Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

Hou, Yong, Wu, Kui, Shi, Xulian, Li, Fuqiang, Song, Luting, Wu, Hanjie, Dean, Michael, Li, Guibo, Tsang, Shirley, Jiang, Runze, Zhang, Xiaolong, Li, Bo, Liu, Geng, Bedekar, Niharika, Lu, Na, Xie, Guoyun, Liang, Han, Chang, Liao, Wang, Ting, Chen, Jianghao, Li, Yingrui, Zhang, Xiuqing, Yang, Huanming, Xu, Xun, Wang, Ling and Wang, Jun (2015) Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing. GigaScience, 4 1-16. doi:10.1186/s13742-015-0068-3


Author Hou, Yong
Wu, Kui
Shi, Xulian
Li, Fuqiang
Song, Luting
Wu, Hanjie
Dean, Michael
Li, Guibo
Tsang, Shirley
Jiang, Runze
Zhang, Xiaolong
Li, Bo
Liu, Geng
Bedekar, Niharika
Lu, Na
Xie, Guoyun
Liang, Han
Chang, Liao
Wang, Ting
Chen, Jianghao
Li, Yingrui
Zhang, Xiuqing
Yang, Huanming
Xu, Xun
Wang, Ling
Wang, Jun
Title Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing
Journal name GigaScience   Check publisher's open access policy
ISSN 2047-217X
Publication date 2015-08-06
Year available 2015
Sub-type Article (original research)
DOI 10.1186/s13742-015-0068-3
Open Access Status DOI
Volume 4
Start page 1
End page 16
Total pages 16
Place of publication BioMed Central
Publisher London, United Kingdom
Collection year 2016
Language eng
Formatted 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.
Keyword Whole genome amplification
Single-cell resequencing
Variations detection
DOP-PCR
MDA
MALBAC
Next-generation sequencing
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
Institute for Molecular Bioscience - Publications
 
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Created: Sat, 05 Sep 2015, 03:52:19 EST by Mr Mathew Carter on behalf of Institute for Molecular Bioscience