Bead-based approaches for increased sensitivity and multiplexing of CRISPR diagnostics

Sameed M. Siddiqui; Nicole L. Welch; Tien G. Nguyen; Amaya Razmi; Tianyi Chang; Rebecca Senft; Jon Arizti-Sanz; Marzieh E. Mirhashemi; David R. Stirling; Cheri M. Ackerman; Beth A. Cimini; Paul C. Blainey; Pardis C. Sabeti; Cameron Myhrvold

doi:10.1038/s41551-025-01498-2

Bead-based approaches for increased sensitivity and multiplexing of CRISPR diagnostics

Sameed M. Siddiqui, Nicole L. Welch, Tien G. Nguyen, Amaya Razmi, Tianyi Chang, Rebecca Senft, Jon Arizti-Sanz, Marzieh E. Mirhashemi, David R. Stirling, Cheri M. Ackerman, Beth A. Cimini, Paul C. Blainey, Pardis C. Sabeti, Cameron Myhrvold

Research output: Contribution to journal › Article › peer-review

Abstract

CRISPR-based diagnostics have emerged as a promising tool for fast, accurate and portable pathogen detection. There has been rapid progress in pre-amplification processes and CRISPR-related enzymes used in these approaches, but the development of reporter systems and reaction platforms has lagged behind. In this paper, we develop bead-based techniques to address these gaps. First, we develop a novel bead-based split-luciferase reporter system with up to 20× sensitivity compared with standard fluorescence-based reporter design in CRISPR diagnostics. Second, we develop a highly deployable, bead-based platform capable of detecting nine distinct viral targets in parallelized, droplet-based reactions, with sensitivity reaching as low as 2.5 copies per µl of input RNA. We demonstrate the enhanced performance of both approaches on synthetic and clinical sample sensitivity, speed, multiplexing and deployability.

Original language	English (US)
Journal	Nature Biomedical Engineering
DOIs	https://doi.org/10.1038/s41551-025-01498-2
State	Accepted/In press - 2025

All Science Journal Classification (ASJC) codes

Biotechnology
Bioengineering
Medicine (miscellaneous)
Biomedical Engineering
Computer Science Applications

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10.1038/s41551-025-01498-2

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Siddiqui, S. M., Welch, N. L., Nguyen, T. G., Razmi, A., Chang, T., Senft, R., Arizti-Sanz, J., Mirhashemi, M. E., Stirling, D. R., Ackerman, C. M., Cimini, B. A., Blainey, P. C., Sabeti, P. C., & Myhrvold, C. (Accepted/In press). Bead-based approaches for increased sensitivity and multiplexing of CRISPR diagnostics. Nature Biomedical Engineering. https://doi.org/10.1038/s41551-025-01498-2

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title = "Bead-based approaches for increased sensitivity and multiplexing of CRISPR diagnostics",

abstract = "CRISPR-based diagnostics have emerged as a promising tool for fast, accurate and portable pathogen detection. There has been rapid progress in pre-amplification processes and CRISPR-related enzymes used in these approaches, but the development of reporter systems and reaction platforms has lagged behind. In this paper, we develop bead-based techniques to address these gaps. First, we develop a novel bead-based split-luciferase reporter system with up to 20× sensitivity compared with standard fluorescence-based reporter design in CRISPR diagnostics. Second, we develop a highly deployable, bead-based platform capable of detecting nine distinct viral targets in parallelized, droplet-based reactions, with sensitivity reaching as low as 2.5 copies per µl of input RNA. We demonstrate the enhanced performance of both approaches on synthetic and clinical sample sensitivity, speed, multiplexing and deployability.",

author = "Siddiqui, \{Sameed M.\} and Welch, \{Nicole L.\} and Nguyen, \{Tien G.\} and Amaya Razmi and Tianyi Chang and Rebecca Senft and Jon Arizti-Sanz and Mirhashemi, \{Marzieh E.\} and Stirling, \{David R.\} and Ackerman, \{Cheri M.\} and Cimini, \{Beth A.\} and Blainey, \{Paul C.\} and Sabeti, \{Pardis C.\} and Cameron Myhrvold",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2025.",

year = "2025",

doi = "10.1038/s41551-025-01498-2",

language = "English (US)",

journal = "Nature Biomedical Engineering",

issn = "2157-846X",

publisher = "Nature Research",

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TY - JOUR

T1 - Bead-based approaches for increased sensitivity and multiplexing of CRISPR diagnostics

AU - Siddiqui, Sameed M.

AU - Welch, Nicole L.

AU - Nguyen, Tien G.

AU - Razmi, Amaya

AU - Chang, Tianyi

AU - Senft, Rebecca

AU - Arizti-Sanz, Jon

AU - Mirhashemi, Marzieh E.

AU - Stirling, David R.

AU - Ackerman, Cheri M.

AU - Cimini, Beth A.

AU - Blainey, Paul C.

AU - Sabeti, Pardis C.

AU - Myhrvold, Cameron

PY - 2025

Y1 - 2025

N2 - CRISPR-based diagnostics have emerged as a promising tool for fast, accurate and portable pathogen detection. There has been rapid progress in pre-amplification processes and CRISPR-related enzymes used in these approaches, but the development of reporter systems and reaction platforms has lagged behind. In this paper, we develop bead-based techniques to address these gaps. First, we develop a novel bead-based split-luciferase reporter system with up to 20× sensitivity compared with standard fluorescence-based reporter design in CRISPR diagnostics. Second, we develop a highly deployable, bead-based platform capable of detecting nine distinct viral targets in parallelized, droplet-based reactions, with sensitivity reaching as low as 2.5 copies per µl of input RNA. We demonstrate the enhanced performance of both approaches on synthetic and clinical sample sensitivity, speed, multiplexing and deployability.

AB - CRISPR-based diagnostics have emerged as a promising tool for fast, accurate and portable pathogen detection. There has been rapid progress in pre-amplification processes and CRISPR-related enzymes used in these approaches, but the development of reporter systems and reaction platforms has lagged behind. In this paper, we develop bead-based techniques to address these gaps. First, we develop a novel bead-based split-luciferase reporter system with up to 20× sensitivity compared with standard fluorescence-based reporter design in CRISPR diagnostics. Second, we develop a highly deployable, bead-based platform capable of detecting nine distinct viral targets in parallelized, droplet-based reactions, with sensitivity reaching as low as 2.5 copies per µl of input RNA. We demonstrate the enhanced performance of both approaches on synthetic and clinical sample sensitivity, speed, multiplexing and deployability.

UR - https://www.scopus.com/pages/publications/105016766904

UR - https://www.scopus.com/inward/citedby.url?scp=105016766904&partnerID=8YFLogxK

U2 - 10.1038/s41551-025-01498-2

DO - 10.1038/s41551-025-01498-2

M3 - Article

C2 - 40983646

AN - SCOPUS:105016766904

SN - 2157-846X

JO - Nature Biomedical Engineering

JF - Nature Biomedical Engineering

ER -

Bead-based approaches for increased sensitivity and multiplexing of CRISPR diagnostics

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