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	Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants
	Xi, Ruibin ; Lee, Semin ; Xia, Yuchao ; Kim, Tae-Min ; Park, Peter J.
	2016
关键词	ACUTE MYELOID-LEUKEMIA LARGE GENE LISTS SEQUENCING DATA BREAST-CANCER STRUCTURAL VARIATION POPULATION-SCALE FUSION PARTNER RECTAL-CANCER HUMAN COLON MUTATIONS
英文摘要	Whole-genome sequencing data allow detection of copy number variation (CNV) at high resolution. However, estimation based on read coverage along the genome suffers from bias due to GC content and other factors. Here, we develop an algorithm called BIC-seq2 that combines normalization of the data at the nucleotide level and Bayesian information criterion-based segmentation to detect both somatic and germline CNVs accurately. Analysis of simulation data showed that this method outperforms existing methods. We apply this algorithm to low coverage whole-genome sequencing data from peripheral blood of nearly a thousand patients across eleven cancer types in The Cancer Genome Atlas ( TCGA) to identify cancer-predisposing CNV regions. We confirm known regions and discover new ones including those covering KMT2C, GOLPH3, ERBB2 and PLAG1. Analysis of colorectal cancer genomes in particular reveals novel recurrent CNVs including deletions at two chromatin-remodeling genes RERE and NPM2. This method will be useful to many researchers interested in profiling CNVs from whole-genome sequencing data.; National Institutes of Health (NIH) [R01EY024230]; Ludwig Cancer Center; National Natural Science Foundation of China [11471022, 71532001]; National Key Basic Research Program of China [2015CB856000]; Recruitment Program of Global Youth Experts of China; NSFC; National Key Basic Research Program of China; SCI(E); PubMed; ARTICLE; ruibinxi@math.pku.edu.cn; peter_park@harvard.edu; 13; 6274-6286; 44
语种	英语
出处	PubMed ; SCI
出版者	NUCLEIC ACIDS RESEARCH
内容类型	其他
源URL	[http://hdl.handle.net/20.500.11897/433471]
专题	数学科学学院 生命科学学院
推荐引用方式 GB/T 7714	Xi, Ruibin,Lee, Semin,Xia, Yuchao,et al. Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants. 2016-01-01.

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