GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data

Genome Biol. 2008;9(5):R86. doi: 10.1186/gb-2008-9-5-r86. Epub 2008 May 23.


Absolute tumor DNA copy numbers can currently be achieved only on a single gene basis by using fluorescence in situ hybridization (FISH). We present GeneCount, a method for genome-wide calculation of absolute copy numbers from clinical array comparative genomic hybridization data. The tumor cell fraction is reliably estimated in the model. Data consistent with FISH results are achieved. We demonstrate significant improvements over existing methods for exploring gene dosages and intratumor copy number heterogeneity in cancers.

Publication types

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

MeSH terms

  • Carcinoma, Squamous Cell / genetics
  • DNA, Neoplasm / genetics*
  • Female
  • Gene Dosage*
  • Humans
  • Lymphoma, Non-Hodgkin / genetics
  • Nucleic Acid Hybridization / methods*
  • Translocation, Genetic
  • Uterine Cervical Neoplasms / genetics


  • DNA, Neoplasm