Abstract
Advances in whole genome amplification (WGA) techniques enable understanding of the genomic sequence at a single cell level. Demand for single cell dedicated WGA kits (scWGA) has led to the development of several commercial kit. To this point, no robust comparison of all available kits was performed. Here, we benchmark an economical assay, comparing all commercially available scWGA kits. Our comparison is based on targeted sequencing of thousands of genomic loci, including highly mutable regions, from a large cohort of human single cells. Using this approach we have demonstrated the superiority of Ampli1 in genome coverage and of RepliG in reduced error rate. In summary, we show that no single kit is optimal across all categories, highlighting the need for a dedicated kit selection in accordance with experimental requirements.
Highlights
Advances in whole genome amplification (WGA) techniques enable understanding of the genomic sequence at a single cell level
Several single cell dedicated WGA kits (scWGA) kit comparisons were published[5,6,7,8,9,10,11,12], none has yet to compare all of the available kits in a single comparison, and at most, selected kits that represent the same category were selected for comparison
In order to create a comprehensive analysis of scWGA kits we aimed to pick and analyze a uniform population of cells using all commercially available scWGA kits (Table 1)
Summary
Advances in whole genome amplification (WGA) techniques enable understanding of the genomic sequence at a single cell level. Our comparison is based on targeted sequencing of thousands of genomic loci, including highly mutable regions, from a large cohort of human single cells. Using this approach we have demonstrated the superiority of Ampli[1] in genome coverage and of RepliG in reduced error rate. Biochemical biases may occur mainly due to damaged cells or by amplification bias Examples for such bias are in vitro mutation, loss of genomic regions (allelic drop out-ADO) and non-uniform amplification that may disrupt copy number variation (CNV) analysis or lead to ADO in cases of shallow NGS coverage. The following aspects were analyzed: genome coverage, reproducibility of amplification between SCs (intersecting successfully amplified loci) and, due to the instable nature of STR in vitro amplicon, the error-rate of each scWGA kit
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