Comparison of whole genome amplification techniques for human single cell exome sequencing

Erik Borgström; Marta Paterlini; Jeff E Mold; Jonas Frisen; Joakim Lundeberg

doi:10.1371/journal.pone.0171566

Comparison of whole genome amplification techniques for human single cell exome sequencing

PLoS One. 2017 Feb 16;12(2):e0171566. doi: 10.1371/journal.pone.0171566. eCollection 2017.

Authors

Erik Borgström¹, Marta Paterlini², Jeff E Mold², Jonas Frisen², Joakim Lundeberg¹

Affiliations

¹ Scilifelab, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
² CMB, Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

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.

Discussion: 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.

Publication types

Comparative Study

MeSH terms

Exome / genetics*
Genome, Human*
High-Throughput Nucleotide Sequencing / methods*
Humans
Nucleic Acid Amplification Techniques / methods*
Polymorphism, Single Nucleotide / genetics*
Sequence Analysis, DNA / methods
Single-Cell Analysis / methods*

Grants and funding

This work was supported by: Swedish Research Council, Knut and Alice Wallenberg Foundation, Swedish Cancer Society, European Research Council, Karolinska Institutet, Tobias Foundation, Torsten Söderbergs Foundation, and StratRegen. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.