Related Experiment Video

Updated: Jul 9, 2026

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
09:16

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants

Published on: February 21, 2015

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

K H Hallor1, J Staaf, G Jönsson

  • 1Department of Clinical Genetics, Lund University Hospital, Lund SE-221 85, Sweden. Karolin.Hansen_Hallor@med.lu.se

British Journal of Cancer
|December 12, 2007
PubMed

Insights

Chordoma development involves DNA copy number changes, primarily deletions. Loss of CDKN2A/CDKN2B genes in 9p21 is a key step in chordoma tumor formation.

Area of Science:

  • Oncology
  • Genetics
  • Cancer Research

Background:

  • Chordoma development's initiating somatic genetic events remain unidentified.
  • Previous studies show chordomas have near-diploid or hypodiploid karyotypes with various chromosomal rearrangements.
  • No consistent structural chromosome aberration has been reported in chordoma.

Purpose of the Study:

  • To characterize DNA copy number changes in chordoma using array-based methods.
  • To identify consistent genetic alterations associated with chordoma development.
  • To investigate the role of specific gene loci in chordoma pathogenesis.

Main Methods:

  • Array comparative genomic hybridization (aCGH) was used to analyze DNA copy number alterations in chordoma samples.
  • Fluorescence in situ hybridization (FISH) was employed to corroborate findings for specific loci.

Main Results:

  • All investigated chordoma samples exhibited copy number alterations.
  • Deletions were more frequent than gains, with imbalances observed across all chromosomes.
  • Homozygous or heterozygous loss of the CDKN2A and CDKN2B loci at 9p21 was found in 70% of tumors.

Conclusions:

  • DNA copy number changes, particularly deletions, are a significant mechanism in chordoma development.
  • The loss of CDKN2A and CDKN2B genes is strongly implicated as a crucial event in chordoma pathogenesis.
  • Array-based genomic analysis provides valuable insights into the genetic landscape of chordoma.

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