Loren Data's SAM Daily™

FBO DAILY ISSUE OF JUNE 09, 2011 FBO #3484
MODIFICATION

D -- Next Generation Genome Sequencing Bioinformatics Pipeline

Notice Date

6/7/2011
 

Notice Type

Modification/Amendment
 

NAICS

541690 — Other Scientific and Technical Consulting 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

1086925
 

Archive Date

6/29/2011
 

Point of Contact

Anne Oliver, Phone: 301-827-6764, Gina Jackson, Phone: 301-827-1982
 

E-Mail Address

anne.oliver@fda.hhs.gov, gina.jackson@fda.hhs.gov
(anne.oliver@fda.hhs.gov, gina.jackson@fda.hhs.gov)
 

Small Business Set-Aside

Total Small Business
 

Description

This amendment is to modify the RFI instruction. No other changes. This RFI is set aside for Small Business. Description of Services/Supplies: Next Generation Genome Sequencing Bioinformatics Pipeline This is a Request for Information (RFI) to identify the capabilities of the marketplace of all interested parties. This is not a request for Proposals. This request is for information and planning purposes as part of market survey only and shall not be construed as a solicitation or as an obligation on the part of the Food and Drug Administration (FDA) for any future solicitation. No official solicitation exists; therefore, please do not request a copy of a solicitation. If in the future an official solicitation is released, there is no guarantee that sources responding to this RFI will be included on the source list. Telephone inquiries will not be accepted. The FDA makes no implied or in fact contract by issuing this RFI. Acknowledgement of receipt of responses will not be made, nor will respondents be notified of the FDA's view of the information received. Do not send any material that requires a non-disclosure agreement or that may be business sensitive. Responses received that include a non-disclosure agreement or identify information that is business sensitive will not be accepted. Responses to this notice will not be returned. 1. Mission and Objectives Whole genome DNA sequencing (WGS) with next generation platforms is no longer restricted to large sequencing centers but can be conducted in private laboratories with relative ease. In addition, these platforms no longer come with the "big science" price tag of millions but can be fairly inexpensive (as little as $60k) with prices becoming all the more competitive. However, these newer systems yield raw sequencing reads that require significant bioinformatic expertise to utilize, manipulate, and ultimately conduct comparative assessments considering the size and volume of a given data set. Adding to the complexity is the evolving scale of information to be extracted from the massive sequencing datasets indicative of the starting material: from single strain, mixed populations, and extending into full metagenomic communities. From a general perspective, WGS is becoming entrenched in the near future as the state-of-the-art gold standard and will require individual laboratory competency and utility in this area. It is clear that the current bottleneck is secondary and tertiary extraction/derivatives of the information that currently requires highly trained bioinformatics personnel. It is ultimately a cost benefit to automate the process pipeline to translate raw sequence to useable and recognizable data based on comparative assessments. This work may ultimately support and integrate WGS data, in a modular fashion, into the Pathogen Annotated Tracking and Resource Network (PATRN) that is currently under contract in CFSAN/OARSA/DVA. Certainly, a variation on this fundamental need can translate into the functional genomics realm to enumerate, categorize, and characterize in true digital quantity and quality changes occurring at the RNA level. In aggregate, this work supports FDA/CFSAN related-mission to delineate and/or develop methodology for the microbiological and molecular identification of foodborne pathogenic bacteria. In addition, this pipeline may allow unique markers to surface rapidly that are important not only in identification and subtyping but relate to host or food reservoir. Deliverables The desired deliverable for this requisition would involve a simplified (point and click) bioinformatic software-based utility package for handling/integrating raw genomic sequence data reads from a next generation sequencing platform. The utility package would essentially convert raw reads with proper interfacing with genomic sequence databases (such as GenBank) into easily identifiable DNA polymorphisms with functional genomic annotation information as outlined in the statement of work. 2. Period of Performance/Basis 10/1/2011 To 09/30/2012 3. Source Selection Procedures/Criteria The equipment must meet the technical requirements listed under the SOW/PWS. The evaluation factors for this solicitation will be the ability to meet the technical requirements, compatibility with existing systems and past performance will comprise the major percentage of the evaluation factors. The Government reserves the right to select the system that will offer best value. The vendor will have an established record of being able to service their systems, provide technical assistance and have the service contracts available for additional funding. 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 purchase order to other than the lowest price technically acceptable quote. The Government will evaluate information based on the following evaluation criteria: 1) Technical Capability factor "Meeting or Exceeding the Requirement," and 2) Price. Technical Capability is significantly more important than price. 4. EIT. Approval of the OPDIV/OS Section 508 Official or designee is required when claiming an exception to Section 508 of the Rehabilitation Act (see the HHS Section 508 policy at http://www.hhs.gov/od/508policy/index.html ) This may ultimately support and integrate whole genome sequencing into the Pathogen Annotated Tracking and Resource Network (PATRN) that is currently under contract in CFSAN/OARSA/DVA. Statement of Work (SOW)/Performance Work Statement (PWS) Sequencing Pipeline Development for Single Strain Analysis • Produce consensus sequence of raw reads • Assemble contiguous fragments based on internal alignment and complementarily • Intermediate assemblies aligned and scaffolded to sequenced archetype or reference genomes • Gene and regulatory element annotations of contiguous fragments • Identification of novel gene features, single nucleotide polymorphisms (SNPs) • Export capability and location relative to reference genome of novel features • Identification of functional SNPs: SNPs coded as synonymous, nonsynonymous (including classification of nonsense, missense etc), potential regulatory or ribosomal element involvement including promoters and terminators • Classification of SNPs and genes into virulence-related elements • Categorization unaligned/novel insertions or deletions • Comparative capacity with multiple de novo strain sequences (Option Year) - • Metagenomic (community) pipeline TBD • Transcriptomic pipeline TBD RFI Instructions: Please complete, Source selection procedures/criteria, describing your company's capabilities; Size of Business and Estimated Dollar Value Range. Responses shall have the following information: • Identified with the RFI number; • Be no more than ten (10) pages in length; • Not to submit marketing materials; • Submit the response to the email indicated above. FDA makes no implied or in fact contract by issuing this RFI. Acknowledgement of receipt of responses will not be made, nor will respondents be notified of the FDA's view of the information received. Size of Business State whether your company is a large business, small business (and also state your socioeconomic status), College/University, or a non-profit organization. Estimated Dollar Value Range Based on the government's mission, objectives, and scope of work, what dollar value range would you determine to be the most accurate rough estimate. 0 Under $150,000.00 0 Over $150,000.00 and Under $500,000.00 0 Over $500,000.00 and Under $1,000,000.00 According to FAR Part 10, Market Research, the results of the market research will be used to: (i) Determine if sources capable of satisfying the agency's requirements exist; (ii) Determine if commercial items or, to the extent commercial items suitable to meet the agency's needs are not available, non-developmental items are available that- (A) Meet the agency's requirements; (B) Could be modified to meet the agency's requirements; or (C) Could meet the agency's requirements if those requirements were modified to a reasonable extent; (iii) Determine the extent to which commercial items or non-developmental items could be incorporated at the component level; (iv) Determine the practices of firms engaged in producing, distributing, and supporting commercial items, such as type of contract, terms for warranties, buyer financing, maintenance and packaging, and marking; (v) Ensure maximum practicable use of recovered materials and promote energy conservation and efficiency; and (vi) Determine whether bundling is necessary and justified. (vii) Assess the availability of electronic and information technology that meets all or part of the applicable accessibility standards issued by the Architectural and Transportation Barriers Compliance Board at 36 CFR Part 1194. The extent of market research will vary, depending on such factors as urgency, estimated dollar value, complexity, and past experience. The contracting officer may use market research conducted within 18 months before the award of any task or delivery order if the information is still current, accurate, and relevant. Market research involves obtaining information specific to the item being acquired and should include- (i) Whether the Government's needs could be met by- (A) Items of a type customarily available in the commercial marketplace; (B) Items of a type customarily available in the commercial marketplace with modifications; or (C) Items used exclusively for governmental purposes; (ii) Customary practices regarding customizing, modifying or tailoring of items to meet customer needs and associated costs; (iii) Customary practices, including warranty, buyer financing, discounts, contract type considering the nature and risk associated with the requirement, etc., under which commercial sales of the products or services are made; (iv) The requirements of any laws and regulations unique to the item being acquired; (v) The availability of items that contain recovered materials and items that are energy efficient; (vi) The distribution and support capabilities of potential suppliers, including alternative arrangements and cost estimates; and (vii) Size and status of potential sources.
 

Web Link

FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/FDA/DCASC/1086925/listing.html)
 

Place of Performance

Address: 5100 Pint Branch PKWY, College Park, Maryland, 20740, United States

Zip Code: 20740
 

Record

SN02466744-W 20110609/110607235540-2060fcd50c5934d2b72b753aa495beab (fbodaily.com)
 

Source

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

---

| FSG Index  |  This Issue's Index  |  Today's FBO Daily Index Page |