Clinical presentation, particularly early in the course of disease, is only rarely pathognomonic of infection with a specific infectious agent. As a result, diagnosis is complex with many different organisms causing similar symptoms. Given that effective intervention requires accurate diagnosis and that the probability of success diminishes over time, tests that enable rapid, efficient differential diagnosis have potential to decrease morbidity, mortality, and social and economic costs of infectious diseases. Polymerase chain reaction (PCR) is not well suited to highly multiplexed microbiological analyses because primer interactions can reduce sensitivity and the repertoire of reporter systems is typically limited to 10 to 20 targets. DNA microarrays allow extensive multiplexing but existing assays are less sensitive than agent-specific PCR and require amplification, fluorescent labeling and several hours for processing. Next generation sequencing has unlimited multiplex potential. However, current platforms require hours to days for sample processing and bioinformatic analysis and are too complex for most point-of-care applications. In this project we will develop a single-molecule field-effect transistor (smFET) diagnostic assay platform. This application draws on our recent work, in which we have shown that the conductance of a carbon nanotube with a single covalently tethered DNA probe molecule is exquisitely sensitive to the increased charge that results from hybridization of a complementary DNA strand. smFET arrays on active complementary metal-oxide-semiconductor (CMOS) substrates will allow genomic materials to be assayed to concentrations approaching 1 fM (or 600 molecule per mL), comparable to qPCR, but while allowing multiplexing comparable to microarrays. We will specifically apply this technology to a genomic diagnostic platform that will allow efficient, low-cost differential diagnosis of infectious diseases. Our objectives we will be to optimize and develop the sensor to detect target concentration as low as 1 fM and develop approaches to distinguish mismatches through analysis of binding kinetics;integrate these devices onto CMOS measurement substrates, further improving electronic performance and allowing parallel multiplexing;test the platform with clinical samples in a staged strategy that begins in minimal biocontainment with nucleic acid templates, proceeds to work with potentially infectious materials in biocontainment;reduce the form factor for the device to that of a portable USB stick;and build software and bioinformatics infrastructure to support this platform for deployment in the field and clinics.

Public Health Relevance

The smFET assay technology developed here will allow for rapid, efficient differential diagnosis of infectious diseases in the clinic. Given that effective intervention requires accurate diagnosis and that the probability of success diminishes over time, these tests have the potential to decrease morbidity, mortality, and the social and economic costs of infectious diseases.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Program--Cooperative Agreements (U19)
Project #
Application #
Study Section
Special Emphasis Panel (ZAI1-LR-M (J1))
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Columbia University
New York
United States
Zip Code
Lindow, Janet C; Wunder Jr, Elsio A; Popper, Stephen J et al. (2016) Cathelicidin Insufficiency in Patients with Fatal Leptospirosis. PLoS Pathog 12:e1005943
Bouilly, Delphine; Hon, Jason; Daly, Nathan S et al. (2016) Single-Molecule Reaction Chemistry in Patterned Nanowells. Nano Lett 16:4679-85
Bacharach, Eran; Mishra, Nischay; Briese, Thomas et al. (2016) Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia. MBio 7:e00431-16
Beall, Anne; Yount, Boyd; Lin, Chun-Ming et al. (2016) Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A. MBio 7:e01451-15
Forero, Adriana; Tisoncik-Go, Jennifer; Watanabe, Tokiko et al. (2016) The 1918 Influenza Virus PB2 Protein Enhances Virulence through the Disruption of Inflammatory and Wnt-Mediated Signaling in Mice. J Virol 90:2240-53
Tisoncik-Go, Jennifer; Gasper, David J; Kyle, Jennifer E et al. (2016) Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism. Cell Host Microbe 19:254-66
Warren, Steven B; Vernick, Sefi; Romano, Ethan et al. (2016) Complementary Metal-Oxide-Semiconductor Integrated Carbon Nanotube Arrays: Toward Wide-Bandwidth Single-Molecule Sensing Systems. Nano Lett 16:2674-9
Strouts, Fiona R; Popper, Stephen J; Partidos, Charalambos D et al. (2016) Early Transcriptional Signatures of the Immune Response to a Live Attenuated Tetravalent Dengue Vaccine Candidate in Non-human Primates. PLoS Negl Trop Dis 10:e0004731
Menachery, Vineet D; Yount Jr, Boyd L; Sims, Amy C et al. (2016) SARS-like WIV1-CoV poised for human emergence. Proc Natl Acad Sci U S A 113:3048-53
Tokarz, Rafal; Sameroff, Stephen; Hesse, Richard A et al. (2015) Discovery of a novel nidovirus in cattle with respiratory disease. J Gen Virol 96:2188-93

Showing the most recent 10 out of 32 publications