TruePrime solutions for liquid biopsy samples: whole genome amplification of cell-free DNA and single circulating tumor cells

TruePrime is the name of a novel multiple displacement amplification (MDA) technology based on the combination of Phi29 DNA polymerase with the recently discovered primase/polymerase TthPrimPol (Picher et al, Nat. Commun. 2016). In this setup, TthPrimPol synthesizes the DNA primers needed for Phi29 DNA pol in the course of the reaction, which allows the exponential amplification of DNA, resulting in advantages over the traditional methods based on random synthetic primers, such as complete absence of primer artefacts, higher sensitivity down to the femtogram range, high reproducibility, little bias in genome coverage, and superior variant detection.

TruePrime DNA amplification technology works with all kind of DNA samples used on genomics analysis but has been specifically adjusted to liquid biopsy samples such apoptotic (mononucleosomal) cell-free DNA and genomic DNA from single CTCs.

Here we show the results obtained from liquid and tumor tissue biopsies from five different colon cancer patients, comparing targeted (Ion Torrent) and whole genome (Illumina) sequencing data obtained from TruePrime-amplified cell-free DNA and CTC samples with the corresponding non-amplified cell-free DNA and genomic DNA isolated from formalin-fixed paraffin-embedded (FFPE) tumor tissue, resulting in a more sensitive and reliable variant detection and therefore demonstrating the usefulness of TruePrime solutions for liquid biopsy analysis.