A new and improved ‘gold standard’ for complete plasmid verification

Knowledge Exchange overview

During this Knowledge Exchange, three presenters from Oxford Nanopore Technologies shared a comprehensive overview of the workflow for rapid, cost-effective sequencing of complete plasmid constructs.

Abstract

Aaron began by introducing why the field is moving towards routine whole plasmid verification, and how the Oxford Nanopore workflow enables any lab to implement a new and improved plasmid sequencing solution. Jemma then walked attendees through the protocol for plasmid sequencing using Oxford Nanopore Rapid Barcoding Kits. Followed by Stephen, who introduced EPI2ME bioinformatics and covered democratising data analyses for non-bioinformaticians.

The benefits of plasmid sequencing

Viewers learnt how to implement this end-to-end workflow to characterise the sequence of entire plasmid constructs rapidly, locally and at a competitive price. This enabled several advantages over other methods. For example, users could:

•    Easily verify if the plasmid insert and backbone are free of mutations
•    Completely avoid the need for primers and complicated primer walking
•    Resolve repetitive regions, dimers and deletions
•    Work across range of plasmid/BAC sizes and complexities
•    Implement a simple end-to-end workflow with rapid turnaround time
•    Keep the process in-house or at a local institution, ensuring data remains secure

Aaron Pomerantz is the Segment Marketing Manager at Oxford Nanopore, where he covers synthetic biology, microbiology and infectious disease. He received his PhD from UC Berkeley in the Department of Integrative Biology, employing genomics, genome editing, and bioimaging techniques in non-model organisms, as well as in-field nanopore sequencing in the Amazon rainforest. In his role as Segment Marketing Manager, he drives development of new areas in the research life sciences market.

Jemma Jordan is a Director within the Product Management team at Oxford Nanopore and is responsible for their range of library preparation kits. She has a PhD in Biochemistry and over a decade of laboratory experience developing and optimising assays and workflows.

Stephen Rudd is a Director at Oxford Nanopore where he is responsible for the bioinformatic products and imagines user journeys that begin with a collection of FASTQ files. He has two decades of experience in genome bioinformatics support and works with the Customer Workflows team towards demystifying bioinformatics. Through our EPI2ME Labs environment, we hope to support laboratory scientists with simplified solutions to complex computational tasks.