Rapid in situ identification of biological samples via DNA amplicon sequencing using miniaturized laboratory equipment

Aaron Pomerantz, Kristoffer Sahlin, Nina Vasiljevic, Adeline Seah, Marisa Lim, Emily Humble, Susan Kennedy, Henrik Krehenwinkel, Sven Winter, Rob Ogden, Stefan Prost

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

In many parts of the world, human-mediated environmental change is depleting biodiversity faster than it can be characterized, while invasive species cause agricultural damage, threaten human health, and disrupt native habitats. Consequently, the application of effective approaches for rapid surveillance and identification of biological specimens is increasingly important to inform conservation and biosurveillance efforts. Taxonomic assignments have been greatly advanced using sequence-based applications, such as DNA barcoding, a diagnostic technique that utilizes polymerase chain reaction (PCR) and DNA sequence analysis of standardized genetic regions. However, in many biodiversity hotspots, endeavors are often hindered by a lack of laboratory infrastructure, funding for biodiversity research, and restrictions on the transport of biological samples. A promising development is the advent of low-cost, miniaturized scientific equipment. Such tools can be assembled into functional laboratories to carry out genetic analyses in situ, at local institutions, field stations, or classrooms. Here, we outline the steps required to perform amplicon sequencing applications, from DNA isolation to nanopore sequencing and downstream data analysis, all of which can be conducted outside of a conventional laboratory environment using miniaturized scientific equipment, without reliance on internet connectivity. Depending on sample type, the protocol (from DNA extraction to full bioinformatic analyses) can be completed within 10 hours and with appropriate quality controls can be used for diagnostic identification of samples independent of core genomic facilities that are required for alternative methods.

Original languageEnglish
Pages (from-to)1415-1443
JournalNature Protocols
Volume17
Early online date11 Apr 2022
DOIs
Publication statusPublished - 1 Jun 2022

Keywords / Materials (for Non-textual outputs)

  • Nanopore
  • DNA barcoding
  • biodiversity
  • biosurveillance

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