The Role for NGS-based Technologies in a Post-Pandemic World
By Prasanna Thwar , PhD , director , Assay Development , Clear Labs
Illustration : Curtis Nishimura for Clear Labs
Next-generation sequencing ( NGS ) - based methods have existed for more than a decade , but their utility has been predominantly limited to research and applied life sciences . It has had limited use in clinical laboratories and is used more extensively by public health laboratories for foodborne outbreak investigations . Its adoption for other applications in public health laboratories has varied due to a number of challenges . The COVID-19 pandemic , however , has showcased how NGS is paramount to addressing a global biothreat .
First , metagenomic NGS helped identify SARS-CoV-2 as the pathogen responsible for COVID-19 . Then , whole genome sequencing ( WGS ) of the viral isolate provided the exact genome sequence that led to the development of nucleic acid diagnostic tests and an mRNA vaccine . As the pandemic has evolved , WGS has become the go-to method for tracking transmission , resolving outbreaks , monitoring new variants , choosing clinical trial cohorts and even helping to inform quarantine measures .
Several hurdles have limited the widespread adoption of NGS technologies thus far — cost vs . value , workflow complexity , lack of proper standards and controls , and subsequent apprehension from regulatory bodies and payors . Some of these hurdles will continue to exist beyond the pandemic . For assisting public health laboratories to adopt the best platforms for their specific laboratories , here are 10 considerations that can help with successful implementation of NGS-based technologies in the postpandemic world .
1 . NGS workflows are often long , cumbersome and prone to human error . For successful widespread adoption , the entire workflow needs to be automated with preferably no human intervention , similar to commercial nucleic acid amplification tests ( NAATs ).
2 . While partial , segmented solutions provide flexibility to customize or use different vendors , end-to-end integrated solutions should include hardware , consumables , reagent kits and all the workflow steps that enable adoption , reduce variability and lessen validation burden .
3 . While existing tools for NGS analysis cater to general use cases , there is a critical need for software that is optimized for , and seamlessly integrated with , sequencing platforms .
4 . If NGS is to be used on a regular basis for detecting pathogens , the timeto-result needs to be improved to generate results within an actionable timeframe .
20 LAB MATTERS Summer 2021