A remark on copy number variation detection methods

doi:10.1371/journal.pone.0196226

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	A remark on copy number variation detection methods
	Li, Shuo 1,3; Dou, Xialiang 1,4; Gao, Ruiqi 1,5; Ge, Xinzhou 1,5; Qian, Minping 1; Wan, Lin2
	2018-04-27
发表期刊	PLOS ONE
ISSN	1932-6203
卷号	13 期号:4 页码:11
摘要	Copy number variations (CNVs) are gain and loss of DNA sequence of a genome. High throughput platforms such as microarrays and next generation sequencing technologies (NGS) have been applied for genome wide copy number losses. Although progress has been made in both approaches, the accuracy and consistency of CNV calling from the two platforms remain in dispute. In this study, we perform a deep analysis on copy number losses on 254 human DNA samples, which have both SNP microarray data and NGS data publicly available from Hapmap Project and 1000 Genomes Project respectively. We show that the copy number losses reported from Hapmap Project and 1000 Genome Project only have < 30% overlap, while these reports are required to have cross-platform (e.g. PCR, microarray and high-throughput sequencing) experimental supporting by their corresponding projects, even though state-of-art calling methods were employed. On the other hand, copy number losses are found directly from HapMap microarray data by an accurate algorithm, i.e. CNVhac, almost all of which have lower read mapping depth in NGS data; furthermore, 88% of which can be supported by the sequences with breakpoint in NGS data. Our results suggest the ability of microarray calling CNVs and the possible introduction of false negatives from the unessential requirement of the additional cross-platform supporting. The inconsistency of CNV reports from Hapmap Project and 1000 Genomes Project might result from the inadequate information containing in microarray data, the inconsistent detection criteria, or the filtration effect of cross-platform supporting. The statistical test on CNVs called from CNVhac show that the microarray data can offer reliable CNV reports, and majority of CNV candidates can be confirmed by raw sequences. Therefore, the CNV candidates given by a good caller could be highly reliable without cross-platform supporting, so additional experimental information should be applied in need instead of necessarily.
DOI	10.1371/journal.pone.0196226
语种	英语
资助项目	NSFC[11571349] ; NSFC[91630314] ; Strategic Priority Research Program of the CAS[XDB13050000] ; NCMIS of the CAS ; LSC of the CAS ; Youth Innovation Promotion Association of the CAS
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000431013300024
出版者	PUBLIC LIBRARY SCIENCE
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/30215
专题	系统科学研究所
通讯作者	Qian, Minping; Wan, Lin
作者单位	1.Peking Univ, Sch Math Sci, Beijing, Peoples R China 2.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Beijing, Peoples R China 3.Univ Calif Los Angeles, David Geffen Sch Med, Dept Pathol & Lab Med, Los Angeles, CA 90095 USA 4.Univ Chicago, Dept Stat, Chicago, IL 60637 USA 5.Univ Calif Los Angeles, Dept Stat, Los Angeles, CA USA
推荐引用方式 GB/T 7714	Li, Shuo,Dou, Xialiang,Gao, Ruiqi,et al. A remark on copy number variation detection methods[J]. PLOS ONE,2018,13(4):11.
APA	Li, Shuo,Dou, Xialiang,Gao, Ruiqi,Ge, Xinzhou,Qian, Minping,&Wan, Lin.(2018).A remark on copy number variation detection methods.PLOS ONE,13(4),11.
MLA	Li, Shuo,et al."A remark on copy number variation detection methods".PLOS ONE 13.4(2018):11.