title: Performance Evaluation of NIPT in Detection of Chromosomal Copy Number Variants Using Low-Coverage Whole-Genome Sequencing of Plasma DNA.
abstract: OBJECTIVE
  The aim of this study was to assess the performance of noninvasively prenatal testing (NIPT) for fetal copy number variants (CNVs) in clinical samples, using a whole-genome sequencing method.
  
  
  METHODS
  A total of 919 archived maternal plasma samples with karyotyping/microarray results, including 33 CNVs samples and 886 normal samples from September 1, 2011 to May 31, 2013, were enrolled in this study. The samples were randomly rearranged and blindly sequenced by low-coverage (about 7M reads) whole-genome sequencing of plasma DNA. Fetal CNVs were detected by Fetal Copy-number Analysis through Maternal Plasma Sequencing (FCAPS) to compare to the karyotyping/microarray results. Sensitivity, specificity and were evaluated.
  
  
  RESULTS
  33 samples with deletions/duplications ranging from 1 to 129 Mb were detected with the consistent CNV size and location to karyotyping/microarray results in the study. Ten false positive results and two false negative results were obtained. The sensitivity and specificity of detection deletions/duplications were 84.21% and 98.42%, respectively.
  
  
  CONCLUSIONS
  Whole-genome sequencing-based NIPT has high performance in detecting genome-wide CNVs, in particular >10Mb CNVs using the current FCAPS algorithm. It is possible to implement the current method in NIPT to prenatally screening for fetal CNVs.
authors.affiliation: BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.|BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Hongtai
authors.initials: H
authors.lastname: Liu
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Ya
authors.initials: Y
authors.lastname: Gao
authors.affiliation: Shenzhen People's Hospital, the Second Clinical Medical School of Jinan University, Shenzhen, 518020, China.
authors.forename: Zhiyang
authors.initials: Z
authors.lastname: Hu
authors.affiliation: Shenzhen People's Hospital, the Second Clinical Medical School of Jinan University, Shenzhen, 518020, China.
authors.forename: Linhua
authors.initials: L
authors.lastname: Lin
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Xuyang
authors.initials: X
authors.lastname: Yin
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.|BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Dayang
authors.initials: D
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.|Section of Molecular Disease Biology, Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen N, Denmark.
authors.forename: Fang
authors.initials: F
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Jiang
authors.affiliation: Shenzhen People's Hospital, the Second Clinical Medical School of Jinan University, Shenzhen, 518020, China.
authors.forename: Jinghui
authors.initials: J
authors.lastname: Ren
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
mesh_terms: D000328:Adult; D004247:DNA / Q000097:blood / Q000235:genetics*; D056915:DNA Copy Number Variations / Q000235:genetics*; D005260:Female; D015894:Genome, Human / Q000235:genetics; D005865:Gestational Age; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D007621:Karyotyping; D011247:Pregnancy; D011296:Prenatal Diagnosis / Q000379:methods*; D012680:Sensitivity and Specificity; D055815:Young Adult
chemical_list: D004247:DNA