Global copy number profiling of cancer genomes

Bioinformatics. 2016 Mar 15;32(6):926-8. doi: 10.1093/bioinformatics/btv676. Epub 2015 Nov 16.


In this article, we introduce a robust and efficient strategy for deriving global and allele-specific copy number alternations (CNA) from cancer whole exome sequencing data based on Log R ratios and B-allele frequencies. Applying the approach to the analysis of over 200 skin cancer samples, we demonstrate its utility for discovering distinct CNA events and for deriving ancillary information such as tumor purity.

Availability and implementation: CONTACT: or

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Algorithms
  • DNA Copy Number Variations*
  • Gene Frequency
  • Genome, Human
  • Humans
  • Neoplasms
  • Sequence Analysis, DNA