A research and development project aimed at development of high content multiplex assays capable of simultaneous detection of 35 NIAID Category A, B, and C viral agents plus quantification of cytokine/chemokine responses in patients is proposed. Lawrence Livermore National Laboratory (LLNL), NanoString Technologies Corp. (NT), the University of Texas Medical Branch, and the University of California San Francisco propose to develop a molecular detection assay that will simultaneously detect the presence of any of 35 Category A, B, or C viruses in a patient sample and determine the disease state of the patient. The system envisioned will take advantage of LLNL's bioinformatics and viral assay development capabilities as well as NT's novel platform enabling direct quantification of nucleic acid molecules in clinically relevant samples. The assay will require minimal sample preparation with no need for amplification or enzymatic reactions. An integrated, quantitative, highly specific and sensitive [1 copy per cell] assay system with automated data analysis &output, requiring less than 20 minutes of hands-on manipulation and minimal sample preparation is envisioned. The system will allow simultaneous and sensitive multiplex detection of up to 700 analytes per sample. Initial throughput of up to 72 samples per instrument per 24 hour period is envisioned. The system will enable rapid modifications to the nucleic acid detection "codesets" such that the system can integrate new diagnostic tests for other agents (modified agents, high priority agents or others) and other host response genes. Finally, the system envisioned will require minimal operator training and expertise.

Public Health Relevance

Statement Lawrence Livermore National Laboratory (LLNL), NanoString Technologies Corp. (NT), the University of Texas Medical Branch, and the University of California San Francisco propose to develop a molecular detection assay that will simultaneously detect the presence of any of 35 Category A, B, or C viruses in a patient sample (blood, sputum, or cerebrospinal fluid are envisioned) and determine the cytokine expression profile in that sample to determine disease state. The system envisioned will take advantage of LLNL's bioinformatics and viral assay development capabilities- especially those related to biodefense as well as NT's novel platform enabling direct quantification of RNA and DNA molecules in clinically relevant samples. The assay will require minimal sample preparation with no need for amplification or enzymatic reactions. Furthermore, UTMB's high containment and animal facilities will be critical to obtaining test materials and initial validation of our approach while UCSF's clinical samples will be invaluable for final validation on actual human clinical samples-a critical first step to CLIA waver and later FDA approval. An integrated, quantitative, highly specific and sensitive [1 copy per cell] assay system with automated data analysis &output, requiring less than 20 minutes of hands-on manipulation and minimal sample preparation is envisioned. The system will allow simultaneous and sensitive multiplex detection of up to 700 analytes per sample. Initial throughput of up to 72 samples per instrument per 24 hour period is envisioned. The system will enable rapid modifications to the nucleic acid detection codesets such that the system can integrate new diagnostic tests for other agents (modified agents, high priority agents or others) and other host response genes. Finally, the system envisioned will require minimal operator training and expertise.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI093500-03
Application #
8453480
Study Section
Special Emphasis Panel (ZAI1-LG-M (J3))
Program Officer
Dugan, Vivien Grace
Project Start
2011-05-01
Project End
2014-04-30
Budget Start
2013-05-01
Budget End
2014-04-30
Support Year
3
Fiscal Year
2013
Total Cost
$291,764
Indirect Cost
$102,048
Name
Lawrence Livermore National Laboratory
Department
Type
DUNS #
827171463
City
Livermore
State
CA
Country
United States
Zip Code
94550
Peña, José; Plante, Jessica A; Carillo, Alda Celena et al. (2014) Multiplexed digital mRNA profiling of the inflammatory response in the West Nile Swiss Webster mouse model. PLoS Negl Trop Dis 8:e3216