ArticleNature communications2022
Designing highly multiplex PCR primer sets with Simulated Annealing Design using Dimer Likelihood Estimation (SADDLE).
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Anchored random reverse primer sequencing for quantitative detection of novel gene fusions.Nature biomedical engineering · 2026Article
- Primer design through submodular function estimation.Bioinformatics (Oxford, England) · 2026Article
- Leveraging Next-Generation Tools for Genetic Assessment and Demographic Monitoring in Threatened and Elusive Humboldt Martens.Evolutionary applications · 2026Article
- Enzymatic DNA Reaction Networks for Orchestrating Stimuli-Dependent Temporal Molecular Pulse.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Universal primer mediated multiplex asymmetric PCR coupled with hybridization-based electrochemical biosensing for rapid, simultaneous and label-free detection of multiple pathogens.Mikrochimica acta · 2026Article
- Wastewater intelligence predicts the emergence of clinically-relevant and drug-resistant Candidozyma auris at healthcare facilities.Nature communications · 2026Article
- Research progress on nucleic acid amplification-based detection technologies for phytopathogenic fungi.Applied microbiology and biotechnology · 2026Review
- Machine learning-directed massively parallel programmable nucleic acid amplification.Science advances · 2026Article
- Accelerating primer design for amplicon sequencing using large language model-powered agents.Nature biomedical engineering · 2026Article
- Efficient amplicon panels for evaluating hybridization and genetic structure in the Schistosoma haematobium species group.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2026Article
- TaqMan qPCR quantification of the Cytb gene for precise determination of camel milk in dairy products.PloS one · 2026Article
- Clinical features ofFrontiers in cellular and infection microbiology · 2026Article
- Species-level enumeration of low-concentration lactic acid bacteria in breast milk.Food chemistry. Molecular sciences · 2025Article
- [Overview of PCR-based Diagnostic Assays for Emerging Infectious Disease Pathogens].Jugan geon-gang gwa jilbyeong · 2025Review
- Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut.Nature biotechnology · 2025Article
- Empowering low-crosstalk, dynamic-decision random access of DNA storage via 384-multiplexed nanopore signatures.Nature communications · 2025Article
- Highly sensitive and multiplex detection of nine potential bioterrorism viral agents in a single reaction by multiplex probe amplification (MPA) with melting curve analysis.Microbiology spectrum · 2025Article
- Multiplex nucleic acid polymerase assay for eight severe hemorrhagic fever viruses based on dual-probe hybridization and melting curve analysis.Infectious medicine · 2025Article
- Application of targeted metagenomic next-generation sequencing in pneumonia patients.Microbiology spectrum · 2025Article
- Infectious disease diagnostic device using rapid and efficient qPCR assays on a multi-target chip: idream-qPCR.Microsystems & nanoengineering · 2025Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
One major challenge in the design of highly multiplexed PCR primer sets is the large number of potential primer dimer species that grows quadratically with the number of primers to be designed. Simultaneously, there are exponentially many choices for multiplex primer sequence selection, resulting in systematic evaluation approaches being computationally intractable. Here, we present and experimentally validate Simulated Annealing Design using Dimer Likelihood Estimation (SADDLE), a stochastic algorithm for design of multiplex PCR primer sets that minimize primer dimer formation. In a 96-plex PCR primer set (192 primers), the fraction of primer dimers decreases from 90.7% in a naively designed primer set to 4.9% in our optimized primer set. Even when scaling to 384-plex (768 primers), the optimized primer set maintains low dimer fraction. In addition to NGS, SADDLE-designed primer sets can also be used in qPCR settings to allow highly multiplexed detection of gene fusions in cDNA, with a single-tube assay comprising 60 primers detecting 56 distinct gene fusions recurrently observed in lung cancer.
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