SOURCES SOUGHT
B -- VAQUITA PORPOISE REFERENCE GENOME SEQUENCE
- Notice Date
- 1/12/2018
- Notice Type
- Sources Sought
- NAICS
- 541990
— All Other Professional, Scientific, and Technical Services
- Contracting Office
- Department of Commerce, National Oceanic and Atmospheric Administration (NOAA), National Marine Fisheries Service, SSMC 3, 1315 East West Highway, Silver Spring, Maryland, 20910, United States
- ZIP Code
- 20910
- Solicitation Number
- SWFSC-18-SS01
- Archive Date
- 2/14/2018
- Point of Contact
- Karen K. Beck, Phone: 858-334-2846
- E-Mail Address
-
Karen.Beck@noaa.gov
(Karen.Beck@noaa.gov)
- Small Business Set-Aside
- N/A
- Description
- Sources Sought - VAQUITA PORPOISE REFERENCE GENOME SEQUENCE SWFSC-18-SS01 THIS IS A SOURCES SOUGHT ANNOUNCEMENT. IT IS NOT A SOLICITATION, NOR DOES IT GUARANTEE A SOLICITATION WILL BE ISSUED. REQUESTS FOR A SOLICITATION WILL NOT RECEIVE A RESPONSE. Any information submitted in response to this Sources Sought Announcement is strictly voluntary. The Government will neither award a contract solely based on this notice, nor pay for any information submitted by respondents. This notice is a request by the Government to collect information from interested vendors for the purpose of market research. A draft Statement of Work is provided for informational purposes only. Failing to provide a response to this announcement will not prohibit/exclude an interested vendor from participating in a future solicitation. The Government requirement is for sequencing, assembly and annotation of the complete vaquita porpoise reference genome, including public presentation and storage of the contributing sequence data and genome assemblies. The North American Industry Classification Code (NAICS) is 541990 with a size standard of 15.0 million. Interested Contractors are requested to provide the following information in response to this Sources Sought Announcement: 1) A statement that you believe your firm has the capability to meet all above stated requirements. 2) Your firm's DUNS number & CAGE code; 3) Your firm's SBA certified small business concern status. Specifically identify if your firm is HUBZone-certified, Service Disabled Veteran Owned, or in the SBA's 8(a) program, etc. If your firm is not small, please state that it is a large business. 4) A brief description of your firm's past experience (within past 3 years) providing similar product. The information provided in response to this announcement is limited to five pages or less. All information shall be provided free of charge to the Government. The Government will not return any data provided in response to this announcement. This request for information does not constitute a commitment, implied or otherwise, that a procurement action will be issued. The Government shall not be liable for or suffer any consequential damages for proprietary information not properly identified. Proprietary information will be safeguarded in accordance with the applicable Government regulations. Responses shall be provided to Contracting Officer, Karen Beck via email at Karen.Beck@noaa.gov no later than 3:00 PM (Pacific Standard Time) on Thursday, January 18, 2018. STATEMENT OF WORK VAQUITA PORPOISE REFERENCE GENOME SEQUENCE I. Introduction The vaquita porpoise (Phocoena sinus) is the most endangered marine mammal, with an estimated population of <15 individuals remaining in a small region of the northern Gulf of California, Mexico. In November, 2017, an adult female was captured as part of an effort to bring vaquitas into captivity for breeding and protection. The female died in captivity, and a complete necropsy was completed with collection of multiple tissues for cell culture and genomic analysis. The current project goal is to use the high-quality DNA available from the cultured cells from this vaquita to generated the complete reference genome sequence of the vaquita. In order to meet the standards of a reference genome, multiple sequencing and DNA mapping technologies and analytical methods need to be employed, providing long and short-read DNA fragments and chromosome anchors to allow a de novo assembly, and sequencing of cDNA from expressed genes in the cultured cells to aid in gene identification and annotation. The completed reference genome will be a public resource representing the porpoise lineage of cetaceans, and allow for completion ongoing genomic research of the vaquita to understand its unique evolutionary history, issues relevant to conservation of the species, and genetic diversity important for conservation and studies of evolution and population genetics of cetaceans. II. Background: Previous genetic analysis of vaquita porpoises have indicated little or no genetic diversity, suggesting potential increased risk of genetic issues as the population declines. As genomic technologies have become available, we have begun genomic analysis of vaquitas, based on historical samples in the SWFSC genetics collection. Initial mitochondrial genome analysis indicates that there is more diversity than previously thought. High-coverage genome sequences have been generated for 20 vaquita samples collected between 1985 and 2017, but these sequences are limited to short fragments that need to be aligned to a reference genome for appropriate organization and analysis. No porpoise reference genome currently exists, so the goal of this project is to generate the first complete reference genome for a porpoise. Recent collection of fresh tissues from a vaquita, and successful culture of cells from the tissue, provide the first opportunity to obtain sufficient quality and quantity of DNA to generate the reference genome. III. Period of Performance: From receipt of cultured cells, sample preparation, sequencing, mapping, assembly and annotation of the reference genome is expected to take 3 to 6 months from date of award. The project will be considered complete when both the raw data and annotated reference genome sequences are made publicly available through public genome databases (US NCBI GenBank, European Ensembl Genome Browser). IV. Technical Specifications: The goal is to generate a reference genome that meets internationally agreed standards of high-quality, error-free, near gapless, chromosome-level, haplotype-phased, and annotated reference genome assembly. Cultured cells will be shipped to the genome sequencing laboratory for DNA and RNA extraction, multiple genomic library preparations (for each of the sequencing and mapping technologies), genomic sequencing and mapping, and de novo assembly of the reference genome. The required technologies include PacBio long-read and Illumina short-read sequencing, 10X Genomics, Hi-C, and BioNano scaffolding, and IsoSeq RNA sequencing for gene annotation). RNA sequencing will allow direct identification and organizational annotation of a portion of the vaquita genes, and multiple analytical pipelines will be used to further annotate all genes. Multiple bioinformatics and analytical techniques are required to complete the de novo assembly and annotation. Both the raw data and the completed reference genome will be made publicly available through arrangement with a public web-hosting organization and through public genome databases in the US and Europe. V. Description of Work and Services: • Task 1. Extraction of DNA and RNA from cultured cells • Task 2. Construction of appropriate DNA libraries for sequencing • Task 3. Multiple sequencing and genome mapping technologies to generate data. • Task 4. De novo assembly and annotation of the reference genome • Task 5. Public web hosting of raw data and reference genome VI. Deliverables: A complete reference genome sequence will be made available to the project leader as soon as it is completed, to aid in ongoing assembly and analysis of multiple vaquita genomes. All raw sequence data will be made available to the public through a web-based data server, and complete annotated reference genome will be made available through the international genome databases GenBank (US NCBI) and Ensembl Genome Browser (EU). VII. Required Knowledge and Experience: Selected individuals must have the following qualifications: • Expertise in next generation sequencing techniques (specifically with the Illumina, PacBio, BioNano, 10x Genomics, Hi-C, and RNA IsoSeq platforms), and genomic library generation for the respective techniques. • Expertise in processing next generation sequencing data. • Expertise in de novo genomic assembly, mapping, and genome annotation. • Statistical and bioinformatics analytical expertise. • Access to computing facilities for the above analyses, and ability to permanently provide public access to the raw data, and make the completed reference genome available through international genome databases.
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/DOC/NOAA/NMFSJJ/SWFSC-18-SS01/listing.html)
- Place of Performance
- Address: Vendor's location, United States
- Record
- SN04788729-W 20180114/180112230653-81a6dc01ceb16699f6d1da61d7381ee0 (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
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