The Ultimate qPCR Experiment: Producing Publication Quality, Reproducible Data the First Time

https://research.bangor.ac.uk/portal/files/29192587/untitled.pdf

Comparison of virus concentration methods for the RT-qPCR-based recovery of murine hepatitis virus, a surrogate for SARS-CoV-2 from untreated wastewater.

This project was funded in part by USGS's Ecosystems Mission Area, Invasive Species Program, the intramural research program of the U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center and an Ignite Grant #IGN071717 from Innovate BC. We thank Nick Akins, Lauren Bergman, Leah Botkin, Erica Mize, Nikolas Grueneis, Xin Guan, Danyang (Sandy) Shen, Nathan Thompson, Kyle Von Ruden, Alvi Wadud, and Kristyne Wozney for technical support.

/pdf/reporting-the-limits-of-detection-and-quantification-for-s9xijpbpe5.pdf

Reporting the limits of detection and quantification for environmental DNA assays

qPCR primer design revisited.

DNA analysis has seen an incredible development in terms of instrumentation, assays and applications over the last years. Massively parallel sequencing (MPS) and digital PCR are now broadly applied in research and diagnostics, and quantitative PCR is used for more and more practises. All these techniques are based on in vitro DNA polymerization and fluorescence measurements. A major limitation for successful analysis is the various sample-related substances that interfere with the analysis, i.e. PCR inhibitors. PCR inhibition affects library preparation in MPS analysis and skews quantification in qPCR, and some inhibitors have been found to quench the fluorescence of the applied fluorophores. Here, we provide a deeper understanding of mechanisms of specific PCR inhibitors and how these impact specific analytical techniques. This background knowledge is necessary in order to take full advantage of modern DNA analysis techniques, specifically for analysis of samples with low amounts of template and high amounts of background material. The classical solution to handle PCR inhibition is to purify or dilute DNA extracts, which leads to DNA loss. Applying inhibitor-tolerant DNA polymerases, either single enzymes or blends, provides a more straightforward and powerful solution. This review includes mechanisms of specific PCR inhibitors as well as solutions to the inhibition problem in relation to cutting-edge DNA analysis.

/pdf/pcr-inhibition-in-qpcr-dpcr-and-mps-mechanisms-and-solutions-4sc0f5efbv.pdf

PCR inhibition in qPCR, dPCR and MPS-mechanisms and solutions.

Methods to determine limit of detection and limit of quantification in quantitative real-time PCR (qPCR).

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Methods to determine limit of detection and limit of quantification in quantitative real-time PCR (qPCR).