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FBO DAILY ISSUE OF JUNE 14, 2009 FBO #2757
SOLICITATION NOTICE

B -- Sequencing food born pathogens

Notice Date

6/12/2009
 

Notice Type

Combined Synopsis/Solicitation
 

NAICS

611710 — Educational Support Services
 

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

1057342
 

Archive Date

7/12/2009
 

Point of Contact

Jaclyn Stielper, , Doreen Williams , Phone: 301-827-3366
 

E-Mail Address

jaclyn.stielper@fda.hhs.gov, doreen.williams@fda.hhs.gov
(jaclyn.stielper@fda.hhs.gov, doreen.williams@fda.hhs.gov)
 

Small Business Set-Aside

N/A
 

Description

This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in FAR 12.6, simplified acquisition procedures and the resultant purchase order will include all applicable provisions and clauses in effect through the Federal Acquisition Circular 05-30. This announcement constitutes the only full and open competition solicitation and a written solicitation will not be issued. This synopsis, NAICS code 541380, is to notify contractors that the government intends to issue a Firm Fixed Price Purchase Order in accordance with FAR Part 13.106 for the following statement of work, under the simplified acquisition procedures. Any firm that believes it is capable of providing the required service as stated herein may submit a capability statement to document its ability to provide the required services. A determination to compete this procurement based on a response to this notice is solely within the discretion of the Government. The Government reserves the right to award a contract without discussions if the Contracting Officer determines that the initial offer(s) is/are providing the Best Value and discussions are not necessary. Award will be made to the party whose quote offers the best value to the Government, technical, price, and other factors considered. The Government may award this contract to other than the lowest price technically acceptable quote. The Government will evaluate information based on the following evaluation criteria: 1) Technical Capability factor described to "Meet or Exceed the Requirement," 2) Past Performance and 3) Price. Technical Capability and Past Performance is significantly more important than price. This solicitation is issued as a Request for Quote (RFQ). The Food and Drug Administration (FDA) intends to award a purchase order for the service of sequencing food born pathogens. The Statement of Work is as follows: Background One of the FDA missions in the Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, is to develop efficient and rapid identification of food born pathogens such as Escherichia coli O157:H7, Salmonella species, Cronobacter species and other enteric bacterial food contaminants and to relate those food born samples to clinical samples, especially in the case of food borne outbreaks of disease. For the last 20 years, pulsed field gel electrophoresis (PFGE) has been the standard used by the CDC and FDA through Pulse Net to characterize outbreak strains. Both increased knowledge and changing technologies are changing the way outbreak strains need to be identified. Specifically, the knowledge of entire genome sequences of over a hundred bacteria, variants in these sequences, and technologies of optical mapping, PCR, DNA microarrays (chips), mass spectroscopy, nucleotide signatures (snps), DNA sequencing and several other new technologies all promise potentially more rapid, less expensive, and better identification of food born pathogens. As part of ongoing research on the cost, speed and usefulness of these different technologies we have been comparing sequencing, optical mapping, DNA microchip arrays, and other technologies. Sequences of new Cronobacter species would provide critical information for ongoing outbreak analysis and would allow the evaluation of these other technologies for identifying Cronobacter isolates. Objective The purpose of this contract is to ensure the timely delivery of genomic DNA sequences from ten Cronobacter species. The quality, cost, and speed of examining a strain of food born bacteria will be compared to other technologies of strain examination and identification. Project Scope This contract will provide ten genomic sequences to the Division of Molecular Biology FDA. Description of Work; Three phases 2.0.1 Sequencing. An isolate of the strain of bacteria to be sequenced is grown and genomic DNA is prepared at the FDA. DNA is sent to the contractor’s facility for sequencing. Several upgrades have been implemented into 454 DNA sequencing, including paired end sequencing to improve sequencing efficiency, and other improvements in overall sequence read length and batch efficiency. 454 GS FLX Titanium Series combines 400-500 base shotgun and multi-span paired end reads (3 Kb, 8 Kb, 20 Kb) to produce for a 4-5 million base pair bacterial chromosome, 99-100% coverage in a ¼ plate run, with 15 x oversampling in a run time of a week. Genomic DNA is sheared into 20 Kb, 8 Kb or 3 Kb fragments and adaptors are added to the end of each fragment. A paired end library is constructed; DNA fragments containing added adaptors are isolated and amplified for sequencing. Extra long 400-500 base pair shotgun reads can sequence through many genomic repeats. 2.0.2 Contig assembly. All the initial sequencing runs produce hundreds of sequences. They must be assembled by computers and specially designed software. From this assembly process for a bacterial genome 2-200 contigs are created for one genome. 2.0.3 Annotation. Using known sequences, software packages have been devised to compare the 2-200 contigs to known genes. These programs are undergoing improvements in efficiency, speed and cost. Their contribution to the overall cost of a genome sequence is decreasing with new programs. Task Deliverables and Milestones: Genomic sequences (electronic or on CD), four strains at one time. Criteria for Acceptance Deliverables will be submitted to the Principal Investigator who initiated the request. We expect greater than 95% genome coverage of each strain, in approximately 2-300 contigs. Period of Performance July 7, 2009 through December 15, 2009 Location, Work Schedule and Travel Unless otherwise directed, contractors will adhere to standard work hours, working no more than 40 hours per week and observe all U.S. Government holidays. Security and Privacy It is not anticipated that the contractor will be exposed to sensitive Agency information or data. But, the contractor agrees that contract personnel will not divulge or release information or data developed or obtained in connection with performance of this contract, unless made public by FDA or upon written approval by the Project Officer. The contractor will complete an NPI (Non-Public Information) Agreement prior to award being made. Contractor Conformance with Applicable Laws, Regulations, Policies and Standards The Contractor shall be responsible for knowledge of and compliance with all applicable federal information technology and information management laws, regulations, policies and standards at the government-wide, HHS and FDA levels. At the government-wide level, these include Office of Management and Budget (OMB), National Institute of Standards and Technology (NIST) and General Accounting Office (GAO). These can be primarily found at or through the Federal CIO Council website at: http://www.cio.gov. HHS documents are found at: http://www.cdc.gov/irmo. Past Experience The contractor must be able to demonstrate past experience directly relevant to the types of work needed. Such experience includes projects performed in the past two years similar in scope to the requirements of this Statement of Work. Payment Terms Payment to be made within 30 days of delivery of sequence. CCR: Vendors must be registered in the Central Contractor Register (CCR) prior to the award of a contract. You may register by going to www.ccr.gov. You will need your Dun & Bradstreet number and banking information. QUESTIONS DEADLINE: All questions are to be submitted via email to Jaclyn.Stielper@fda.hhs.gov no later than June 23, 2009, 4:30pm EST. QUOTATIONS DUE: All quotations are due, via email to: Jaclyn.Stielper@fda.hhs.gov, no later than 4:30 PM, EST on June 27, 2009. PROVISIONS and CLAUSES: The provision at FAR 52.212-1, Instructions to Offerors Commercial Items applies to this solicitation. The following agenda has been attached to this provision: None. Offerors shall include a completed copy of the provision at FAR 52.212-3, Offeror Representations and Certifications Commercial Items. The clause at FAR 52.212-4, Contract Terms and Conditions, Commercial Items applies to this acquisition. The following agenda has been attached to the clause: None. The clause at FAR 52.212-5 Contract Terms and Conditions Required to Implement Statues or Executive Orders, Commercial Items applies to this acquisition. The following FAR clauses cited are applicable: FAR 52.217-8, FAR 52.217-9, FAR 52.222-26, FAR 52.222-35, FAR 52.222-36, and FAR 52.232-33. Clauses and provisions are incorporated by reference and apply to this acquisition. Responses to this notice must be sent via email to Jaclyn.Stielper@fda.hhs.gov. Telephone calls will not be accepted.
 

Web Link

FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/FDA/DCASC/1057342/listing.html)
 

Place of Performance

Address: 8301 Muirkirk Road, Laurel, Maryland, 20708, United States

Zip Code: 20708
 

Record

SN01843759-W 20090614/090612235819-486897b4a5430ca1d5b049675844708a (fbodaily.com)
 

Source

FedBizOpps Link to This Notice
(may not be valid after Archive Date)

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