title: Global copy number profiling of cancer genomes.
abstract: 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.
  
  
  
  https://github.com/xfwang/CLOSE CONTACT: xuefeng.wang@stonybrook.edu or michael.krauthammer@yale.edu
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Family, Population & Preventive Medicine, Stony Brook University, Stony Brook, NY 11794, USA, Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Xuefeng
authors.initials: X
authors.lastname: Wang
authors.affiliation: Departments of Biostatistics and Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
authors.forename: Mengjie
authors.initials: M
authors.lastname: Chen
authors.affiliation: Department of Biostatistics.
authors.forename: Xiaoqing
authors.initials: X
authors.lastname: Yu
authors.affiliation: Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Natapol
authors.initials: N
authors.lastname: Pornputtapong
authors.affiliation: Department of Statistics, University of California, Davis, CA 9516, USA.
authors.forename: Hao
authors.initials: H
authors.lastname: Chen
authors.affiliation: Department of Statistics, The Wharton School, University of Pennsylvania, PA 19104, USA and.
authors.forename: Nancy R
authors.initials: NR
authors.lastname: Zhang
authors.affiliation: Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA.
authors.forename: R Scott
authors.initials: RS
authors.lastname: Powers
authors.affiliation: Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Krauthammer
mesh_terms: D000465:Algorithms; D056915:DNA Copy Number Variations; D005787:Gene Frequency; D015894:Genome, Human; D006801:Humans; D009369:Neoplasms; D017422:Sequence Analysis, DNA