{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T23:08:59Z","timestamp":1777072139714,"version":"3.51.4"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008468","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,1,12]],"date-time":"2021-01-12T00:00:00Z","timestamp":1610409600000}}],"reference-count":22,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2020,12,30]],"date-time":"2020-12-30T00:00:00Z","timestamp":1609286400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Russian State funded budget","award":["\u0410\u0410\u0410\u0410-\u041017-117020210025-5"],"award-info":[{"award-number":["\u0410\u0410\u0410\u0410-\u041017-117020210025-5"]}]},{"name":"Russian State funded budget","award":["\u0410\u0410\u0410\u0410-\u041017-117020210025-5"],"award-info":[{"award-number":["\u0410\u0410\u0410\u0410-\u041017-117020210025-5"]}]},{"name":"Russian State funded budget","award":["\u0410\u0410\u0410\u0410-\u041017-117020210025-5"],"award-info":[{"award-number":["\u0410\u0410\u0410\u0410-\u041017-117020210025-5"]}]},{"name":"Russian State funded budget","award":["\u0410\u0410\u0410\u0410-\u041017-117020210025-5"],"award-info":[{"award-number":["\u0410\u0410\u0410\u0410-\u041017-117020210025-5"]}]},{"name":"Russian State funded budget","award":["\u0410\u0410\u0410\u0410-\u041017-117020210025-5"],"award-info":[{"award-number":["\u0410\u0410\u0410\u0410-\u041017-117020210025-5"]}]},{"name":"Russian State funded budget","award":["\u0410\u0410\u0410\u0410-\u041017-117020210025-5"],"award-info":[{"award-number":["\u0410\u0410\u0410\u0410-\u041017-117020210025-5"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    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\n                    <jats:italic>LRRK2<\/jats:italic>\n                    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\n                    <jats:italic>Salmonella enterica<\/jats:italic>\n                    ,\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    O157:H7,\n                    <jats:italic>Listeria monocytogenes<\/jats:italic>\n                    , and\n                    <jats:italic>Staphylococcus aureus<\/jats:italic>\n                    considering variable positions of the genomes.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1008468","type":"journal-article","created":{"date-parts":[[2020,12,30]],"date-time":"2020-12-30T14:57:06Z","timestamp":1609340226000},"page":"e1008468","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":27,"title":["NGS-PrimerPlex: High-throughput primer design for multiplex polymerase chain reactions"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4822-0251","authenticated-orcid":true,"given":"Andrey","family":"Kechin","sequence":"first","affiliation":[]},{"given":"Viktoria","family":"Borobova","sequence":"additional","affiliation":[]},{"given":"Ulyana","family":"Boyarskikh","sequence":"additional","affiliation":[]},{"given":"Evgeniy","family":"Khrapov","sequence":"additional","affiliation":[]},{"given":"Sergey","family":"Subbotin","sequence":"additional","affiliation":[]},{"given":"Maxim","family":"Filipenko","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,12,30]]},"reference":[{"key":"pcbi.1008468.ref001","doi-asserted-by":"crossref","first-page":"1489","DOI":"10.1007\/s00414-017-1567-9","article-title":"FlexPlex27\u2014highly multiplexed rapid DNA identification for law enforcement, kinship, and military applications","volume":"131","author":"R Grover","year":"2017","journal-title":"Int J Legal Med"},{"key":"pcbi.1008468.ref002","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.aca.2014.04.017","article-title":"Segmented continuous-flow multiplex polymerase chain reaction microfluidics for high-throughput and rapid foodborne pathogen detection","volume":"826","author":"B Shu","year":"2014","journal-title":"Anal Chim Acta"},{"key":"pcbi.1008468.ref003","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1126\/science.aar3247","article-title":"Detection and localization of surgically resectable cancers with a multi-analyte blood test","volume":"359","author":"JD Cohen","year":"2018","journal-title":"Science"},{"key":"pcbi.1008468.ref004","doi-asserted-by":"crossref","DOI":"10.7314\/APJCP.2015.16.17.7935","article-title":"Massive parallel sequencing for diagnostic genetic testing of BRCA genes\u2014A single center experience","volume":"16","author":"NA Ermolenko","year":"2015","journal-title":"Asian Pacific J Cancer Prev"},{"key":"pcbi.1008468.ref005","volume-title":"Cold Spring Harb Protoc","author":"MR Green","year":"2019"},{"key":"pcbi.1008468.ref006","doi-asserted-by":"crossref","first-page":"1479","DOI":"10.1038\/nm.3729","article-title":"Anchored multiplex PCR for targeted next-generation sequencing","volume":"20","author":"Z Zheng","year":"2014","journal-title":"Nat Med."},{"key":"pcbi.1008468.ref007","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1007\/s40291-015-0174-z","article-title":"Nested PCR Assay for Eight Pathogens: A Rapid Tool for Diagnosis of Bacterial Meningitis","volume":"20","author":"SP Bhagchandani","year":"2016","journal-title":"Mol Diagn Ther. 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