Universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR) for SNP genotyping

Abstract Background The detection and identification of single nucleotide polymorphism (SNP) is essential for determining patient disease susceptibility and the delivery of medicines targeted to the individual. At present, SNP genotyping technology includes Sanger sequencing, TaqMan-probe quantitati...

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Autores principales:	Baowei Li, Yanran Liu, Xiaodan Hao, Jinhua Dong, Limei Chen, Haimei Li, Wei Wu, Ying Liu, Jianxun Wang, Yin Wang, Peifeng Li
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	UPIP-qPCR Intermediate primer Universal probe SNP genotyping Sanger sequencing Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/6e04b79e072348569f454e7bbdd7f48c
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spelling	oai:doaj.org-article:6e04b79e072348569f454e7bbdd7f48c2021-11-28T12:23:00ZUniversal probe-based intermediate primer-triggered qPCR (UPIP-qPCR) for SNP genotyping10.1186/s12864-021-08148-21471-2164https://doaj.org/article/6e04b79e072348569f454e7bbdd7f48c2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08148-2https://doaj.org/toc/1471-2164Abstract Background The detection and identification of single nucleotide polymorphism (SNP) is essential for determining patient disease susceptibility and the delivery of medicines targeted to the individual. At present, SNP genotyping technology includes Sanger sequencing, TaqMan-probe quantitative polymerase chain reaction (qPCR), amplification-refractory mutation system (ARMS)-PCR, and Kompetitive Allele-Specific PCR (KASP). However, these technologies have some disadvantages: the high cost of development and detection, long and time consuming protocols, and high false positive rates. Focusing on these limitations, we proposed a new SNP detection method named universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR). In this method, only two types of fluorescence-labeled probes were used for SNP genotyping, thus greatly reducing the cost of development and detection for SNP genotyping. Results In the amplification process of UPIP-qPCR, unlabeled intermediate primers with template-specific recognition functions could trigger probe hydrolysis and specific signal release. UPIP-qPCR can be used successfully and widely for SNP genotyping. The sensitivity of UPIP-qPCR in SNP genotyping was 0.01 ng, the call rate was more than 99.1%, and the accuracy was more than 99.9%. High-throughput DNA microarrays based on intermediate primers can be used for SNP genotyping. Conclusion This novel approach is both cost effective and highly accurate; it is a reliable SNP genotyping method that would serve the needs of the clinician in the provision of targeted medicine.Baowei LiYanran LiuXiaodan HaoJinhua DongLimei ChenHaimei LiWei WuYing LiuJianxun WangYin WangPeifeng LiBMCarticleUPIP-qPCRIntermediate primerUniversal probeSNP genotypingSanger sequencingBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	UPIP-qPCR Intermediate primer Universal probe SNP genotyping Sanger sequencing Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	UPIP-qPCR Intermediate primer Universal probe SNP genotyping Sanger sequencing Biotechnology TP248.13-248.65 Genetics QH426-470 Baowei Li Yanran Liu Xiaodan Hao Jinhua Dong Limei Chen Haimei Li Wei Wu Ying Liu Jianxun Wang Yin Wang Peifeng Li Universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR) for SNP genotyping
description	Abstract Background The detection and identification of single nucleotide polymorphism (SNP) is essential for determining patient disease susceptibility and the delivery of medicines targeted to the individual. At present, SNP genotyping technology includes Sanger sequencing, TaqMan-probe quantitative polymerase chain reaction (qPCR), amplification-refractory mutation system (ARMS)-PCR, and Kompetitive Allele-Specific PCR (KASP). However, these technologies have some disadvantages: the high cost of development and detection, long and time consuming protocols, and high false positive rates. Focusing on these limitations, we proposed a new SNP detection method named universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR). In this method, only two types of fluorescence-labeled probes were used for SNP genotyping, thus greatly reducing the cost of development and detection for SNP genotyping. Results In the amplification process of UPIP-qPCR, unlabeled intermediate primers with template-specific recognition functions could trigger probe hydrolysis and specific signal release. UPIP-qPCR can be used successfully and widely for SNP genotyping. The sensitivity of UPIP-qPCR in SNP genotyping was 0.01 ng, the call rate was more than 99.1%, and the accuracy was more than 99.9%. High-throughput DNA microarrays based on intermediate primers can be used for SNP genotyping. Conclusion This novel approach is both cost effective and highly accurate; it is a reliable SNP genotyping method that would serve the needs of the clinician in the provision of targeted medicine.
format	article
author	Baowei Li Yanran Liu Xiaodan Hao Jinhua Dong Limei Chen Haimei Li Wei Wu Ying Liu Jianxun Wang Yin Wang Peifeng Li
author_facet	Baowei Li Yanran Liu Xiaodan Hao Jinhua Dong Limei Chen Haimei Li Wei Wu Ying Liu Jianxun Wang Yin Wang Peifeng Li
author_sort	Baowei Li
title	Universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR) for SNP genotyping
title_short	Universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR) for SNP genotyping
title_full	Universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR) for SNP genotyping
title_fullStr	Universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR) for SNP genotyping
title_full_unstemmed	Universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR) for SNP genotyping
title_sort	universal probe-based intermediate primer-triggered qpcr (upip-qpcr) for snp genotyping
publisher	BMC
publishDate	2021
url	https://doaj.org/article/6e04b79e072348569f454e7bbdd7f48c
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_version_	1718408022136455168

Universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR) for SNP genotyping

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