The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity

Abstract Background A large number of variants have been employed in various medical applications, such as providing medication instructions, disease susceptibility testing, paternity testing, and tumour diagnosis. A high multiplicity PCR will outperform other technologies because of its lower cost,...

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Autores principales:	Jie Yuan, Ji Yi, Meixiao Zhan, Qingqing Xie, Ting Ting Zhen, Jian Zhou, Zeqing Li, Zhou Li
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Primer design Multiplex Software Web interface Variant Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/3f50ab83bfb846e9b7cf88e7f38070b5
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spelling	oai:doaj.org-article:3f50ab83bfb846e9b7cf88e7f38070b52021-11-21T12:26:40ZThe web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity10.1186/s12864-021-08149-11471-2164https://doaj.org/article/3f50ab83bfb846e9b7cf88e7f38070b52021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08149-1https://doaj.org/toc/1471-2164Abstract Background A large number of variants have been employed in various medical applications, such as providing medication instructions, disease susceptibility testing, paternity testing, and tumour diagnosis. A high multiplicity PCR will outperform other technologies because of its lower cost, reaction time and sample consumption. To conduct a multiplex PCR with higher than 100 plex multiplicity, primers need to be carefully designed to avoid the formation of secondary structures and nonspecific amplification between primers, templates and products. Thus, a user-friendly, highly automated and highly user-defined web-based multiplex PCR primer design software is needed to minimize the work of primer design and experimental verification. Results Ultiplex was developed as a free online multiplex primer design tool with a user-friendly web-based interface ( http://ultiplex.igenebook.cn ). To evaluate the performance of Ultiplex, 294 out of 295 (99.7%) target primers were successfully designed. A total of 275 targets produced qualified primers after primer filtration, and 271 of those targets were successfully clustered into one compatible PCR group and could be covered by 108 primers. The designed primer group stably detected the rs28934573(C > T) mutation at lower than a 0.25% mutation rate in a series of samples with different ratios of HCT-15 and HaCaT cell line DNA. Conclusion Ultiplex is a web-based multiplex PCR primer tool that has several functions, including batch design and compatibility checking for the exclusion of mutual secondary structures and mutual false alignments across the whole genome. It offers flexible arguments for users to define their own references, primer Tm values, product lengths, plex numbers and tag oligos. With its user-friendly reports and web-based interface, Ultiplex will provide assistance for biological applications and research involving genomic variants.Jie YuanJi YiMeixiao ZhanQingqing XieTing Ting ZhenJian ZhouZeqing LiZhou LiBMCarticlePrimer designMultiplexSoftwareWeb interfaceVariantBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-17 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Primer design Multiplex Software Web interface Variant Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Primer design Multiplex Software Web interface Variant Biotechnology TP248.13-248.65 Genetics QH426-470 Jie Yuan Ji Yi Meixiao Zhan Qingqing Xie Ting Ting Zhen Jian Zhou Zeqing Li Zhou Li The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity
description	Abstract Background A large number of variants have been employed in various medical applications, such as providing medication instructions, disease susceptibility testing, paternity testing, and tumour diagnosis. A high multiplicity PCR will outperform other technologies because of its lower cost, reaction time and sample consumption. To conduct a multiplex PCR with higher than 100 plex multiplicity, primers need to be carefully designed to avoid the formation of secondary structures and nonspecific amplification between primers, templates and products. Thus, a user-friendly, highly automated and highly user-defined web-based multiplex PCR primer design software is needed to minimize the work of primer design and experimental verification. Results Ultiplex was developed as a free online multiplex primer design tool with a user-friendly web-based interface ( http://ultiplex.igenebook.cn ). To evaluate the performance of Ultiplex, 294 out of 295 (99.7%) target primers were successfully designed. A total of 275 targets produced qualified primers after primer filtration, and 271 of those targets were successfully clustered into one compatible PCR group and could be covered by 108 primers. The designed primer group stably detected the rs28934573(C > T) mutation at lower than a 0.25% mutation rate in a series of samples with different ratios of HCT-15 and HaCaT cell line DNA. Conclusion Ultiplex is a web-based multiplex PCR primer tool that has several functions, including batch design and compatibility checking for the exclusion of mutual secondary structures and mutual false alignments across the whole genome. It offers flexible arguments for users to define their own references, primer Tm values, product lengths, plex numbers and tag oligos. With its user-friendly reports and web-based interface, Ultiplex will provide assistance for biological applications and research involving genomic variants.
format	article
author	Jie Yuan Ji Yi Meixiao Zhan Qingqing Xie Ting Ting Zhen Jian Zhou Zeqing Li Zhou Li
author_facet	Jie Yuan Ji Yi Meixiao Zhan Qingqing Xie Ting Ting Zhen Jian Zhou Zeqing Li Zhou Li
author_sort	Jie Yuan
title	The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity
title_short	The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity
title_full	The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity
title_fullStr	The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity
title_full_unstemmed	The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity
title_sort	web-based multiplex pcr primer design software ultiplex and the associated experimental workflow: up to 100- plex multiplicity
publisher	BMC
publishDate	2021
url	https://doaj.org/article/3f50ab83bfb846e9b7cf88e7f38070b5
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The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity

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