数字农科院2.0

MultiPrime: A reliable and efficient tool for targeted next-generation sequencing

文献类型： 外文期刊

作者： Xia, Han;Zhang, Zhe;Luo, Chen;Wei, Kangfei;Li, Xuming;Mu, Xiyu;Duan, Meilin;Zhu, Chuanlong;Jin, Luyi;He, Xiaoqing;Tang, Lingjie;Hu, Long;Guan, Yuanlin;Lam, David C. C.;Yang, Junbo

作者机构：

关键词： （0-1-5）degenerate primer design;minimal primer set;multiplex PCR;targeted next-generation sequencing

期刊名称： iMeta

ISSN： 2770-5986

年卷期： 2024 年 2 卷 4 期

页码：

收录情况： SCIE（2024版）

摘要： We present multiPrime, a novel tool that automatically designs minimal primer sets for targeted next-generation sequencing, tailored to specific microbiomes or genes. MultiPrime enhances primer coverage by designing primers with mismatch tolerance and ensures both high compatibility and specificity. We evaluated the performance of multiPrime using a data set of 43,016 sequences from eight viruses. Our results demonstrated that multiPrime outperformed conventional tools, and the primer set designed by multiPrime successfully amplified the target amplicons. Furthermore, we expanded the application of multiPrime to 30 types of viruses and validated the work efficacy of multiPrime-designed primers in 80 clinical specimens. The subsequent sequencing outcomes from these primers indicated a sensitivity of 94% and a specificity of 89%. This study introduces multiPrime, a novel tool tailored for the wide-ranging detection of target sequences through targeted next-generation sequencing (tNGS). By integrating degenerate primer design principles with effective mismatch handling, multiPrime demonstrates enhanced precision and specificity in the identification of diverse sequence types. This breakthrough presents a prospective pathway for optimizing the development of tNGS. In performance comparison, multiPrime excelled over conventional tools in terms of execution time, primer coverage, and the number of candidate primers. It offers a streamlined and versatile solution for the rapid and cost-effective detection of diverse microbiomes.Highlightsimage MultiPrime is a user-friendly and one-step tool for designing targeted next-generation sequencing primer sets.It integrates degenerate primer design theory with mismatch handling, resulting in improved accuracy and specificity in detecting broad-spectrum sequences.It outperformed conventional programs in terms of run time, primer number, and primer coverage.The versatility and potential of multiPrime are highlighted by its potential application in detecting single or multiple genes, exons, antisense strands, RNA, or other specific DNA segments.

分类号：

  • 相关文献

[1]Construction of SNP genetic maps based on targeted next-generation sequencing and QTL mapping of vital agronomic traits in faba bean (Vicia faba L.). Meng wei LI,Yu hua HE,Rong LIU,Guan LI,Dong WANG,Yi shan JI,Xin YAN,Shu xian HUANG,Chen yu WANG,Yu MA,Bei LIU,Tao YANG,Xu xiao ZONG. 2023

[2]Development of multiplex PCR assay for rapid detection of Riemerella anatipestifer, Escherichia coli, and Salmonella enterica simultaneously from ducks. Hu, Qinghai,Tu, Jing,Han, Xiangan,Zhu, Yinyu,Ding, Chan,Yu, Shengqing,Ding, Chan,Yu, Shengqing. 2011

[3]Efficient multiplex simple sequence repeat genotyping of the oomycete plant pathogen Phytophthora infestans. Li, Ying,Cooke, David E. L.,Li, Ying,Jacobsen, Evert,Li, Ying,van der Lee, Theo. 2013

[4]Development of two multiplex PCR assays targeting improvement of bread-making and noodle qualities in common wheat. Zhang, X. K.,Liu, L.,He, Z. H.,Sun, D. J.,He, X. Y.,Xu, Z. H.,Zhang, P. P.,Chen, F.,Xia, X. C.,Zhang, X. K.,He, Z. H.. 2008

[5]Development of one-tube multiplex polymerase chain reaction (PCR) for detecting Mycobacterium bovis. Quan, Zhang,Haiming, Tan,Xiaoya, Cai,Weifeng, Yuan,Hong, Jia,Hongfei, Zhu.

[6]Rapid diagnosis of goose viral infections by multiplex PCR. Chen, Zongyan,Li, Chuanfeng,Li, Guoxin,Yu, Hai,Jiang, Yifeng,Yan, Liping,Meng, Chunchun,Zhou, Yanjun,Tong, Guangzhi,Liu, Guangqing.

[7]Rapid identification of deer products by multiplex PCR assay. Zha, Dai-Ming,Xing, Xiu-Mei,Yang, Fu-He,Zha, Dai-Ming,Zha, Dai-Ming,Xing, Xiu-Mei,Yang, Fu-He,Zha, Dai-Ming,Xing, Xiu-Mei,Yang, Fu-He.

[8]Development of an allele-specific marker for Glu-B3 alleles in common wheat and establishment of a multiplex PCR assay. Sui, Xinxia,Wang, Linhai,Xia, Xianchun,He, Zhonghu,Sui, Xinxia,Wang, Zhenlin,He, Zhonghu. 2010

[9]Development of a multiplex PCR assay for detection and discrimination of Theileria annulata and Theileria sergenti in cattle. Junlong, Liu,Li, Youquan,Liu, Aihong,Guan, Guiquan,Xie, Junren,Yin, Hong,Luo, Jianxun,Junlong, Liu,Li, Youquan,Liu, Aihong,Guan, Guiquan,Xie, Junren,Yin, Hong,Luo, Jianxun.

[10]Optimization of a multiplex PCR assay for detecting transgenic soybean components in feed products. Wang, Xiumin,Teng, Da,Yang, Yalin,Guan, Qingfeng,Wang, Jianhua,Tian, Fang,Wang, Xiumin,Teng, Da,Yang, Yalin,Guan, Qingfeng,Wang, Jianhua,Tian, Fang,Ao, Changjin.

[11]A PCR method targeting internal transcribed spacers: the simultaneous detection of Babesia bigemina and Babesia bovis in cattle. Liu, Junlong,Guan, Guiquan,Liu, Aihong,Li, Youquan,Yin, Hong,Luo, Jianxun.

[12]A multiplex PCR assay for fraud identification of deer products. Zha, Daiming,Xing, Xiumei,Yang, Fuhe,Zha, Daiming,Zha, Daiming,Xing, Xiumei,Yang, Fuhe,Zha, Daiming,Xing, Xiumei,Yang, Fuhe. 2010

[13]Development of a Multiplex RT-PCR Assay for Simultaneous Detection of Four Potential Zoonotic Swine RNA Viruses. Gebremeskel Mamu Werid,He Zhang,Yassein M. Ibrahim,Yu Pan,Lin Zhang,Yunfei Xu,Wenli Zhang,Wei Wang,Hongyan Chen,Lizhi Fu,Yue Wang. 2022

[14]A Multiplex Pcr Assay For T.he Simultaneous Detection Of T aenia Hydatigena, T. Multiceps, T. Pisiformis, And Dipylidium Caninum Infections. Zhu, GQ,Li, L,Ohiolei, JA,Wu, YT,Li, WH,Zhang, NZ,Fu, BQ,Yan, HB,Jia, WZ. 2019

[15]Strain-level Identification of Brucella melitensis Reference Strain 63/9 using Multiplex PCR Method by Targeting BMEA_B0162 and BMEA_A1238. Ge Zhang,Hui Jiang,Guangzhi Zhang,Peng Li,Yu Feng,Xingjia Shen,Jiabo Ding. 2024

[16]Occurrence of Trichinella spiralis in farmed wild boars (Sus scrofa): an underrated risk in China. Zhang, Nian-Zhang,Wang, Meng,Chen, Wei-Gang,Gai, Wen-Yan,Dao, Thanh Thi Ha,Li, Ting-Ting,Li, Wen-Hui,Zhang, Hai-Rui,Yin, Hong,Thuy, Nguyen Thi Bich,Fu, Bao-Quan. 2024

作者其他论文 更多>>