TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol
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Updated: Mar 11, 2026
Target Cell Pre-enrichment and Whole Genome Amplification for Single Cell Downstream Characterization
Published on: May 15, 2018
Ángel J Picher1, Bettina Budeus2, Oliver Wafzig2
1SYGNIS Biotech S.L.U., Parque Científico de Madrid, Cantoblanco, Madrid 28049, Spain.
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.
Insights
This study introduces TruePrime, a novel whole genome amplification method for single cells. TruePrime utilizes Thermus thermophilus PrimPol and Phi29 DNA polymerase for superior genome coverage and accuracy in genomic analysis.
Area of Science:
- Genomics
- Molecular Biology
- Biotechnology
Background:
- Single-cell genome sequencing requires DNA amplification, which can introduce bias and errors.
- Existing multiple displacement amplification (MDA) methods have limitations in coverage uniformity and accuracy.
Purpose of the Study:
- To develop a novel MDA method for near-complete whole genome amplification from single cells.
- To improve the accuracy, reproducibility, and coverage of single-cell genomic analysis.
Main Methods:
- Developed a new MDA method, TruePrime, combining Thermus thermophilus PrimPol (TthPrimPol) and Phi29 DNA polymerase (Φ29DNApol).
- TthPrimPol synthesizes DNA primers using dNTPs, enabling highly processive amplification by Φ29DNApol.
Main Results:
- TruePrime achieved near-complete whole genome amplification from single cells.
- Demonstrated superior genome coverage breadth and evenness, high reproducibility, and excellent single-nucleotide variant (SNV) detection rates with low allelic dropout (ADO) and chimera formation.
- Showcased superior copy number variant (CNV) calling compared to random primer-based MDA methods.
Conclusions:
- The TruePrime method significantly improves single-cell whole genome amplification.
- This advancement facilitates more accurate and comprehensive genomic analysis at the single-cell level.
