openPrimeR for multiplex amplification of highly diverse templates

• DOI: 10.1016/j.jim.2020.112752
• Publication Date: 2020-01-25T16:18:52Z
• Authors: Christoph Kreer; Matthias Döring; Nathalie Lehnen; Meryem S. Ercanoglu; Lutz Gieselmann; Domnica Luca; Kanika Jain; Philipp Schommers; Nico Pfeifer; Florian Klein
• Keywords: 570; 0303 health sciences; Genes, Immunoglobulin Heavy Chain; Software Validation; 610; HIV Infections; Templates, Genetic; ddc:no; Proof of Concept Study; 3. Good health; 03 medical and health sciences; Software Design; Case-Control Studies; Host-Pathogen Interactions; HIV-1; Humans; Genes, Immunoglobulin Light Chain; Multiplex Polymerase Chain Reaction; DNA Primers; Gene Library

AbstractTo 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.