title: A quantitative comparison of single-cell whole genome amplification methods.
abstract: Single-cell sequencing is emerging as an important tool for studies of genomic heterogeneity. Whole genome amplification (WGA) is a key step in single-cell sequencing workflows and a multitude of methods have been introduced. Here, we compare three state-of-the-art methods on both bulk and single-cell samples of E. coli DNA: Multiple Displacement Amplification (MDA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC), and the PicoPLEX single-cell WGA kit (NEB-WGA). We considered the effects of reaction gain on coverage uniformity, error rates and the level of background contamination. We compared the suitability of the different WGA methods for the detection of copy-number variations, for the detection of single-nucleotide polymorphisms and for de-novo genome assembly. No single method performed best across all criteria and significant differences in characteristics were observed; the choice of which amplifier to use will depend strongly on the details of the type of question being asked in any given experiment.
authors.affiliation: Department of Applied Physics, Stanford University, Stanford, California, United States of America.
authors.forename: Charles F A
authors.initials: CF
authors.lastname: de Bourcy
authors.affiliation: Department of Applied Physics, Stanford University, Stanford, California, United States of America; Department of Bioengineering, Stanford University, Stanford, California, United States of America; Howard Hughes Medical Institute, Stanford, California, United States of America.
authors.forename: Iwijn
authors.initials: I
authors.lastname: De Vlaminck
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, California, United States of America; Howard Hughes Medical Institute, Stanford, California, United States of America.
authors.forename: Jad N
authors.initials: JN
authors.lastname: Kanbar
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, California, United States of America.
authors.forename: Jianbin
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Applied Physics, Stanford University, Stanford, California, United States of America; Department of Bioengineering, Stanford University, Stanford, California, United States of America; Division of Hematology, Oncology, Stem Cell Transplantation and Cancer Biology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America.
authors.forename: Charles
authors.initials: C
authors.lastname: Gawad
authors.affiliation: Department of Applied Physics, Stanford University, Stanford, California, United States of America; Department of Bioengineering, Stanford University, Stanford, California, United States of America; Howard Hughes Medical Institute, Stanford, California, United States of America.
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Quake
mesh_terms: D056915:DNA Copy Number Variations / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics / Q000379:methods; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D059010:Single-Cell Analysis / Q000379:methods*
chemical_list: D004269:DNA, Bacterial