A quantitative comparison of single-cell whole genome amplification methods.
A quantitative comparison of single-cell whole genome amplification methods.
复制标题
DOI：
10.1371/journal.pone.0105585
复制
发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Quake SR
中科院分区：
文献类型：
--
作者：
de Bourcy CF;De Vlaminck I;Kanbar JN;Wang J;Gawad C;Quake SR
单细胞测序是研究基因组异质性的重要工具。全基因组扩增（WGA）是单细胞测序工作流程中的关键步骤，并且已经引入了多种方法。在这里，我们比较了三个国家的最先进的方法对散装和单细胞样品的E。大肠杆菌DNA：多重置换扩增（MDA）、基于多重退火和环的扩增循环（MALBAC）和PicoPLEX单细胞WGA试剂盒（NEB-WGA）。我们考虑了反应增益对覆盖均匀性、错误率和背景污染水平的影响。我们比较了不同的WGA方法检测拷贝数变异，检测单核苷酸多态性和从头基因组组装的适用性。没有一种方法在所有标准中表现最好，并且观察到特征的显著差异;选择使用哪种放大器将在很大程度上取决于任何给定实验中所问问题类型的细节。
Single-cell sequencing is emerging as an important tool for studies of genomic heterogeneity. Whole genome amplification (WGA) is a key step in single-cell sequencing workflows and a multitude of methods have been introduced. Here, we compare three state-of-the-art methods on both bulk and single-cell samples of E. coli DNA: Multiple Displacement Amplification (MDA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC), and the PicoPLEX single-cell WGA kit (NEB-WGA). We considered the effects of reaction gain on coverage uniformity, error rates and the level of background contamination. We compared the suitability of the different WGA methods for the detection of copy-number variations, for the detection of single-nucleotide polymorphisms and for de-novo genome assembly. No single method performed best across all criteria and significant differences in characteristics were observed; the choice of which amplifier to use will depend strongly on the details of the type of question being asked in any given experiment.
登录
查看更多内容
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
4.5
作者：
Marcy, Yann;Ishoey, Thomas;Lasken, Roger S.;Stockwell, Timothy B.;Walenz, Brian P.;Halpern, Aaron L.;Beeson, Karen Y.;Goldberg, Susanne M. D.;Quake, Stephen R.
通讯作者：
Quake, Stephen R.
影响因子：
3.7
作者：
Blainey PC;Mosier AC;Potanina A;Francis CA;Quake SR
通讯作者：
Quake SR
影响因子：
64.8
作者：
Navin N;Kendall J;Troge J;Andrews P;Rodgers L;McIndoo J;Cook K;Stepansky A;Levy D;Esposito D;Muthuswamy L;Krasnitz A;McCombie WR;Hicks J;Wigler M
通讯作者：
Wigler M
DOI：
10.1073/pnas.1208715109
发表时间：
2012-09-04
影响因子：
11.1
作者：
Schmitt, Michael W.;Kennedy, Scott R.;Loeb, Lawrence A.
通讯作者：
Loeb, Lawrence A.