title: Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications.
abstract: We present a survey of single-cell whole-genome amplification (WGA) methods, including degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR), multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycles (MALBAC). The key parameters to characterize the performance of these methods are defined, including genome coverage, uniformity, reproducibility, unmappable rates, chimera rates, allele dropout rates, false positive rates for calling single-nucleotide variations, and ability to call copy-number variations. Using these parameters, we compare five commercial WGA kits by performing deep sequencing of multiple single cells. We also discuss several major applications of single-cell genomics, including studies of whole-genome de novo mutation rates, the early evolution of cancer genomes, circulating tumor cells (CTCs), meiotic recombination of germ cells, preimplantation genetic diagnosis (PGD), and preimplantation genomic screening (PGS) for in vitro-fertilized embryos.
authors.affiliation: Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Huang
authors.forename: Fei
authors.initials: F
authors.lastname: Ma
authors.forename: Alec
authors.initials: A
authors.lastname: Chapman
authors.forename: Sijia
authors.initials: S
authors.lastname: Lu
authors.forename: Xiaoliang Sunney
authors.initials: XS
authors.lastname: Xie
mesh_terms: D005260:Female; D005307:Fertilization in Vitro; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D005854:Germ Cells / Q000502:physiology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D059645:Mutation Rate; D009369:Neoplasms / Q000235:genetics; D016133:Polymerase Chain Reaction; D011247:Pregnancy; D019836:Preimplantation Diagnosis; D059010:Single-Cell Analysis / Q000379:methods*
keywords: CTC; DOP-PCR; MALBAC; MDA; PGD; PGS; WGA; cancer genomics; in vitro fertilization; single-cell genomics