openPrimeR for multiplex amplification of highly diverse templates

J Immunol Methods. 2020 May:480:112752. doi: 10.1016/j.jim.2020.112752. Epub 2020 Jan 25.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Case-Control Studies
  • DNA Primers*
  • Gene Library
  • Genes, Immunoglobulin Heavy Chain*
  • Genes, Immunoglobulin Light Chain*
  • HIV Infections / genetics
  • HIV Infections / immunology*
  • HIV Infections / virology
  • HIV-1 / immunology
  • Host-Pathogen Interactions
  • Humans
  • Multiplex Polymerase Chain Reaction*
  • Proof of Concept Study
  • Software Design*
  • Software Validation
  • Templates, Genetic*


  • DNA Primers