Comparison of seven single cell whole genome amplification commercial kits using targeted sequencing

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.

A pipeline for copy number profiling of single circulating tumour cells to assess intrapatient tumour heterogeneity

“…Because Ampli 1™ WGA is limited to DNA fragments digested by MseI , chromosomal regions which are CG‐rich or CG‐poor can have poorer coverage. However, with a coverage of 74%, Ampli 1™ WGA has a higher coverage than other single‐cell WGA methods [ 42 , 43 ].…”

New Perspectives for Whole Genome Amplification in Forensic STR Analysis

“…Thus, WGA will leave the legal admissibility or the biostatistical properties of a chosen marker set untouched. By ideally uniformly amplifying the entirety of genomic DNA, WGA methods are open for any particular DNA marker type; however, different WGA methods may be better suited for particular types of markers [88,89]. It will be interesting to see in how far WGA methods might be compatible with or improve upcoming methods of forensic DNA analysis.…”

Whole-Genome Amplification—Surveying Yield, Reproducibility, and Heterozygous Balance, Reported by STR-Targeting MIPs

“…H1 human ES cells (WA01) and single-cell WGA material were banked in our lab by Tamir et al [ 16 ]. Briefly, single H1 cells were picked and deposited in individual wells, cultured for ~2 weeks, then a single clone was selected to generate single-cell WGA materials according to the manufacturer’s manual for each WGA kit.…”

“…The clonal cells were dissociated and picked using the CellCelector (ALS) automated cell picker. The cells were then processed using different single-cell WGA kits (see [ 16 ] Methods section). Following single-cell WGA, the DNA samples were processed targeted for STR loci using the DuMIPs pipeline [ 6 , 17 ].…”

“…Biezuner et al [ 16 ] recently targeted ~1000 non-autosomal short tandem repeat (STR) loci using combinations of multiplex PCR with the Access Array microfluidics platform, covering seven kits and 125 cells but involving multiple rounds of PCR amplifications, cumulatively estimated at ~50 amplification cycles and covering only ~1000 loci on the X chromosome of male-derived cells. The duplex molecular inversion probe (DuMIP, also named the padlock probe) method for lineage discovery used here extends this comparison to a coverage of ~12,000 STR loci across the entire genome, reducing the amplification to ~20 PCR cycles and improving uniformity.…”