Massively multiplexed nucleic acid detection with Cas13

Cheri M. Ackerman, Cameron Myhrvold (), Sri Gowtham Thakku, Catherine A. Freije, Hayden C. Metsky, David K. Yang, Simon H. Ye, Chloe K. Boehm, Tinna-Sólveig F. Kosoko-Thoroddsen, Jared Kehe, Tien G. Nguyen, Amber Carter, Anthony Kulesa, John R. Barnes, Vivien G. Dugan, Deborah T. Hung, Paul C. Blainey () and Pardis C. Sabeti
Additional contact information
Cheri M. Ackerman: Broad Institute of Massachusetts Institute of Technology and Harvard
Cameron Myhrvold: Broad Institute of Massachusetts Institute of Technology and Harvard
Sri Gowtham Thakku: Broad Institute of Massachusetts Institute of Technology and Harvard
Catherine A. Freije: Broad Institute of Massachusetts Institute of Technology and Harvard
Hayden C. Metsky: Broad Institute of Massachusetts Institute of Technology and Harvard
David K. Yang: Broad Institute of Massachusetts Institute of Technology and Harvard
Simon H. Ye: Broad Institute of Massachusetts Institute of Technology and Harvard
Chloe K. Boehm: Broad Institute of Massachusetts Institute of Technology and Harvard
Tinna-Sólveig F. Kosoko-Thoroddsen: Broad Institute of Massachusetts Institute of Technology and Harvard
Jared Kehe: Broad Institute of Massachusetts Institute of Technology and Harvard
Tien G. Nguyen: Broad Institute of Massachusetts Institute of Technology and Harvard
Amber Carter: Broad Institute of Massachusetts Institute of Technology and Harvard
Anthony Kulesa: Broad Institute of Massachusetts Institute of Technology and Harvard
John R. Barnes: Centers for Disease Control and Prevention
Vivien G. Dugan: Centers for Disease Control and Prevention
Deborah T. Hung: Broad Institute of Massachusetts Institute of Technology and Harvard
Paul C. Blainey: Broad Institute of Massachusetts Institute of Technology and Harvard
Pardis C. Sabeti: Broad Institute of Massachusetts Institute of Technology and Harvard

Nature, 2020, vol. 582, issue 7811, 277-282

Abstract: Abstract The great majority of globally circulating pathogens go undetected, undermining patient care and hindering outbreak preparedness and response. To enable routine surveillance and comprehensive diagnostic applications, there is a need for detection technologies that can scale to test many samples1–3 while simultaneously testing for many pathogens4–6. Here, we develop Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN), a platform for scalable, multiplexed pathogen detection. In the CARMEN platform, nanolitre droplets containing CRISPR-based nucleic acid detection reagents7 self-organize in a microwell array8 to pair with droplets of amplified samples, testing each sample against each CRISPR RNA (crRNA) in replicate. The combination of CARMEN and Cas13 detection (CARMEN–Cas13) enables robust testing of more than 4,500 crRNA–target pairs on a single array. Using CARMEN–Cas13, we developed a multiplexed assay that simultaneously differentiates all 169 human-associated viruses with at least 10 published genome sequences and rapidly incorporated an additional crRNA to detect the causative agent of the 2020 COVID-19 pandemic. CARMEN–Cas13 further enables comprehensive subtyping of influenza A strains and multiplexed identification of dozens of HIV drug-resistance mutations. The intrinsic multiplexing and throughput capabilities of CARMEN make it practical to scale, as miniaturization decreases reagent cost per test by more than 300-fold. Scalable, highly multiplexed CRISPR-based nucleic acid detection shifts diagnostic and surveillance efforts from targeted testing of high-priority samples to comprehensive testing of large sample sets, greatly benefiting patients and public health9–11.

Date: 2020
References: Add references at CitEc
Citations: View citations in EconPapers (7)

Downloads: (external link)
https://www.nature.com/articles/s41586-020-2279-8 Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:nature:v:582:y:2020:i:7811:d:10.1038_s41586-020-2279-8

Ordering information: This journal article can be ordered from
https://www.nature.com/

DOI: 10.1038/s41586-020-2279-8

Access Statistics for this article

Nature is currently edited by Magdalena Skipper

More articles in Nature from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().