MassCode Liquid Arrays as a Tool for Multiplexed High-Throughput Genetic Profiling

Richmond, Gregory S.; Khine, Htet; Zhou, Tina T.; Ryan, Daniel E.; Brand, Tony; McBride, Mary T.; Killeen, Kevin

doi:10.1371/journal.pone.0018967

Cited by 6 publications

(4 citation statements)

References 45 publications

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“…Concerning Infantis and Virchow, the same three markers have been selected: the SCH-2097 markers (probe and couple of primers) and the r probe [ 12 , 14 ]. These results were coherent as SCH-2097 markers target the rfb gene cluster used to identify the serogroup C1 while the r probe targets the sequence coding for the r flagellar phase characterizing both S .…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Genome Target Evaluator (GTEvaluator): A workflow exploiting genome dataset to measure the sensitivity and specificity of genetic markers

et al. 2017

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Most of the bacterial typing methods used to discriminate isolates in medical or food safety microbiology are based on genetic markers used as targets in PCR or hybridization experiments. These DNA typing methods are important tools for studying prevalence and epidemiology, for conducting surveillance, investigations and control of biological hazard sources. In that perspective, it is crucial to insure that the chosen genetic markers have the greatest specificity and sensitivity. The wealth of whole-genome sequences available for many bacterial species offers the opportunity to evaluate the performance of these genetic markers. In the present study, we have developed GTEvaluator, a bioinformatics workflow which ranks genetic markers depending on their sensitivity and specificity towards groups of well-defined genomes. GTEvaluator identifies the most performant genetic markers to target individuals among a population. The individuals (i.e. a group of genomes within a collection) are defined by any kind of particular phenotypic or biological properties inside a related population (i.e. collection of genomes). The performance of the genetic markers is computed by a distance value which takes into account both sensitivity and specificity. In this study we report two examples of GTEvaluator application. In the first example Bacillus phenotypic markers were evaluated for their capacity to distinguish B. cereus from B. thuringiensis. In the second experiment, GTEvaluator measured the performance of genetic markers dedicated to the molecular serotyping of Salmonella enterica. In one in silico experiment it was possible to test 64 markers onto 134 genomes corresponding to 14 different serotypes.

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Section: Resultsmentioning

confidence: 99%

“…in 2011 and used in an innovating genotyping method that couple PCR and HPLC to identify Salmonella serotypes. This method was devised as part of a high-throughput mid-plexing analytical system to provide an efficient qualitative differential tool for the detection of several Salmonella serotypes [ 14 ].…”

Section: Methodsmentioning

confidence: 99%

Genome Target Evaluator (GTEvaluator): A workflow exploiting genome dataset to measure the sensitivity and specificity of genetic markers

et al. 2017

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“…Microbiologists need to access to Salmonella serovar genomes from specific sources for many types of analyses such as clustering analyses, source attribution studies or when screening for molecular markers. 10 -13 Obtaining genomes from laboratories around the world is therefore a major advantage. Here, we tested the ability of the SalmoDEST tool to obtain Salmonella genomes from strains isolated from bovine sources worldwide.…”

Section: Methodsmentioning

confidence: 99%

Retrieving Good-Quality Salmonella Genomes From the GenBank Database Using a Python Tool, SalmoDEST

Cherchame

Ilango

Cadel-Six

2022

Bioinform Biol Insights

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With the advent of next-generation whole-genome sequencing (WGS), the need for good-quality and well-characterised Salmonella genomes has increased over the past years. Good-quality complete genomes are often required for assembly reference mapping or phylogenetic single nucleotide polymorphism (SNP) analysis. Complete genomes or contigs from specific sources or serovars are also searched for clustering analysis or source attribution studies. Therefore, new bioinformatics tools are needed for the extraction of good-quality and well-characterised genomes from public databases. Here, we developed SalmoDEST, an open-source Python tool capable of extracting Salmonella genomes with a coverage higher than 50x and genome length over 4Mb from the GenBank database in the form of complete genomes or contigs, with verification of the serovar to which they belong and identification of the corresponding multi locus sequence type (MLST) profile. To validate the ability to SalmoDEST to screen for and retrieve genomes of good quality, we compared our results for S. Typhi complete genome with those available in the literature and extracted Salmonella genomes from bovine sources strains isolated worldwide. Finally, we provide in this study a list of 239 complete genomes for 123 serovars of Salmonella of high quality. SalmoDEST is a handy and easy-to-use open-source tool to extract complete genomes or contigs that can be routinely used in public health, food safety and research laboratories. SalmoDEST (SALMOnella Download gEnome Serotype sT) is available at https://github.com/I-Guy/SalmoDEST .

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“…This issue must be addressed with any method that would utilize this approach. However, PCR followed by MS to identify PCR products has considerable potential for rapid detection of various target organisms (34,35,38) with some promising commercial applications currently available (e.g., the Abbott ID-Plex system (34)). These systems have considerable multiplexing capabilities and can be an intermediate solution between traditional PCR (limited at best to four or five targets per reaction) and full genome sequencing (which is usually more complex due to DNA preparation required, back-end analysis needs, etc.).…”

Section: New Developmentsmentioning

confidence: 99%

Assessment Criteria and Approaches for Rapid Detection Methods To Be Used in the Food Industry

Wiedmann

Wang²,

Post

et al. 2014

Journal of Food Protection

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The number of commercially available kits and methods for rapid detection of foodborne pathogens continues to increase at a considerable pace, and the diversity of methods and assay formats is reaching a point where it is very difficult even for experts to weigh the advantages and disadvantages of different methods and to decide which methods to choose for a certain testing need. Although a number of documents outline quantitative criteria that can be used to evaluate different detection methods (e.g., exclusivity and inclusivity), a diversity of criteria is typically used by industry to select specific methods that are used for pathogen detection. This article is intended to provide an overall outline of criteria that the food industry can use to evaluate new rapid detection methods, with a specific focus on nucleic acid-based detection methods.

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MassCode Liquid Arrays as a Tool for Multiplexed High-Throughput Genetic Profiling

Cited by 6 publications

References 45 publications

Genome Target Evaluator (GTEvaluator): A workflow exploiting genome dataset to measure the sensitivity and specificity of genetic markers

Genome Target Evaluator (GTEvaluator): A workflow exploiting genome dataset to measure the sensitivity and specificity of genetic markers

Retrieving Good-Quality Salmonella Genomes From the GenBank Database Using a Python Tool, SalmoDEST

Assessment Criteria and Approaches for Rapid Detection Methods To Be Used in the Food Industry

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