Centrifugal-Driven Droplet Generation Method with Minimal Waste for Single-Cell Whole Genome Amplification

Abstract

High-quality whole-genome amplification (WGA) of individual cells is the primary step for characterizing the genetic information on single cells in biology and medicine. As the most popular single-cell WGA method, multiple displacement amplification (MDA) is often plagued by the nonuniform amplification. The droplet MDA has been an innovative tool to solve this dilemma by mitigating the amplification bias and increasing the genomic coverage. Despite these advantages, the time-consuming droplet generation process, the waste of small volume samples and the difficulty of parallel operation for multiple single-cell samples remain major obstacles. Herein, we introduce a centrifugal-driven droplet generation method for rapid and convenient generation of uniform droplets from a relatively small volume sample (5 μL) in 60s with more than 98% sample utilization. We have performed quantitative digital droplet PCR using this method, demonstrating its capability of amplifying nucleic acids at the single-molecule level. Single-cell centrifugal-driven droplet MDA (cd-MDA) has also been conducted for single-cell sequencing, achieving uniform amplification and broad genomic coverage. With the single-molecule sensitivity, minimum sample waste, high genomic coverage, and excellent sequencing evenness, this centrifugal-driven droplet generation method is promising for convenient and scalable use in digital PCR and single-cell whole-genome research.