SOURCES SOUGHT
A -- Development of a Multiplex Detection System
- Notice Date
- 5/15/2009
- Notice Type
- Sources Sought
- NAICS
- 541711
— Research and Development in Biotechnology
- Contracting Office
- Department of Health and Human Services, Food and Drug Administration, Office of Acquisitions and Grants Services, 5630 Fishers Lane, Room 2129, Rockville, Maryland, 20857-0001
- ZIP Code
- 20857-0001
- Solicitation Number
- FDA-SOL-09-1055925
- Archive Date
- 6/6/2009
- Point of Contact
- Dominique H Malone, Phone: (301) 827-7227, Doreen Williams , Phone: 301-827-3366
- E-Mail Address
-
dominique.malone@fda.hhs.gov, doreen.williams@fda.hhs.gov
(dominique.malone@fda.hhs.gov, doreen.williams@fda.hhs.gov)
- Small Business Set-Aside
- N/A
- Description
- A. General Information: In accordance with FAR 15.201(e), this request is for planning purposes only, and does not constitute an Invitation for Bids, a Request for Proposals, a Solicitation, a Request for Quotes, or an indication the Government will contract for the items contained in the announcement. This is a Sources Sought regarding potential sources. The intent of this SOURCES SOUGHT announcement is to conduct market research to identify sources to support informed decisions to procure for the required services, i.e., a total small business set-aside action (e.g., SBA Certified 8(a), Service-Disabled Veteran Owned, HUBZone, Small Disadvantaged, Veteran-Owned, Women-Owned,), GSA task order, etc. Our intention is to specifically identify small businesses. This notice is a Request for Information (SOURCES SOUGHT) for all interested qualified small businesses that meet the requirements for this effort. The North American Industrial Classification System (NAICS) code is 541711 with a small business size standard of 500 employees. This is not an invitation for bid, request for quote or other solicitation. B. Project Background: The Food and Drug Administration, Center for Food Safety and Applied Nutrition (CFSAN) has specific regulatory responsibilities directed at ensuring the safety of food, food additive, dietary supplement, and cosmetic products. In part, CFSAN maintains an active research program for the purpose of developing and applying technologies to detect, to identify and evaluate microbial hazards that may contaminate products either naturally or intentionally. CFSAN has a research project in place to develop methods for the isolation and identification of biothreat agents and conventional pathogens in foods. The identification methods currently in place will identify a single agent in a food matrix, which is fine if there is intelligence such as clinical cases of infection that suggest the causative agent of the infection. However, in the event of an unknown with either biothreat or conventional pathogens, separate methods would be needed to screen for all of the microbial agents of concern. This analysis would require a large amount of time that could result in significant morbidity and mortality. Using the multiplex approach such as the Luminex (Bio-plex) system multiple agents could be screened for simultaneously significantly reducing analysis time and removal of contaminated products from the US food supply. C. Objective: The objective of this potential requirement is to assist CFSAN in fulfilling its regulatory responsibilities and guard the American public from intentional or accidental contamination of the food supply with these microbiological agents. D. Draft Project Requirements: Independently, and not as an agent of the Government, furnish the necessary personnel, services, and otherwise do all things necessary for, or incident to, the following: To accomplish the requirements for this requirement the contractor shall have access to both a Biosafety Level 2 (BSL-2) and a Biosafety Level 3 (BLS-3) laboratory registered with the Centers for Disease Control and Prevention or the USDA Animal and Plant Health Inspection Service (APHIS) select agent program that will enable the contractor to obtain purified DNA from fully virulent strains of biothreat agents such as Bacillus anthracis, Yersinia pestis, Francisella tularensis, Brucella spp., and Burkholderia spp. The laboratory shall also have access to genetic material from conventional foodborne pathogens such as Salmonella enterica serotypes, Cronobacter spp., marine vibrios, Listeria spp., Campylobacter spp., norovirus and hepatitis A virus.. This requires that the laboratory shall have access to strain collections of the above listed pathogens to complete the work required for this requirement. The facility isolating the genetic material shall have a USDA Animal and Plant Health Inspection Service (APHIS) import permit to receive specific strains of B. anthracis, F. tularensis, Brucella spp., and Burkholderia spp. that the Government may require for use on this requirement. The facility shall have a security plan in place to safeguard the data generated from this requirement. It is highly desirable that at least one person working directly on this requirement has a security clearance at the Secret Level or above. The contractor shall have knowledge on the isolation of highly purified DNA from gram-negative and gram-negative bacterial cultures as well as viral cultures. The facility shall have the capability to conduct studies and develop DNA-based reagents for the Luminex (Bio-plex) system for the identification of bacterial and viral pathogens. It is highly desirable that the contractor has or is currently developing identification methods for the biothreat using the Bio-plex. If these methods are not currently available, the contractor shall have capability to develop them rapidly and validate them for high priority biothreat agents and foodborne bacterial and viral agents specified by the Center for Food Safety and Applied Nutrition. It is highly desirable that the contractor be familiar with the Bio-plex reagents developed for the CDC Laboratory Response Network (LRN) and the Department of Homeland Security (DHHS), and have knowledge of the validation requirements for reagents utilized by these agencies. The contractor shall work closely with CFSAN throughout this requirement and all services shall be provided in a timely manner 1.All signatures will be designed using a whole-genome approach such that all available complete genomes of different strains of the target species will be compared using multiple genome alignment programs. 2.A consensus alignment using programs such as the Gestalt Workbench developed by Gustavo Glusman will be preformed from the alignments that contain the target sequence conserved among all input genomes. To establish that the organism-conserved sequences do not occur in any other sequenced microbe, the consensus gestalt is compared against database of microbial organisms. An algorithm will be used for electronic subtraction of sequences from the consensus gestalt that was not unique to the pathogen targets of interest and the result will be a uniqueness gestalt that is mined for potential signature candidates. At this stage, a number of constraints specific to the type of assay and/or platform (See Table 2 below) will be imposed on the candidate signatures, further narrowing the signature set. 3.A final in-silico screening will be performed to verify that signatures will detect the pathogen targets and not detect any non-pathogen targets. After automated signature design and electronic screening, a file containing primer/probe sequence information is automatically generated for electronic ordering. Table 2: List of parameters and settings used in generating candidate signatures. Primer Design Parameters ParametersStandard Settings PRIMER_OPT_SIZE20 PRIMER_MIN_SIZE18 PRIMER_MAX_SIZE27 PRIMER_PRODUCT_OPT_SIZE100 PRIMER_PRODUCT_SIZE_RANGE71-250 PRIMER_OPT_TM62 PRIMER_MIN_TM61 PRIMER_MAX_TM63 PRIMER_MIN_GC20 PRIMER_MAX_GC80 PRIMER_PICK_INTERNAL_OLIGO1 PRIMER_INTERNAL_OLIGO_OPT_SIZE31 PRIMER_INTERNAL_OLIGO_MIN_SIZE18 PRIMER_INTERNAL_OLIGO_MAX_SIZE36 PRIMER_INTERNAL_OLIGO_OPT_TM72 PRIMER_INTERNAL_OLIGO_MIN_TM71 PRIMER_INTERNAL_OLIGO_MAX_TM73 4.Assay format will be a single TaqMan RT-PCR signature comprised of an unmodified forward primer, an unmodified reverse primer and a fluorescence resonance energy transfer (FRET) probe labeled with a 5´FAM fluorophore and 3´Black Hole Quencher 1. Assays will be tested on using the appropriate PCR instrumentation. Use of Cepheid Smart Cycler is highly desirable. 5.Data from the single signature development will be provided to CFSAN prior to development of the multi-plex assay. 6.Upon completion of TaqMan signature development, a multiplex panel consisting of multiple signatures per agent that can be used to amplify a single agent or multiple agents in a single sample will be developed. This multiplex will consist of probes with recognition sequences identical to TaqMan signatures developed and coupled through an 18 carbon spacer and a carboxyl moiety to polystyrene fluorescent microbeads or immunomagnetic beads as employed by the Luminex platform. The forward TaqMan primers will be modified by the addition of a 5’ biotin moiety; the reverse primers will remain unmodified. Probe and primer recognition sequences will be identical to the corresponding TaqMan signatures. 7.For the assay protocol, all signatures will be computationally designed with specific constraints on GC-content, melting temperature (TM), and primer-dimer formation (Table 2 above) to enhance multiplex capability. 8.A standardized one-step PCR protocol for bacterial agents and a three-step RT-PCR protocol for viruses using a commercially available RT-PCR kit will be developed for the PCR portions of the work. 9.Endpoint thermal cycling will be followed by gel screening or Multiplex hybridization. PCR amplification will be conducted using one-step amplification kits for ease of assembly and prevention of cross-contamination encountered with two-step procedures. 10.Standardized amounts of background, target, and near-neighbor nucleic acids will be used during screening process. The amount of DNA will be determined for each food matrix in consultation with CFSAN. 11.Each signature will be analyzed for each of the following characteristics. The values associated with each will be determined in consultation with CFSAN for each agent and food matrix. oLimit of detection oRepeatability oSpecificity oRobustness 12.The Cepheid SmartCycler is the preferred instrumentation for development of TaqMan assays and end-point PCR and RT-PCR for gel and Luminex analysis since this is the instrumentation available in the majority of the ORA, FERN and LRN laboratories. However, assays developed on instruments such the BioRad iCycler and ABI 7000 96-well plate real-time PCR instruments that can be transferred to the SmartCycler platform are acceptable. 13.All reagents for all assays shall be available from commercial vendors. 14.The efficacy of the nucleic acid purification extraction and purification process will be assessed using known quantities RNA for the virus assays (e.g synthetic RNA encapsulated by phage MS-2 capsid protein and used as both an end-to-end assay control and extraction efficiency control) and whole bacterial DNA from a non-related non-human pathogen such as Erwinia herbicola. Efficiency of extraction will be accessed by TaqMan RT-PCR for RNA and by TaqMan PCR for DNA. 15.Controls that convey important diagnostic information regarding assay integrity, including reagent addition, quality and concentration, assay operator performance and instrument stability that do not compromise or limit the screening capabilities of the assays shall be incorporated. These controls shall minimize the likelihood of false positives and false negative results and incorporate PCR inhibition and extraction controls. Controls shall include but are not limited to: i.Instrument Control: Luminex control to confirm that the reporter optics within the Bio-Plex instrument are functioning correctly. ii.Negative Control: A Luminex bead conjugated to DNA sequence unique from that of the target organisms to serve as a non-specific binding control in the multiplex PCR assay. iii.Fluorescence control (FC) iv.PCR/RT-PCR Amplification/Inhibition Control E. Capability Statement Requirements Responses to this sources Sought should address the following: 1. Part A. Capabilities and Technical Experience in response with the Statement Work for this requirement. 2. Part B. Technical and Management Approach in response to the Statement of Work for this requirement. 3.Company name, mailing address, e-mail address, telephone and FAX numbers, website address (if available), and the name, telephone number, and e-mail address of a point of contact having the authority and knowledge to clarify responses with Government representatives. 4.Name, title, telephone number, and e-mail addresses of individuals who can verify the demonstrated capabilities identified in the responses. 5.Business size for, size standard $ and status, if qualified as an 8(a) firm (must be certified by SBA), Small Disadvantaged Business (must be certified by SBA), Woman-Owned Small Business, HUBZone firm (must be certified by SBA), and/or Service-Disabled Veteran-Owned Small Business (must be listed in the VetBiz Vendor Information Pages). 6.DUNS number, CAGE Code, Tax Identification Number, and company structure (Corporation, LLC, partnership, joint venture, etc.). Companies also must be registered in the Central Contractor Registry (CCR, at www.ccr.gov) to be considered as potential sources. 7.Identification of the firm's GSA Schedule contract(s) by Schedule number and contract number and SINs that are applicable to this potential requirement are also requested. 8.If the company has a Government approved accounting system, please identify the agency that approved the system. Please submit copies of any documentation such as letters or certificates to in Teaming arrangements are acceptable, and the information required above on the company responding to this announcement, should also be provided for each entity expected to be teammates of the respondent for performance of this work. Interested small business potential offerors are encouraged to respond to this notice. Responses shall directly demonstrate the company’s capability, experience, and/or ability to marshal resources to effectively and efficiently perform each of the tasks described above at a sufficient level of detail; and evidence that the contractor is viable to met the minimum requirements listed above while in compliance with FAR 52.219-14 (“Limitations on Subcontracting”). Respondents shall address their capability, experience and knowledge directly correlated to the Project Requirements discussed in Section D of this document. Interested offerors should submit their capability statement not exceeding fifteen (15) pages in length, excluding standard brochures. SUBMISSIONS ARE DUE on or before 4:30pm, Eastern Time, May 22, 2009. The capabilities response shall be e-mailed to: Dominique.Malone@fda.hhs.gov. Responses to the notice will not be returned. Information provided in response to this notice will be used to assess alternatives available for determining how to proceed in the acquisition process. NO PHONE CALLS WILL BE ACCEPTED. F. Period of Performance The government anticipates an award for this requirement on or around September 1, 2009. The period of performance will have a base year and four options. G. Additional Requirements/ Instructions for Submitting SOURCES SOUGHT Responses to FDA: This notice is for planning purposes only, and does not constitute an Invitation for Bids, a Request for Proposals, a Solicitation, a Request for Quotes, or an indication the Government will contract for the items contained in this announcement. This request is not to be construed as a commitment on the part of the Government to award a contract, nor does the Government intend to pay for any information submitted as a result of this request. The Government will not reimburse respondents for any cost associated with submission of the information being requested or reimburse expenses incurred to interested parties for responses to this announcement. a.Responses to this notice shall be received by the Contract Specialist, Dominique.Malone@fda.hhs.gov on or before 4:30pm, Eastern Time, May 22, 2009. b.Responses to this announcement will not be returned, nor will there be any ensuing discussions or debriefings of any responses. However, information obtained as a result of this announcement may be reflected in the subsequent solicitation, and FDA may contact one or more respondents for clarifications and to enhance the Government’s understanding. This announcement is Government market research, and may result in revisions in both its requirements and its acquisition strategy based on industry responses. c.All transmitted information marked proprietary shall be treated as such. Therefore, businesses should identify any proprietary information in their SOURCES SOUGHT response. Proprietary materials will neither be distributed, nor discussed with, any other organization. Information submitted in response to this SOURCES SOUGHT will be used at the discretion of the Government. Further, the information submitted will remain confidential insofar as permitted by law, including the Freedom of Information and Privacy Acts. H. Other Information: The Government does not reimburse respondents for any cost associated with submission of the information being requested or reimburse expenses incurred to interested parties for responses to this announcement. Any responses received will not be used as a proposal. FDA does reserve the right to utilize any non-proprietary technical information in the anticipated SOW or solicitation. Information received will be considered solely to make informed decisions regarding a potential procurement. Responses to the SOURCES SOUGHT will not be returned and will not be accepted after the due date. All communications shall be by email. Respondents will not be notified of the results of the review of the responses. On behalf of the Food and Drug Administration, thank you for your interest.
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/FDA/DCASC/FDA-SOL-09-1055925/listing.html)
- Place of Performance
- Address: The Contractors Site, United States
- Record
- SN01820332-W 20090517/090516162138-3343f1c9ae869e38004eae2e8df3e1d6 (fbodaily.com)
- Source
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FedBizOpps Link to This Notice
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