TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol

Ángel J. Picher, Bettina Budeus, Oliver Wafzig, Carola Krüger, Sara García-Gómez, María I. Martínez-Jiménez, Alberto Díaz-Talavera, Daniela Weber, Luis Blanco () and Armin Schneider ()
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Ángel J. Picher: SYGNIS Biotech S.L.U., Parque Científico de Madrid
Bettina Budeus: SYGNIS Bioscience GmbH
Oliver Wafzig: SYGNIS Bioscience GmbH
Carola Krüger: SYGNIS Bioscience GmbH
Sara García-Gómez: Centro de Biología Molecular Severo Ochoa (CSIC-UAM)
María I. Martínez-Jiménez: Centro de Biología Molecular Severo Ochoa (CSIC-UAM)
Alberto Díaz-Talavera: Centro de Biología Molecular Severo Ochoa (CSIC-UAM)
Daniela Weber: SYGNIS Bioscience GmbH
Luis Blanco: Centro de Biología Molecular Severo Ochoa (CSIC-UAM)
Armin Schneider: SYGNIS Bioscience GmbH

Nature Communications, 2016, vol. 7, issue 1, 1-16

Abstract: Abstract Sequencing of a single-cell genome requires DNA amplification, a process prone to introducing bias and errors into the amplified genome. Here we introduce a novel multiple displacement amplification (MDA) method based on the unique DNA primase features of Thermus thermophilus (Tth) PrimPol. TthPrimPol displays a potent primase activity preferring dNTPs as substrates unlike conventional primases. A combination of TthPrimPol’s unique ability to synthesize DNA primers with the highly processive Phi29 DNA polymerase (Φ29DNApol) enables near-complete whole genome amplification from single cells. This novel method demonstrates superior breadth and evenness of genome coverage, high reproducibility, excellent single-nucleotide variant (SNV) detection rates with low allelic dropout (ADO) and low chimera formation as exemplified by sequencing HEK293 cells. Moreover, copy number variant (CNV) calling yields superior results compared with random primer-based MDA methods. The advantages of this method, which we named TruePrime, promise to facilitate and improve single-cell genomic analysis.

Date: 2016
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DOI: 10.1038/ncomms13296

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