Abstract
BackgroundWhole 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.ResultsThe 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.DiscussionIn 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.
Highlights
Whole genome amplification (WGA) is currently a prerequisite for single cell whole genome or exome sequencing
The products from the AMPLI1 and Multiple Annealing and Looping Based Amplification Cycles (MALBAC) kits were shown to be most similar to the bulk samples and are recommended for WGA of single cells
The resulting data was evaluated in terms of genomic coverage, allelic dropout and SNP calling
Summary
Whole genome amplification (WGA) is currently a prerequisite for single cell whole genome or exome sequencing. In this study four commercial kits for WGA (AMPLI1, MALBAC, Repli-G and PicoPlex) were used to amplify human single cells. To facilitate the choice of amplification technique for human single cell sequencing we compared four of the most frequently used and commercially available WGA kits; AMPLI1, MALBAC, Repli-G and PicoPlex (S1 Fig).
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