Hi-plex for simple, accurate, and cost-effective amplicon-based targeted DNA sequencing

Bernard J. Pope, Fleur Hammet, Tu Nguyen-Dumont, Daniel J. Park

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Otherpeer-review

1 Citation (Scopus)

Abstract

Hi-Plex is a suite of methods to enable simple, accurate, and cost-effective highly multiplex PCR-based targeted sequencing (Nguyen-Dumont et al., Biotechniques 58:33–36, 2015). At its core is the principle of using gene-specific primers (GSPs) to “seed” (or target) the reaction and universal primers to “drive” the majority of the reaction. In this manner, effects on amplification efficiencies across the target amplicons can, to a large extent, be restricted to early seeding cycles. Product sizes are defined within a relatively narrow range to enable high-specificity size selection, replication uniformity across target sites (including in the context of fragmented input DNA such as that derived from fixed tumor specimens (Nguyen-Dumont et al., Biotechniques 55:69–74, 2013; Nguyen-Dumont et al., Anal Biochem 470:48–51, 2015), and application of high-specificity genetic variant calling algorithms (Pope et al., Source Code Biol Med 9:3, 2014; Park et al., BMC Bioinformatics 17:165, 2016). Hi-Plex offers a streamlined workflow that is suitable for testing large numbers of specimens without the need for automation.

Original languageEnglish
Title of host publicationNext Generation Sequencing
Subtitle of host publicationMethods and Protocols
EditorsSteven R. Head, Phillip Ordoukhanian, Daniel R. Salomon
PublisherHumana Press
Pages53-70
Number of pages18
ISBN (Electronic)9781493975143
ISBN (Print)9781493975129
DOIs
Publication statusPublished - 2018
Externally publishedYes

Publication series

NameMethods in Molecular Biology
PublisherHumana Press, Inc.
Volume1712
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • Amplicon sequencing
  • Hi-Plex
  • Massively parallel sequencing
  • Multiplex PCR
  • Mutation screening
  • Next-generation sequencing
  • Sequence screening
  • Targeted sequencing

Cite this

Pope, B. J., Hammet, F., Nguyen-Dumont, T., & Park, D. J. (2018). Hi-plex for simple, accurate, and cost-effective amplicon-based targeted DNA sequencing. In S. R. Head, P. Ordoukhanian, & D. R. Salomon (Eds.), Next Generation Sequencing: Methods and Protocols (pp. 53-70). (Methods in Molecular Biology; Vol. 1712). Humana Press. https://doi.org/10.1007/978-1-4939-7514-3_5
Pope, Bernard J. ; Hammet, Fleur ; Nguyen-Dumont, Tu ; Park, Daniel J. / Hi-plex for simple, accurate, and cost-effective amplicon-based targeted DNA sequencing. Next Generation Sequencing: Methods and Protocols. editor / Steven R. Head ; Phillip Ordoukhanian ; Daniel R. Salomon. Humana Press, 2018. pp. 53-70 (Methods in Molecular Biology).
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Pope, BJ, Hammet, F, Nguyen-Dumont, T & Park, DJ 2018, Hi-plex for simple, accurate, and cost-effective amplicon-based targeted DNA sequencing. in SR Head, P Ordoukhanian & DR Salomon (eds), Next Generation Sequencing: Methods and Protocols. Methods in Molecular Biology, vol. 1712, Humana Press, pp. 53-70. https://doi.org/10.1007/978-1-4939-7514-3_5

Hi-plex for simple, accurate, and cost-effective amplicon-based targeted DNA sequencing. / Pope, Bernard J.; Hammet, Fleur; Nguyen-Dumont, Tu; Park, Daniel J.

Next Generation Sequencing: Methods and Protocols. ed. / Steven R. Head; Phillip Ordoukhanian; Daniel R. Salomon. Humana Press, 2018. p. 53-70 (Methods in Molecular Biology; Vol. 1712).

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Otherpeer-review

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Pope BJ, Hammet F, Nguyen-Dumont T, Park DJ. Hi-plex for simple, accurate, and cost-effective amplicon-based targeted DNA sequencing. In Head SR, Ordoukhanian P, Salomon DR, editors, Next Generation Sequencing: Methods and Protocols. Humana Press. 2018. p. 53-70. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-7514-3_5