affecting 5 or more out of the 21 investigated tumours were seen on all chromosomes. In general, deletions were more common than gains and no high-level amplification was found, supporting previous findings of primarily losses of large chromosomal regions as an important mechanism in chordoma development. Although small imbalances were commonly found, the vast majority of these were detected in single cases; no small deletion affecting all tumours could be discerned. However, the CDKN2A and CDKN2B loci in 9p21 were homo- or heterozygously lost in 70% of the tumours, a finding corroborated by fluorescence in situ hybridisation, suggesting that inactivation of these genes constitute an important step in chordoma development.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Chordoma / genetics*
  • Chromosome Aberrations*
  • Chromosomes, Human, Pair 9
  • Cyclin-Dependent Kinase Inhibitor p15 / genetics
  • Female
  • Gene Deletion*
  • Gene Dosage
  • Genes, p16*
  • Humans
  • In Situ Hybridization, Fluorescence
  • Male
  • Middle Aged
  • Nucleic Acid Hybridization* / methods
  • Oligonucleotide Array Sequence Analysis*
  • Spinal Neoplasms / genetics*


  • CDKN2B protein, human
  • Cyclin-Dependent Kinase Inhibitor p15