@article{3873,
  keywords = {Animals, Humans, Sensitivity and Specificity, Influenza A virus, Virus Diseases, CRISPR-Cas Systems, Microfluidic Analytical Techniques, Genome, Viral, HIV, CRISPR-Associated Proteins, Betacoronavirus, Drug Resistance, Viral, SARS-CoV-2, RNA, Guide, Kinetoplastida},
  author = {Cheri Ackerman and Cameron Myhrvold and Sri Thakku and Catherine Freije and Hayden Metsky and David Yang and Simon Ye and Chloe Boehm and Tinna-Solveig Kosoko-Thoroddsen and Jared Kehe and Tien Nguyen and Amber Carter and Anthony Kulesa and John Barnes and Vivien Dugan and Deborah Hung and Paul Blainey and Pardis Sabeti},
  title = {Massively multiplexed nucleic acid detection with Cas13.},
  abstract = { <p>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 samples while simultaneously testing for many pathogens. 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 reagents self-organize in a microwell array 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 health.</p> },
  year = {2020},
  journal = {Nature},
  volume = {582},
  pages = {277-282},
  month = {2020 Jun},
  issn = {1476-4687},
  doi = {10.1038/s41586-020-2279-8},
  language = {eng},
}