Molecular cytogenetic characterization of the 11q13 amplicon in head and neck squamous cell carcinoma

Cytogenet Genome Res. 2006;115(2):99-106. doi: 10.1159/000095228.


Amplification of 11q13 DNA sequences and overexpression of CCND1 are common findings in head and neck squamous cell carcinoma (HNSCC), identified in about 30% of the cases. However, little is known about initiation of the amplification and the organization of the amplicon. In order to study the structure of the amplicon in more detail and to learn more about the mechanisms involved in its initiation, prometaphase, metaphase, and anaphase fluorescence in situ hybridization (FISH) with 40 BAC clones spanning a 16-Mb region in chromosome bands 11q12.2 to 11q13.5 was performed in nine HNSCC cell lines with homogeneously staining regions. FISH analysis showed that the size of the amplicon varied among the nine cell lines, the smallest being 2.12 Mb and the largest 8.97 Mb. The smallest overlapping region of amplification was approximately 1.61 Mb, covering the region from BAC 729E14 to BAC 102B19. This region contained several genes previously shown to be amplified and overexpressed in HNSCC, including CCDN1, CTTN, SHANK2, and ORAOV1. The cell lines were also used to study the internal structure of the amplicon. Various patterns of amplified DNA sequences within the amplicon were found among the nine cell lines. Even within the same cell line, different amplicon structures could be found in different cell populations, indicating that the mechanisms involved in the development of the amplicons in HNSCC were more complex than previously assumed. The frequent finding of inverted repeats within the amplicons, however, suggests that breakage-fusion-bridge cycles are important in the initiation, but the fact that such repeats constituted only small parts of the amplicons indicate that they are further rearranged during tumor progression.

Publication types

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

MeSH terms

  • Anaphase
  • Carcinoma, Squamous Cell / genetics*
  • Cell Line, Tumor / ultrastructure
  • Chromosome Banding
  • Chromosome Breakage
  • Chromosomes, Artificial, Bacterial
  • Chromosomes, Human, Pair 11 / genetics*
  • Chromosomes, Human, Pair 11 / ultrastructure
  • DNA Repair
  • DNA, Neoplasm / genetics*
  • Disease Progression
  • Female
  • Gene Amplification*
  • Gene Expression Regulation, Neoplastic
  • Head and Neck Neoplasms / genetics*
  • Humans
  • In Situ Hybridization, Fluorescence*
  • Male
  • Metaphase
  • Repetitive Sequences, Nucleic Acid


  • DNA, Neoplasm