title: Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing.
abstract: BACKGROUND
  Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate-oligonucleotide-primed PCR (DOP-PCR) and multiple annealing and looping-based amplification cycles (MALBAC). However, a comprehensive comparison of variations detection performance between these WGA methods has not yet been performed.
  
  
  RESULTS
  We systematically compared the advantages and disadvantages of different WGA methods, focusing particularly on variations detection. Low-coverage whole-genome sequencing revealed that DOP-PCR had the highest duplication ratio, but an even read distribution and the best reproducibility and accuracy for detection of copy-number variations (CNVs). However, MDA had significantly higher genome recovery sensitivity (~84 %) than DOP-PCR (~6 %) and MALBAC (~52 %) at high sequencing depth. MALBAC and MDA had comparable single-nucleotide variations detection efficiency, false-positive ratio, and allele drop-out ratio. We further demonstrated that SCRS data amplified by either MDA or MALBAC from a gastric cancer cell line could accurately detect gastric cancer CNVs with comparable sensitivity and specificity, including amplifications of 12p11.22 (KRAS) and 9p24.1 (JAK2, CD274, and PDCD1LG2).
  
  
  CONCLUSIONS
  Our findings provide a comprehensive comparison of variations detection performance using SCRS amplified by different WGA methods. It will guide researchers to determine which WGA method is best suited to individual experimental needs at single-cell level.
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Yong
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authors.lastname: Hou
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Kui
authors.initials: K
authors.lastname: Wu
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China ; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 China.
authors.forename: Xulian
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authors.lastname: Shi
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Fuqiang
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authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Luting
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authors.lastname: Song
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Hanjie
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authors.lastname: Wu
authors.affiliation: Cancer and Inflammation Program, National Cancer Institute at Frederick, Building 560, Frederick, MD 21702 USA.
authors.forename: Michael
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authors.lastname: Dean
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Guibo
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authors.lastname: Li
authors.affiliation: BioMatrix, LLC, 3029 Windy Knoll Court, Rockville, MD 20850 USA.
authors.forename: Shirley
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authors.lastname: Tsang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Runze
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authors.lastname: Jiang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China ; Collage of Life Science, University of Chinese Academy of Sciences College, 19A Yuquan Road, Beijing, 100049 China.
authors.forename: Xiaolong
authors.initials: X
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Bo
authors.initials: B
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Geng
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authors.affiliation: Stanford University, 450 Serra Mall, Stanford, CA 94305 USA.
authors.forename: Niharika
authors.initials: N
authors.lastname: Bedekar
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China ; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 China.
authors.forename: Na
authors.initials: N
authors.lastname: Lu
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Guoyun
authors.initials: G
authors.lastname: Xie
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Han
authors.initials: H
authors.lastname: Liang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Liao
authors.initials: L
authors.lastname: Chang
authors.affiliation: Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi'An, 710032 China.
authors.forename: Ting
authors.initials: T
authors.lastname: Wang
authors.affiliation: Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi'An, 710032 China.
authors.forename: Jianghao
authors.initials: J
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.affiliation: The Guangdong Enterprise Key Laboratory of Human Disease Genomics, BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Xiuqing
authors.initials: X
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China ; Princess Al Jawhara Centre of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589 Saudi Arabia ; James D Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, 310058 China.
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi'An, 710032 China.
authors.forename: Ling
authors.initials: L
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China ; Princess Al Jawhara Centre of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589 Saudi Arabia ; Department of Biology and the Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, 1599 Denmark.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
mesh_terms: D056915:DNA Copy Number Variations / Q000235:genetics; D016678:Genome; D059010:Single-Cell Analysis
keywords: DOP-PCR; MALBAC; MDA; Next-generation sequencing; Single-cell resequencing; Variations detection; Whole genome amplification