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SALT LAKE CITY, UT, United States

Thatcher S.A.,Biofire Diagnostics, Inc.
Clinical Chemistry | Year: 2015

Background: Effective upstream preparation of nucleic acid (NA) is important for molecular techniques that detect unique DNA or RNA sequences. The isolated NA should be extracted efficiently and purified away from inhibitors of a downstream molecular assay.Content: Many NA sample preparation techniques and commercial kits are available. Techniques for cell lysis and isolation or purification of NA were discovered in early NA characterization studies, evolved in the 20th century with molecular techniques, and still serve as the foundation for current methods. Advances in solid phase extraction methods with nonhazardous chemicals and automated systems have changed the way NA is prepared. Factors to consider when selecting NA preparation methods for molecular detection include lysis (from sources as diverse as human cells, viruses, bacterial spores, or protozoan oocysts), DNA vs RNA, sample background, appropriate preparation chemicals, and required detection limits. Methods are also selected on the basis of requirements for a particular application, such as sample volume or removal of inhibitors. Sometimes tradeoffs are made.Summary: Good automated and manual methods are available to effectively prepare NA for molecular detection in under an hour. Numerous systems are available for various applications, including techniques that are flexible for multiple sample types, are capable of processing large batches, can be performed in <10 min, or that can yield high-purity NA. When methods are selected using the most applicable combination of lysis isolation efficiency and concentration, NA preparation can be very effective, even for molecular detection of multiple targets from the same sample. © 2014 American Association for Clinical Chemistry.

Biofire Diagnostics, Inc. | Date: 2012-11-09

Vials for loading a fluid system are provided. The illustrative vials are configured to minimize air bubbles from being transferred into the fluid system. Certain vial embodiments are provided with filters to allow microbes to pass into the fluidic system, while retaining larger particulate matter.

Biofire Diagnostics, Inc. | Date: 2013-02-12

Devices, containers, and methods are provided for performing biological analysis in a closed environment. Illustrative biological analyses include nucleic acid amplification and detection and immuno-PCR.

Optical systems and apparatuses configured for enabling substantially simultaneous observation of a plurality of points in an array from a common reference point. Without the optical systems and apparatuses disclosed herein, less than all of the plurality of points can be observed substantially simultaneously from the common reference point.

Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 452.63K | Year: 2013

DESCRIPTION (provided by applicant): Meningitis and encephalitis are inflammatory, often infectious, processes of the central nervous system that can result in significant morbidity and mortality. Prompt, appropriate therapy is crucial, but determining theinfectious etiology can be difficult and time-consuming. A wide-range of pathogens can be involved including both bacteria and viruses. Culture is the standard for diagnosis of bacterial Meningoencephalitis (ME), PCR of viral nucleic acid is the standardfor aseptic causes. However the current methods are either 1) too slow to be clinically relevant; 2) technically complex; 3) limited in the number of targets r 4) not cleared by the FDA. Idaho Technology (ITI) has developed a lab in a pouch PCR-based diagnostic system termed FilmArray that is rapid, easy to use, and can test for large panels of infectious agents simultaneously. A FilmArray pouch that can detect 15 respiratory pathogens was cleared by the FDA as a CLIA moderate complexity test. We propose to apply the FilmArray technology to the problem of ME diagnosis. SA1: Develop a FilmArray Meningoencephalitis (FAME) panel: We will construct a FilmArray pouch that combines PCR assays from existing panels with five new assays to detect the following ME-causing organisms directly from cerebrospinal fluid (CSF): Enterobacteriaceae, E. coli, Enterococcus species, H. influenza, L. monocytogenes, Mycoplasma pneumoniae, N. meningitidis, P. aeruginosa, Staphylococci species, S. aureus, Streptococcus species, S. agalactiae, S. pneumoniae, S. pyogenes, viridians streptococci, Adenovirus, Enterovirus, Parechovirus, HSV1, HSV2, VZV, EBV, CMV, HHV-6. SA2: Optimize nucleic acid extraction for virus and bacteria from CSF: CSF is one of the less complex sample matrices that have been processed on the FilmArray (when compared to nasal swabs, blood culture and stool). However, detecting bacteria, and virus, directly from CSF, may require the highest possible sensitivity. We will optimize the nucleic acid purificationsteps internal to the pouch as well as investigate simple steps to concentrate bacteria and viruses before the pouch SA3: Test the FAME panel on 300 CSF samples: Our collaborators will test CSF samples from pediatric and adult patients with suspected ME. We will compare these results to their standard assays performed on the samples, supplemented with the results of the comparator assays described in SA1. A successful outcome of this proposal will be a FilmArray pouch capable of detecting and identifying the common ME pathogens. It will be ready for the analytical and clinical trials necessary for a 510(k) submission to the FDA. This would be the subject of a future phase II submission. PUBLIC HEALTH RELEVANCE PUBLIC HEALTH RELEVANCE: Meningitis and encephalitis are life threatening inflammations of the brain and spinal cord which are often caused by infectious agents. Rapid, comprehensive, diagnosis of the virus or bacteria responsible for these conditions is critical for determining the most effective treatment. We will apply Idaho Technology's automated, multiplex nucleic acid test platform (the FilmArray) to the problem of meningoencephalitis diagnosis.

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