Global copy number profiling of cancer genomes.

TitleGlobal copy number profiling of cancer genomes.
Publication TypeJournal Article
Year of Publication2016
AuthorsWang, Xuefeng, Mengjie Chen, Xiaoqing Yu, Natapol Pornputtapong, Hao Chen, Nancy R. Zhang, Scott R Powers, and Michael Krauthammer
JournalBioinformatics
Volume32
Issue6
Pagination926-8
Date Published2016 03 15
ISSN1367-4811
KeywordsAlgorithms, DNA Copy Number Variations, Gene Frequency, Genome, Human, Humans, Neoplasms, Sequence Analysis, DNA
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.eduSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI10.1093/bioinformatics/btv676
Alternate JournalBioinformatics
Original PublicationGlobal copy number profiling of cancer genomes.
PubMed ID26576652
PubMed Central IDPMC4907391
Grant ListR01 CA082659 / CA / NCI NIH HHS / United States
R01 GM105785 / GM / NIGMS NIH HHS / United States
T15 LM007056 / LM / NLM NIH HHS / United States
P50 CA121974 / CA / NCI NIH HHS / United States
P30 CA045508 / CA / NCI NIH HHS / United States
U01 CA168409 / CA / NCI NIH HHS / United States
P01 CA142538 / CA / NCI NIH HHS / United States
P30 CA016359 / CA / NCI NIH HHS / United States
Project: