Comparison of multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC) in single-cell sequencing.

Minfeng Chen,Xuesong Hu,Fei Ling,Dan Zou,Shengjie Gao,Pengfei Song,Shancen Zhao,Deyou Zheng

doi:10.1371/journal.pone.0114520

Abstract

Single-cell sequencing promotes our understanding of the heterogeneity of cellular populations, including the haplotypes and genomic variability among different generation of cells. Whole-genome amplification is crucial to generate sufficient DNA fragments for single-cell sequencing projects. Using sequencing data from single sperms, we quantitatively compare two prevailing amplification methods that extensively applied in single-cell sequencing, multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Our results show that MALBAC, as a combination of modified MDA and tweaked PCR, has a higher level of uniformity, specificity and reproducibility.

Highlights

Single-cell studies by whole genome amplification were proposed to investigate cellular behaviors from a broad range of environmental and clinical specimens
27 Gb and 26 Gb raw sequencing data was downloaded for each multiple displacement amplification (MDA)-based and multiple annealing and looping-based amplification cycles (MALBAC)-based sample, respectively (S1 Table)
Whole-genome amplification strategy is imperative for a single-cell sequencing project

Summary

Introduction

Single-cell studies by whole genome amplification were proposed to investigate cellular behaviors from a broad range of environmental and clinical specimens. There have been several studies on genome-wide sequencing of single cells, which opened an era for investigating. The quality and quantity of DNA samples are critical for high-throughput sequencing and genetic analysis. These studies rely on whole-genome amplification from a single cell to generate enough DNA for sequencing library construction [7,8,9,10,11]. A crucial innovation in single-cell sequencing is to put in place strategies for whole-genome amplification with minimal amplification bias

Methods

Results

Conclusion