Comparison of whole genome amplification techniques for human single cell exome sequencing.
Comparison of whole genome amplification techniques for human single cell exome sequencing.
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DOI：
10.1371/journal.pone.0171566
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Lundeberg J
中科院分区：
文献类型：
--
作者：
Borgström E;Paterlini M;Mold JE;Frisen J;Lundeberg J
全基因组扩增（WGA）目前是单细胞全基因组或外显子组测序的先决条件。根据所使用的方法，伪影形成率、等位基因丢失和基因组序列覆盖率可能会有显着差异。在分析目标覆盖率和读取深度分布时，观察到评估协议之间的最大差异。这些差异也对下游变体调用产生了影响。总之，AMPLI1 和 MALBAC 试剂盒的产品与批量样品最相似，因此推荐用于单细胞的 WGA。在本研究中，使用四种 WGA 商业试剂盒（AMPLI1、MALBAC、Repli-G 和 PicoPlex）来扩增人类单细胞。 WGA 产品与同一来源的非扩增批量样品一起进行外显子组测序。根据基因组覆盖度、等位基因缺失和 SNP 调用对所得数据进行评估。
Whole genome amplification (WGA) is currently a prerequisite for single cell whole genome or exome sequencing. Depending on the method used the rate of artifact formation, allelic dropout and sequence coverage over the genome may differ significantly. The largest difference between the evaluated protocols was observed when analyzing the target coverage and read depth distribution. These differences also had impact on the downstream variant calling. Conclusively, the products from the AMPLI1 and MALBAC kits were shown to be most similar to the bulk samples and are therefore recommended for WGA of single cells. In this study four commercial kits for WGA (AMPLI1, MALBAC, Repli-G and PicoPlex) were used to amplify human single cells. The WGA products were exome sequenced together with non-amplified bulk samples from the same source. The resulting data was evaluated in terms of genomic coverage, allelic dropout and SNP calling.