GLAPD: Whole Genome Based LAMP Primer Design for a Set of Target Genomes

Abstract

Loop-mediated isothermal amplification (LAMP) technology has been applied in a wide range of fields such as detection of foodborne bacteria and clinical pathogens due to its simplicity and efficiency. However, existing LAMP primer designing systems require a conserved gene or a short genome region as input, and they can't design group-specific primers. With the growing number of whole genomes available, it is possible to design better primers to target a set of genomes with high specificity based on whole genomes. We present here a whole Genome based LAMP primer designer (GLAPD), a new system to design LAMP primer for a set of target genomes using whole genomes. Candidate single primer regions are identified genome wide and then combined into LAMP primer sets. For a given set of target genomes, only primer sets amplifying them and only these genomes will be output. In order to accelerate the primer designing, a GPU version is provided as well. The effectiveness of primers designed by GLAPD has been assessed for a wide range of foodborne bacteria. GLAPD can be accessed at http://cgm.sjtu.edu.

Diagnostic accuracy of loop-mediated isothermal amplification coupled to nanopore sequencing (LamPORE) for the detection of SARS-CoV-2 infection at scale in symptomatic and asymptomatic populations

“…Another potential inherent advantage is the ability to multiplex gene targets allowing the detection of multiple respiratory pathogens [ 18 ] such as SARS-CoV-2, influenza and respiratory syncytial virus (RSV). It is not known what the upper limit of multiplexing of LAMP primers is, and they are considerably more complex to design than PCR primers [ 19 ]. Given the advantages of LAMP in terms of speed of amplification [ 8 ] and sensitivity of detection, an exploration of LAMP multiplexing is urgently required.…”

Loop-Mediated Isothermal Amplification (LAMP) Assay for Detecting Burkholderia cepacia Complex in Non-Sterile Pharmaceutical Products

“…LAMP relies on 6 different primers, suggesting a higher degree of specificity than conventional PCR and qPCR using two primers [ 17 , 18 ]. This makes LAMP assay not only susceptible to the formation of primer dimers, but also cross contamination by aerosol leading to false-positive results much easier than conventional PCR and qPCR [ 19 , 32 , 33 , 34 ]. Indeed, in this study, we have observed some qPCR negative samples (< 100 fg/μL) with C T values between 35 to 40, which triggered color changes that were caused by non-specific amplification products (data not shown).…”

Diagnostic accuracy of Loop mediated isothermal amplification coupled to Nanopore sequencing for the detection of SARS-CoV-2 infection at scale in symptomatic and asymptomatic populations

“…Another potential inherent advantage is the ability to multiplex gene targets allowing the detection of multiple respiratory pathogens (16) such as SARS-CoV-2, influenza and respiratory syncytial virus (RSV). It is not known what the upper limit of multiplexing of LAMP primers is, and they are considerably more complex to design than PCR primers (17). Given the advantages of LAMP in terms of speed of amplification (9) and sensitivity of detection, an exploration of LAMP multiplexing is urgently required.…”