Key result
openPrimeR, an R-based tool for evaluating and designing multiplex PCR primers, successfully generated highly effective primer sets for the amplification of highly mutated immunoglobulins.
openPrimeR provides a functional tool for designing multiplex PCR primers to achieve full target coverage of highly diverse templates like immune receptors.
May aid multiplex PCR primer design for diverse immune receptors; leaves open prospective validation before clinical use.
To study the diversity of immune receptors and pathogens, multiplex PCR has become a central approach in research and diagnostics. However, insufficient primer design against highly diverse templates often prevents amplification and therefore limits the correct understanding of biological processes. Here, we present openPrimeR, an R-based tool for evaluating and designing multiplex PCR primers. openPrimeR provides a functional and intuitive interface and uses either a greedy algorithm or an integer linear program to compute the minimal set of primers that performs full target coverage. As proof of concept, we used openPrimeR to find optimal primer sets for the amplification of highly mutated immunoglobulins. Comprehensive analyses on specifically generated immunoglobulin variable gene segment libraries resulted in the composition of highly effective primer sets (oPR-IGHV, oPR-IGKV and oPR-IGLV) that demonstrated to be particularly suitable for the isolation of novel human antibodies.
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Kreer et al. (2020) studied this question. openPrimeR was evaluated on Minimal set of primers that performs full target coverage. openPrimeR, an R-based tool for evaluating and designing multiplex PCR primers, successfully generated highly effective primer sets for the amplification of highly mutated immunoglobulins.
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