Xuefeng Wang1, Mengjie Chen2, Xiaoqing Yu3, Natapol Pornputtapong4, Hao Chen5, Nancy R Zhang6, R Scott Powers7, Michael Krauthammer4. 1. 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. 2. Departments of Biostatistics and Genetics, University of North Carolina, Chapel Hill, NC 27599, USA. 3. Department of Biostatistics. 4. Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA. 5. Department of Statistics, University of California, Davis, CA 9516, USA. 6. Department of Statistics, The Wharton School, University of Pennsylvania, PA 19104, USA and. 7. Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA.
Abstract
UNLABELLED: 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: https://github.com/xfwang/CLOSE CONTACT: xuefeng.wang@stonybrook.edu or michael.krauthammer@yale.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
UNLABELLED: 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: https://github.com/xfwang/CLOSE CONTACT: xuefeng.wang@stonybrook.edu or michael.krauthammer@yale.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Kai Wang; Mingyao Li; Dexter Hadley; Rui Liu; Joseph Glessner; Struan F A Grant; Hakon Hakonarson; Maja Bucan Journal: Genome Res Date: 2007-10-05 Impact factor: 9.043
Authors: Peter Van Loo; Silje H Nordgard; Ole Christian Lingjærde; Hege G Russnes; Inga H Rye; Wei Sun; Victor J Weigman; Peter Marynen; Anders Zetterberg; Bjørn Naume; Charles M Perou; Anne-Lise Børresen-Dale; Vessela N Kristensen Journal: Proc Natl Acad Sci U S A Date: 2010-09-13 Impact factor: 11.205
Authors: Thomas LaFramboise; Barbara A Weir; Xiaojun Zhao; Rameen Beroukhim; Cheng Li; David Harrington; William R Sellers; Matthew Meyerson Journal: PLoS Comput Biol Date: 2005-11-25 Impact factor: 4.475
Authors: F Favero; T Joshi; A M Marquard; N J Birkbak; M Krzystanek; Q Li; Z Szallasi; A C Eklund Journal: Ann Oncol Date: 2014-10-15 Impact factor: 32.976
Authors: Scott L Carter; Kristian Cibulskis; Elena Helman; Aaron McKenna; Hui Shen; Travis Zack; Peter W Laird; Robert C Onofrio; Wendy Winckler; Barbara A Weir; Rameen Beroukhim; David Pellman; Douglas A Levine; Eric S Lander; Matthew Meyerson; Gad Getz Journal: Nat Biotechnol Date: 2012-05 Impact factor: 54.908
Authors: Markus Riester; Angad P Singh; A Rose Brannon; Kun Yu; Catarina D Campbell; Derek Y Chiang; Michael P Morrissey Journal: Source Code Biol Med Date: 2016-12-15