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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

NGS-PrimerPlex: High-throughput primer design for multiplex polymerase chain reactions.

Andrey Kechin^1,2, Viktoria Borobova^1,2, Ulyana Boyarskikh¹

¹Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.

Plos Computational Biology

|December 30, 2020

Summary

NGS-PrimerPlex is a new tool for designing primers for multiplex PCR, enabling efficient genome target enrichment for next-generation sequencing (NGS) panels. It automates primer design for genes and bacterial pathogens, improving sequencing accuracy and coverage.

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Last Updated: Nov 23, 2025

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Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

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Published on: September 3, 2009

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Multiplex PCR is crucial for developing targeted next-generation sequencing (NGS) panels.
Existing primer design tools may lack versatility for complex amplicon-based enrichment strategies.

Purpose of the Study:

To introduce NGS-PrimerPlex, a command-line application for designing primers for various amplicon-based genome target enrichment methods.
To demonstrate the application of NGS-PrimerPlex in human gene sequencing and bacterial pathogen detection.

Main Methods:

NGS-PrimerPlex supports nested and anchored multiplex PCR, primer redistribution, and extension of existing NGS panels.
The software considers secondary structures, non-target amplicons, primer overlaps, and single-nucleotide polymorphisms (SNPs).
Automated input region definition from gene lists or specific genomic features (e.g., exons) is supported.

Main Results:

An NGS panel for LRRK2 gene sequencing was successfully created, achieving 97.4% median coverage in 354 DNA samples.
Primers were designed for detecting foodborne pathogens (Salmonella enterica, E. coli O157:H7, Listeria monocytogenes, Staphylococcus aureus) in bacterial genomes.

Conclusions:

NGS-PrimerPlex is an efficient and versatile tool for designing primers for diverse NGS applications, from human genetics to pathogen surveillance.
The software facilitates automated and accurate primer design, enhancing the development of targeted sequencing panels.