Comparative analysis of whole genome amplification kits for single cell genome analysis

Single-cell whole genome sequencing (scWGS) enables detailed analysis of genomic heterogeneity at the cellular level. Comprehensive characterization of the cell genome requires whole genome amplification (WGA). Here, we systematically compared two WGA technologies, Multiple Displacement Amplification (MDA) and Primary Template-directed Amplification (PTA), commercially available in the Qiagen REPLI-g kit and BioSkryb ResolveDNA kit, respectively. BioSkryb PTA sequencing libraries consistently outperformed Qiagen MDA across most quality metrics, including genome coverage breadth and uniformity. In copy number variation (CNV) detection, PTA calls showed higher accuracy and sensitivity, including reliable detection of small CNVs at low sequencing depth. Furthermore, SNP array genotyping of the same WGA products confirmed the findings from sequencing while also providing allelic information. Moreover, BioSkryb PTA CNV detection from SNP arrays matched the performance of low-pass sequencing, supporting its utility as an alternative for WGA quality control and single-cell CNV profiling. Overall, BioSkryb PTA kit demonstrated superior performance over Qiagen MDA kit for single cell genome analysis.