title: Comparison of whole genome amplification techniques for human single cell exome sequencing.
abstract: BACKGROUND
  Whole genome amplification (WGA) is currently a prerequisite for single cell whole genome or exome sequencing. Depending on the method used the rate of artifact formation, allelic dropout and sequence coverage over the genome may differ significantly.
  
  
  RESULTS
  The largest difference between the evaluated protocols was observed when analyzing the target coverage and read depth distribution. These differences also had impact on the downstream variant calling. Conclusively, the products from the AMPLI1 and MALBAC kits were shown to be most similar to the bulk samples and are therefore recommended for WGA of single cells.
  
  
  CONCLUSIONS
  In this study four commercial kits for WGA (AMPLI1, MALBAC, Repli-G and PicoPlex) were used to amplify human single cells. The WGA products were exome sequenced together with non-amplified bulk samples from the same source. The resulting data was evaluated in terms of genomic coverage, allelic dropout and SNP calling.
authors.affiliation: Scilifelab, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Borgström
authors.affiliation: CMB, Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Marta
authors.initials: M
authors.lastname: Paterlini
authors.affiliation: CMB, Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Jeff E
authors.initials: JE
authors.lastname: Mold
authors.affiliation: CMB, Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Jonas
authors.initials: J
authors.lastname: Frisen
authors.affiliation: Scilifelab, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Joakim
authors.initials: J
authors.lastname: Lundeberg
mesh_terms: D059472:Exome / Q000235:genetics*; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D059010:Single-Cell Analysis / Q000379:methods*