High-throughput single-cell whole-genome amplification through centrifugal emulsification and eMDA

Commun Biol. 2019 Apr 29:2:147. doi: 10.1038/s42003-019-0401-y. eCollection 2019.

Abstract

Single-cell whole-genome sequencing (scWGS) is mainly used to probe intercellular genomic variations, focusing on the copy number variations or alterations and the single-nucleotide variations (SNVs) occurring within single cells. Single-cell whole-genome amplification (scWGA) needs to be applied before scWGS but is challenging due to the low copy number of DNA. Besides, many genomic variations are rare within a population of cells, so the throughput of currently available scWGA methods is far from satisfactory. Here, we integrate a one-step micro-capillary array (MiCA)-based centrifugal droplet generation technique with emulsion multiple displacement amplification (eMDA) and demonstrate a high-throughput scWGA method, MiCA-eMDA. MiCA-eMDA increases the single-run throughput of scWGA to a few dozen, and enables the assessment of copy number variations and alterations at 50-kb resolution. Downstream target enrichment further enables the detection of SNVs with 20% allele drop-out.

Keywords: DNA; DNA sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Centrifugation / methods*
  • DNA / genetics
  • DNA Copy Number Variations
  • Emulsions / chemistry*
  • Genome, Human / genetics
  • Genomics / methods*
  • HeLa Cells
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Lipid Droplets / chemistry
  • Nucleic Acid Amplification Techniques / methods*
  • Polymorphism, Single Nucleotide
  • Single-Cell Analysis / methods*
  • Whole Genome Sequencing / methods*

Substances

  • Emulsions
  • DNA