1. Global copy number profiling of cancer genomes
- Author
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Wang, Xuefeng, Chen, Mengjie, Yu, Xiaoqing, Pornputtapong, Natapol, Chen, Hao, Zhang, Nancy R, Powers, R Scott, and Krauthammer, Michael
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Mathematical Sciences ,Statistics ,Cancer ,Biotechnology ,Human Genome ,Algorithms ,DNA Copy Number Variations ,Gene Frequency ,Genome ,Human ,Humans ,Neoplasms ,Sequence Analysis ,DNA ,Information and Computing Sciences ,Bioinformatics ,Biological sciences ,Information and computing sciences ,Mathematical sciences - Abstract
UnlabelledIn 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 implementationhttps://github.com/xfwang/CLOSE CONTACT: xuefeng.wang@stonybrook.edu or michael.krauthammer@yale.eduSupplementary informationSupplementary data are available at Bioinformatics online.
- Published
- 2016