MODIFICATION
66 -- T-5000 Biosensor System with one year hardware and software warranty
- Notice Date
- 6/27/2007
- Notice Type
- Modification
- NAICS
- 339111
— Laboratory Apparatus and Furniture Manufacturing
- Contracting Office
- Department of Health and Human Services, Food and Drug Administration, Office of Acquisitions and Grants Services, 5630 Fishers Lane, Room 2129, Rockville, MD, 20857-0001, UNITED STATES
- ZIP Code
- 00000
- Solicitation Number
- Reference-Number-FDA1031318
- Response Due
- 7/12/2007
- Archive Date
- 7/27/2007
- Description
- The non-competitive award will be made in accordance with FAR Part 12 Acquisition of Commercial Items and FAR 13, Simplified Acquisition Procedures. The Food and Drug Administration (FDA) intends to award a Purchase Order on a non-competitive, sole source basis purchase to ISIS Pharmaceuticals, Inc. Carlsbad, California 92008. The system that we require will use an integrated sample preparation and measurement approach. It will use robotics to extract and isolate DNA from samples, followed by transfer to a PCR thermal cycler to amplify the DNA after introduction of particular, and specifically chosen, primers. Once the amplification has been completed, the sample will be robotically handled and cleaned up, followed by analysis using electrospray mass spectrometry. A mass spectrometry measurement of the PCR amplicons gives a detailed organism fingerprint, which provides much more information than a simple yes/no answer provided by probes in real-time PCR; detection is not limited to previously known organisms. The approach can rapidly identify organisms in a mixture without additional sample preparation steps. By adjusting the primer selection, the method can be made general or specific and can rapidly identify mutations (within the amplified region). The approach can handle many different types of samples including: air, soil, water, mucosal swabs and washes, sterile fluids (blood, CSF, urine), hair, teeth, and bone, making it very amenable to food matrices. The approach is also high throughput, allowing for the analysis of 600-1200 samples per 24 hour period. The main specifications for the system are: 1. PCR-based amplification of DNA from samples to produce amplicons of 100-120 base pair length, using carefully selected primers that can classify organisms generally or specifically. 2. Robotic cleanup of PCR amplicons. 3. Electrospray TOF-MS analysis of amplicons at high mass accuracy (<20 ppm). 4. High throughput analysis capability of over 1500 PCR products per day. 5. Analysis of the masses of complementary DNA strands to identify unique composition (based on DNA strand complements) of bases in strand. 6. Comparison of base composition to library of known base compositions (for given primers) for known organisms The unique specifications of this system include: 1. PCR Assay and clean-up kit: This kit contains ten 96-well plates with pre-selected PCR primers that amplify carefully selected regions of DNA to produce products in the size range compatible with the mass range and resolving power of the mass spectrometer. These PCR primers are selected based on the target study and can provide general or specific information about the nature of the organisms in question. The primers are specifically designed by IBIS. Internal standards are also included in the kits. 2. Automated desalting and cleanup module: This component consists of a robotic heat sealer which seals the 96-well plates so that they cannot be contaminated, followed by robotic desalting and clean-up of the PCR amplicons. Desalting is done on magnetic beads. This system is designed to minimize the possibility of sample contamination. 3. Sample injection fluidics module: A custom fluidics module is designed to sample each purified mixture with minimal cross contamination and introduce it into a liquid stream at a carefully controlled flow rate for subsequent ESI-MS analysis. The system alternates between high flow rates (for cleaning between samples) and lower flow rates (200 microliters per minute) for the analytical steps. The module precisely controls injection volumes as well. The injection system controls the voltages on the electrospray source so that the system is not electrospraying while higher cleaning flow rates are being used between samples. 4. Mass spectrometer system for DNA detection: This component consists of a Bruker MicrOTOF electrospray time-of-flight mass spectrometer (ESI-TOF) for analysis of PCR products introduced by the sample injection fluidics module. This instrument consists of an orthogonal injection time-of-flight mass spectrometer with an off-axis sprayer. The orthogonal injection source allows for ion accumulation prior to MS analysis to improve sensitivity. The TOF contains a reflectron to insure high mass resolution. The mass spectrometer is controlled by Bruker MicrOTOF software. The instrument has the following specifications: a. Standard mass range 50 ? 3,000 m/z b. Extended mass range 50 ? 20,000 m/z c. Mass resolution >10,000 FWHM in standard configuration and >15,000 FWHM with MicrOTOF focus d. Mass accuracy of 3 ppm (RMS) error with internal calibration e. Mass accuracy of 5 ppm (RMS) error with external calibration f. Acquisition rate of 20 Hz (full mass range profile mass spectra to hard disk) g. Polarity switching for both, positive and negative ions h. ESI orthogonal electrospray source (1?l ?1 ml/min) i. MicrOTOF instrument control software 5. IBIS Control and Analysis Software a. Robotics Software: controls and coordinates the sample handling and sample injection processes by controlling the robotic components of the system. This includes the cleanup and injection portion of the analysis. b. Control software: This component manages the liquid flow system and the mass spectrometer (by interfacing with the mass spectrometer software), as well as integrates the total operation of the system c. Sample tracking software d. Relational database: Curated database of genomics information that contains base counts (composition) for primer pairs for microorganisms. This database contains sequences generated by known primers for a large number of microorganisms. The information is maintained for primers that are designed to differentiate at the family level (e.g. enterobacter) and at the species and strain level. This database is a unique and indispensable part of the system, since base compositions stored in this database will be compared with those generated experimentally. This component is critical for rapid detection and proper identification of bacteria. e. Data Processor: Analyzes mass spectrometry data from both forward and reverse strands of amplified DNA to generate the unique base composition for the sequence in question. It function is to then compare the generated base composition to a database of known base compositions that would be generated from sequences produced for a given set of primers. FDA intends to make an award fifteen (15) days from the date of this notice. This is not a request for quotes; however sources may submit descriptive literature, fully documenting their capabilities, which will be considered by the Government. A determination to compete this procurement based on response(s) to this notice is solely within the discretion of the Government. All responses or questions regarding this posting must be in writing and can be sent via email to patricia.wright@fda.hhs.gov. No phone calls will be accepted. An award will be made immediately after the response date of this notice. The award will be made in accordance with FAR Part 13, Simplified Acquisition Procedures.
- Record
- SN01328879-W 20070629/070627220442 (fbodaily.com)
- Source
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