Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays

Genome Biol. 2009;10(11):R128. doi: 10.1186/gb-2009-10-11-r128. Epub 2009 Nov 11.


We describe a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured with single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. Assignments were verified by DNA indexes of primary tumors and karyotypes of cell lines. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Allelic Imbalance
  • Automation
  • Breast Neoplasms / genetics*
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic*
  • Genome*
  • Genomics
  • Genotype
  • Homozygote
  • Humans
  • Karyotyping
  • Loss of Heterozygosity
  • Models, Genetic
  • Ploidies
  • Polymorphism, Single Nucleotide*