A method to validate viral copy-number assay involving a hybrid amplicon and duplex droplet digital PCR

TL;DR

This paper introduces a new method using a synthetic DNA fragment to validate viral copy-number assays, offering a faster and more efficient alternative to traditional reference controls.

Contribution

The novel contribution is the development of a hybrid amplicon as a reference material for validating VCN assays using duplex ddPCR.

Findings

The hybrid amplicon demonstrated comparable performance to cell reference standards in validating VCN assays.

The method showed good precision, accuracy, and robustness across varying DNA input amounts.

The hybrid amplicon can be used as a routine quality control measure for digital PCR assays.

Abstract

Viral copy-number (VCN) assay is a powerful, effective method to quantify toxicity, cellular kinetics, and durability of virus-modified cell therapy products. The qualification and validation of assay requires reference control. Traditionally, plasmids and cell lines are used as reference controls, but development and qualification of those controls require considerable time and resources. We propose a reference synthetic DNA fragment containing amplicons of woodchuck hepatitis virus posttranscriptional regulatory element (WPRE) and ribonuclease P protein subunit p30 (RPP30), connected by HindIII restriction enzyme cutting site, as a useful tool to qualify and validate duplex droplet digital PCR (ddPCR) assays for VCN. Using this hybrid amplicon, we qualified the duplex WPRE/RPP30 ddPCR assay by determining range of quantification, precision, bias, and robustness of the assay. The varying amount of input DNA showed upper limit, lower limit, and linearity of the assay. Coefficient of variation (CV) and % recovery showed assay precision and accuracy, respectively. Furthermore, the hybrid amplicon was used to determine assay robustness with potential conditions of variability. The hybrid amplicon was a comparable alternative to cell reference standards for validating VCN assay. In conclusion, WPRE-RPP30 hybrid amplicon can be used as a routine quality control measure to validate digital PCR assays.

During viral copy-number assay development, positive reference control is critical to ensure validity and reliability. This manuscript describes the use of hybrid amplicon method as reference material as a quicker alternative for assay development. The hybrid amplicons and cell reference are excellent reference materials for validation of VCN assay.

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