SOURCES SOUGHT
R -- DNS SEQUENCING TO CHARACTERIZE COMPLEX MIXTURES OF FISH EGGS
- Notice Date
- 4/14/2011
- Notice Type
- Sources Sought
- NAICS
- 541990
— All Other Professional, Scientific, and Technical Services
- Contracting Office
- Department of Commerce, National Oceanic and Atmospheric Administration (NOAA), Eastern Region Acquisition Division-KC, 601 East 12th Street, Room 1756, Kansas City, Missouri, 64106, United States
- ZIP Code
- 64106
- Solicitation Number
- NFFN7600-11-04003SLW
- Point of Contact
- Sharon L. Walker, Phone: (816)426-7470
- E-Mail Address
-
sharon.walker@noaa.gov
(sharon.walker@noaa.gov)
- Small Business Set-Aside
- Total Small Business
- Description
- The U.S. Department of Commerce (DOC), National Marine Fisheries Service, (NMFS) in Miami, FL, acquires services the University of south Carolina for using massively parallel DNA Sequencing to Characterize complex Mixtures of Fish Eggs. Massively parallel DNA sequencing is the ‘next' generation sequencing technology that currently promises hundreds of megabases of DNA sequence per reaction. Small fragments are generally characterized from a single genome (currently ~ 400 bp), and then assembled into a series of over-lapping fragments representing the entire genome under investigation. Recent modifications to this basic technique have allowed the possibility to sequence small fragments from hundreds of individuals rather than hundreds of fragments from a single individual. The technique uses 'barcodes' or short oligonucleotide tags that uniquely define individuals. In the current context, individuals would represent unique collections of fish eggs, and fragments would represent small DNA sequences that carry mutations unique to each species in the sample. DNA would be isolated from all eggs within a sample, this DNA would be used as template to amplify a diagnostic locus whose information content could identify individual species in the collection, and the resulting count of sequences unique to each species representative of the number of individual eggs that can be assigned to each species. For this approach to work, an assay that targets a locus with sufficient discriminatory power to define species and that has available a large database of sequences from voucher specimens is necessary. The University of South Carolina is the only known source that has on hand hundreds of sequences representing many fishes found in the Gulf of Mexico, including tunas, billfishes, snappers and groupers; these species have been characterized with a hort section of the mitochondrial DNA 16s rRNA locus. This locus will be used to characterize eggs to species where feasible and sequence information is available. Description of Work: Oligonucleotides will be ‘labeled' with unique barcode sequences defining each sample of eggs and used to amplify individual 16s rRNA sequences from 800 selected eggs from the entire CUFES sample (40 individual samples, 20 eggs per sample = 800 total). Each individual will be sequenced in its entirety, then characterized and matched against current snapper/grouper databases or used in BLAST searches against sequences in GenBank. These sequences will form the basis for ‘proof of concept' of massively parallel DNA sequencing. Two complementary approaches will be taken. First, 16s rRNA amplifications from 800 individual eggs will be pooled in equimolar amounts. Each individual collection will be ‘labeled' with a unique barcode primer, then all PCR products characterized via pyrosequencing. This pyrosequencing run serves as a positive control' that is, we expect to see the same number of individual taxa as in the 800 separately characterized sequences and in the same amounts, barring any inherent bias in the normalization of PCR products across 800 samples. Second, they will pool equimolar amounts of total genomic DNA isolated from each egg into their respective samples (20 eggs/sample), uniquely barcode each sample, amplify the 16s rRNA fragment using template from each sample (40 samples total), equalize the contribution of each amplified sample to the final template, and subject this final template to pyrosequencing. If no bias exists in terms of, for example, egg volume contribution to each sample, or implicit in the designed oligonucleotides, then we expect to see the same taxa in the same proportions as the 800 individually characterized eggs. Assuming no bias exists, then any future characterizations will use pooled eggs from each sample to isolate and amplify target DNA. Otherwise, if a bias does exist, then individual DNA isolation and amplification, irrespective of sample, would be most reliable, and yield quantitative information on species composition. The proposed contract action is for services for which the Government intends to solicit and negotiate with only one known source the Baruch Institute located at the University of South Carolina, Columbia, SC. They are the only known company able to provide the service for the existing government requirement. The Baruch has prior experience in producing DNA barcoding databases for tunas, billfishes, snappers, groupers and sharks, and continuing work on larval identification. Their prior experience and technique barcoding will help form the basis of this proposed proof of concept. The researchers from the Baruch Institute have years of experience in the genetic analysis of fishes, and a history of experience in this form of using massively parallel DNA sequencing to characterize complex mixtures of fish eggs. Interested persons may identify their interest and capability to respond to the requirement or submit proposals. This is not a request for competitive proposals. However, all proposals received within ten (10) days after the date of publication of this synopsis will be considered by the Government. A determination by the Government not to compete with this proposed contract based upon responses to this notice is solely within the discretion of the Government. Information received will be considered solely for the purpose of determining whether to conduct a competitive procurement. All responsible sources may submit a proposal, which shall be considered by the agency. Interested firms shall include, in writing, the company name, address, point of contact, telephone number, and business size; a statement regarding their detailed capabilities and qualifications to support their ability to provide this service, and any additional supporting literature. Submissions received in response to this notice shall be evaluated based on the technical ability and demonstrated past experience to meet the requirements described in the description section above. Vendor must provide a DUNS number (http://www.dnb.com/us/ ) and register with the Central Contractors Registration (http://www.ccr.gov/ ). Responses should be emailed to sharon.walker@noaa.gov or faxed to 816-274-6983, Attn: Sharon Walker.
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/DOC/NOAA/CASC/NFFN7600-11-04003SLW/listing.html)
- Record
- SN02424790-W 20110416/110414234457-00b4ff31b0aeafa6abf75dddd61fe6a7 (fbodaily.com)
- Source
-
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