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.

中文翻译：

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openPrimeR用于高度多样化模板的多重扩增。

为了研究免疫受体和病原体的多样性，多重PCR已成为研究和诊断的主要方法。然而，针对高度多样化的模板的引物设计不足通常会阻止扩增，因此限制了对生物学过程的正确理解。在这里，我们介绍openPrimeR，这是一种基于R的工具，用于评估和设计多重PCR引物。openPrimeR提供了功能直观的界面，并使用贪婪算法或整数线性程序来计算执行完整靶标覆盖的最小引物集。作为概念验证，我们使用openPrimeR查找用于扩增高度突变的免疫球蛋白的最佳引物组。