E-MTAB-11711
Whole Genome Amplification – surveying yield, reproducibility and heterozygous balance, reported by MIPs targeting STRs
Whole Genome Amplification (WGA) is a crucial first step to nearly all single cell genomic analyses with following steps focusing solely on its products. Therefore, bias and variance caused by the WGA process add numerous challenges to the world of single cell genomics. Short Tandem Repeats (STRs) are sensitive genomic markers used widely in population genetics, forensics and retrospective lineage tracing. By extending a previous evaluation of common WGA kits(T, O et al. 2021) targeting ~1000 STR loci across the male X chromosome, to ~12,000 across the entire genome via a DuplexMIPS system, heterogeneous STR loci can be discovered in abundance, and better used to analyze the efficacy and effectiveness of various WGA kits. We show that while best overall yield is obtained using RepliG-SC, maximum uniformity between alleles and reproducibility across cells is maximized by Ampli1, rendering it as the best candidate for comparative heterozygous analysis of SC genomes.
Whole Genome Amplification (WGA) is a crucial first step to nearly all single cell genomic analyses with following steps focusing solely on its products. Therefore, bias and variance caused by the WGA process add numerous challenges to the world of single cell genomics. Short Tandem Repeats (STRs) are sensitive genomic markers used widely in population genetics, forensics and retrospective lineage tracing. By extending a previous evaluation of common WGA kits(T, O et al. 2021) targeting ~1000 STR loci across the male X chromosome, to ~12,000 across the entire genome via a DuplexMIPS system, heterogeneous STR loci can be discovered in abundance, and better used to analyze the efficacy and effectiveness of various WGA kits. We show that while best overall yield is obtained using RepliG-SC, maximum uniformity between alleles and reproducibility across cells is maximized by Ampli1, rendering it as the best candidate for comparative heterozygous analysis of SC genomes.