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NGS-PrimerPlex : High-throughput primer design for multiplex polymerase chain reactions. / Kechin, Andrey; Borobova, Viktoria; Boyarskikh, Ulyana et al.

In: PLoS Computational Biology, Vol. 16, No. 12, e1008468, 30.12.2020.

Research output: Contribution to journalArticlepeer-review

Harvard

Kechin, A, Borobova, V, Boyarskikh, U, Khrapov, E, Subbotin, S & Filipenko, M 2020, 'NGS-PrimerPlex: High-throughput primer design for multiplex polymerase chain reactions', PLoS Computational Biology, vol. 16, no. 12, e1008468. https://doi.org/10.1371/journal.pcbi.1008468

APA

Kechin, A., Borobova, V., Boyarskikh, U., Khrapov, E., Subbotin, S., & Filipenko, M. (2020). NGS-PrimerPlex: High-throughput primer design for multiplex polymerase chain reactions. PLoS Computational Biology, 16(12), [e1008468]. https://doi.org/10.1371/journal.pcbi.1008468

Vancouver

Kechin A, Borobova V, Boyarskikh U, Khrapov E, Subbotin S, Filipenko M. NGS-PrimerPlex: High-throughput primer design for multiplex polymerase chain reactions. PLoS Computational Biology. 2020 Dec 30;16(12):e1008468. doi: 10.1371/journal.pcbi.1008468

Author

Kechin, Andrey ; Borobova, Viktoria ; Boyarskikh, Ulyana et al. / NGS-PrimerPlex : High-throughput primer design for multiplex polymerase chain reactions. In: PLoS Computational Biology. 2020 ; Vol. 16, No. 12.

BibTeX

@article{871a200a6f4f44b8a5ddc3bd5240d929,
title = "NGS-PrimerPlex: High-throughput primer design for multiplex polymerase chain reactions",
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.",
keywords = "READS, TOOL",
author = "Andrey Kechin and Viktoria Borobova and Ulyana Boyarskikh and Evgeniy Khrapov and Sergey Subbotin and Maxim Filipenko",
note = "Publisher Copyright: {\textcopyright} 2020 Kechin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.",
year = "2020",
month = dec,
day = "30",
doi = "10.1371/journal.pcbi.1008468",
language = "English",
volume = "16",
journal = "PLoS Computational Biology",
issn = "1553-734X",
publisher = "Public Library of Science",
number = "12",

}

RIS

TY - JOUR

T1 - NGS-PrimerPlex

T2 - High-throughput primer design for multiplex polymerase chain reactions

AU - Kechin, Andrey

AU - Borobova, Viktoria

AU - Boyarskikh, Ulyana

AU - Khrapov, Evgeniy

AU - Subbotin, Sergey

AU - Filipenko, Maxim

N1 - Publisher Copyright: © 2020 Kechin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2020/12/30

Y1 - 2020/12/30

N2 - 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.

AB - 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.

KW - READS

KW - TOOL

UR - http://www.scopus.com/inward/record.url?scp=85098951720&partnerID=8YFLogxK

U2 - 10.1371/journal.pcbi.1008468

DO - 10.1371/journal.pcbi.1008468

M3 - Article

C2 - 33378360

AN - SCOPUS:85098951720

VL - 16

JO - PLoS Computational Biology

JF - PLoS Computational Biology

SN - 1553-734X

IS - 12

M1 - e1008468

ER -

ID: 27372689