A high-throughput pipeline for scalable kit-free RNA extraction

Ping Han; Maybelle K Go; Jeng Yeong Chow; Bo Xue; Yan Ping Lim; Michael A Crone; Marko Storch; Paul S Freemont; Wen Shan Yew

doi:10.1038/s41598-021-02742-w

A high-throughput pipeline for scalable kit-free RNA extraction

Sci Rep. 2021 Dec 1;11(1):23260. doi: 10.1038/s41598-021-02742-w.

Authors

Ping Han^#^{1

2

3}, Maybelle K Go^#^{1

2

3}, Jeng Yeong Chow^#^{1

2

3}, Bo Xue^#^{1

2

3}, Yan Ping Lim^{1

2

3}, Michael A Crone^{4

5

6}, Marko Storch^{4

5}, Paul S Freemont^{4

5

6}, Wen Shan Yew^{7

8

9}

Affiliations

¹ Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.
² Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore.
³ Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.
⁴ Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London, SW7 2AZ, UK.
⁵ London Biofoundry, Translation and Innovation Hub, Imperial College White City Campus, London, W12 0BZ, UK.
⁶ UK Dementia Research Institute Centre for Care Research and Technology, Based at Imperial College London and the, University of Surrey, London, UK.
⁷ Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore. wenshanyew@nus.edu.sg.
⁸ Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore. wenshanyew@nus.edu.sg.
⁹ Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore. wenshanyew@nus.edu.sg.

^# Contributed equally.

Abstract

An overreliance on commercial, kit-based RNA extraction in the molecular diagnoses of infectious disease presents a challenge in the event of supply chain disruptions and can potentially hinder testing capacity in times of need. In this study, we adapted a well-established, robust TRIzol-based RNA extraction protocol into a high-throughput format through miniaturization and automation. The workflow was validated by RT-qPCR assay for SARS-CoV-2 detection to illustrate its scalability without interference to downstream diagnostic sensitivity and accuracy. This semi-automated, kit-free approach offers a versatile alternative to prevailing integrated solid-phase RNA extraction proprietary systems, with the added advantage of improved cost-effectiveness for high volume acquisition of quality RNA whether for use in clinical diagnoses or for diverse molecular applications.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19 / diagnosis*
COVID-19 / virology
COVID-19 Testing / methods*
High-Throughput Screening Assays / methods*
Humans
Molecular Diagnostic Techniques / methods
RNA, Viral / analysis
RNA, Viral / genetics*
RNA, Viral / isolation & purification*
ROC Curve
Real-Time Polymerase Chain Reaction / methods*
SARS-CoV-2 / genetics*

Substances

RNA, Viral