ArticlePLoS computational biology2020
NGS-PrimerPlex: High-throughput primer design for multiplex polymerase chain reactions.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 33 citations in OpenAlex.
- Approaches to Thoroughbred Horse Identification in Diverse Sample Types Using Multiplexed SNP-PCR Sequencing Panels.Animal genetics · 2026Article
- Germline de novo mutation rate of the highly heterozygous amphioxus genome.Molecular biology and evolution · 2026Article
- Article
- A Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species.Molecular ecology resources · 2025Article
- Automated highly multiplex detection system for respiratory pathogens in canines.Frontiers in veterinary science · 2025Article
- primerJinn: a tool for rationally designing multiplex PCR primer sets for amplicon sequencing and performing in silico PCR.BMC bioinformatics · 2023Article
- Article
- Detecting Microsatellite Instability in Endometrial, Colon, and Stomach Cancers Using Targeted NGS.Cancers · 2023Article
- High-throughput primer design by scoring in piecewise logistic model for multiple polymerase chain reaction variants.Scientific reports · 2022Article
- Target Enrichment Approaches for Next-Generation Sequencing Applications in Oncology.Diagnostics (Basel, Switzerland) · 2022Review
- Designing highly multiplex PCR primer sets with Simulated Annealing Design using Dimer Likelihood Estimation (SADDLE).Nature communications · 2022Article
- Molecular Characterization of Microbiota in Cerebrospinal Fluid From Patients With CSF Shunt Infections Using Whole Genome Amplification Followed by Shotgun Sequencing.Frontiers in cellular and infection microbiology · 2021Article
- Testing forOncoTargets and therapy · 2021Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Multiplex polymerase chain reaction (PCR) has multiple applications in molecular biology, including developing new targeted next-generation sequencing (NGS) panels. We present NGS-PrimerPlex, an efficient and versatile command-line application that designs primers for different refined types of amplicon-based genome target enrichment. It supports nested and anchored multiplex PCR, redistribution among multiplex reactions of primers constructed earlier, and extension of existing NGS-panels. The primer design process takes into consideration the formation of secondary structures, non-target amplicons between all primers of a pool, primers and high-frequent genome single-nucleotide polymorphisms (SNPs) overlapping. Moreover, users of NGS-PrimerPlex are free from manually defining input genome regions, because it can be done automatically from a list of genes or their parts like exon or codon numbers. Using the program, the NGS-panel for sequencing the LRRK2 gene coding regions was created, and 354 DNA samples were studied successfully with a median coverage of 97.4% of target regions by at least 30 reads. To show that NGS-PrimerPlex can also be applied for bacterial genomes, we designed primers to detect foodborne pathogens Salmonella enterica, Escherichia coli O157:H7, Listeria monocytogenes, and Staphylococcus aureus considering variable positions of the genomes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.