1. Stringent Base Specific and Optimization-Free Multiplex Mediator Probe ddPCR for the Quantification of Point Mutations in Circulating Tumor DNA
- Author
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Inga Höffkes, Max Deuter, Felix von Stetten, Nikolas von Bubnoff, Michael Lehnert, Julius Wehrle, Florian Scherer, Peter Juelg, Nadine Borst, Tobias Hutzenlaub, Roland Zengerle, Elena Kipf, and Franziska Schlenker
- Subjects
Cancer Research ,point mutations ,mediator probe PCR ,medicine.disease_cause ,standardized universal reporter ,Article ,colorectal carcinoma ,Multiplex polymerase chain reaction ,medicine ,Multiplex ,Digital polymerase chain reaction ,Liquid biopsy ,RC254-282 ,Detection limit ,circulating tumor DNA ,Chemistry ,digital PCR ,Point mutation ,treatment response ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,ctDNA ,multiplex PCR ,Molecular biology ,optimization-free ,genomic DNA ,Oncology ,KRAS - Abstract
Simple Summary Cancer treatment strategies and their follow-up monitoring are changing to personalized therapies, based on molecular genetic information from the individual person. Liquid biopsy, where this molecular information is derived from body fluids such as blood, has the potential to provide a systemic fingerprint of cancer dynamics, and, compared to tissue biopsy, is much less invasive for the patient. We used the previously published mediator probe PCR technology for liquid biopsy detection of several mutations in one reaction, so-called digital multiplex PCR. Quantification of point mutations in plasma eluates from follow-up patients using 4-plex digital assays showed a comparable performance to reference 2-plex assays. As a key feature, the presented multiplex assays require no laborious optimization as they use the same concentrations and cycling conditions for all targets. This allows for flexible design and interchangeable target panels, thus the assay is easily adaptable for individual patient monitoring and reduces sample consumption. Abstract There is an increasing demand for optimization-free multiplex assays to rapidly establish comprehensive target panels for cancer monitoring by liquid biopsy. We present the mediator probe (MP) PCR for the quantification of the seven most frequent point mutations and corresponding wild types (KRAS and BRAF) in colorectal carcinoma. Standardized parameters for the digital assay were derived using design of experiments. Without further optimization, the limit of detection (LoD) was determined through spiking experiments with synthetic mutant DNA in human genomic DNA. The limit of blank (LoB) was measured in cfDNA plasma eluates from healthy volunteers. The 2-plex and 4-plex MP ddPCR assays showed a LoB of 0 copies/mL except for 4-plex KRAS G13D (9.82 copies/mL) and 4-plex BRAF V600E (16.29 copies/mL) and allele frequencies of 0.004% ≤ LoD ≤ 0.38% with R2 ≥ 0.98. The quantification of point mutations in patient plasma eluates (18 patients) during follow-up using the 4-plex MP ddPCR showed a comparable performance to the reference assays. The presented multiplex assays need no laborious optimization, as they use the same concentrations and cycling conditions for all targets. This facilitates assay certification, allows a fast and flexible design process, and is thus easily adaptable for individual patient monitoring.
- Published
- 2021