DNA Sequencing Library Preps and Indexing
Sources Sought Synopsis
THIS IS A REQUEST FOR INFORMATION (RFI) ONLY - The Government is currently conducting market research to gather information and identify potential sources for the requirement identified below. A solicitation is not available at this time, and requests for a solicitation will not receive a response. This notice does not constitute a commitment by the United States Government.
NOAA's Acquisition & Grants Office, Western Acquisition Division-Boulder, in support of the National Marine Fisheries Service seeks potential vendors to provide DNA sequencing library preps and indexing, in accordance with the statement of work.
Please provide the following information as requested:
1) A statement that you believe that your firm has the capability to meet these requirements and perform these services. Please include relevant experience and other pertinent information that demonstrates your ability to complete the requirement.
2) Your firm's DUNS number & CAGE code;
3) Your firm's SBA certified small business concern status. Specifically identify if your firm is a small business, HUBZone-certified, Service Disabled Veteran Owned, Woman Owned or SBA 8(a) program certified;
All information received in response to this notice shall be treated as Business Sensitive or confidential to the responder, exempt from public release under the Freedom of Information Act.
All information submitted in response to this announcement is voluntary; the United States Government will not pay for information requested nor will it compensate any respondent for any cost incurred in developing information provided to the United States Government. Proprietary information submitted should be marked appropriately. All submitted information shall remain with the U.S. Government and will not be returned.
The response date for this request for information is no later than COB July 22, 2014.
No collect calls will be accepted. All responses may be submitted via e-mail to Diana Romero, Purchasing Agent, at [email protected]. The phone number for the Purchasing Agent is (303) 497-3761.
NOAA/NATIONAL MARINE FISHERIES SERVICE
SOUTHWEST FISHERIES SCIENCE CENTER
FISHERIES RESOURCES DIVISION
Performance Period: Estimated: August 01, 2014 through January 09, 2016
I. Introduction
Seriola species have traditionally been a major component of global commercial and recreational fisheries and in recent years aquaculture value of these fish has grown into a ~$1.3 billion industry. The California yellowtail (Seriola lalandi) is a strong candidate for development of offshore commercial aquaculture in southern California and neighboring Baja California. Although artificial propagation and production from broodstock populations have been successful, the number of juveniles produced has not yet reached a sustainable level where it can satisfy the aquaculture demand. This is driven primarily by highly variable rates of various deformities, growth rate, and swim bladder inflation. As southern California is at the northern range of the species, it's likely that culture of this species would greatly benefit from identifying locally selected traits to improve broodstock selection.
II. Background
Genetic resources have been developed and used extensively in agriculture and livestock breeding for decades to improve product quality and quantity and more recently these approaches have been applied to a handful of aquaculture species (e.g. salmon, tilapia). Modern genetic approaches extend beyond parentage or family-based analyses to entire genome sequencing, gene expression, targeting of gene variants, and marker-assisted selection. These techniques have the potential to rapidly improve broodstock selection, characterize variation (both beneficial and detrimental), and provide methods to improve production in targeted species.
To address the lack of genetic resources available for S. lalandi we have assembled a high-quality draft genome and are exploring early developmental gene expression. To build upon our success and generate additional genetic resources to address key difficulties in Seriola aquaculture, we propose to use next generation sequencing to identify genomic regions linked to sex determination while simultaneously screening wild diversity for signatures of local selection that may be linked to traits of interest (e.g. cold tolerance, growth rate). Through identification of these markers we will assemble a toolkit by which hatchery facilities can selectively identify broodstock that possess the traits of interest. A sex-linked marker would not only allow minimally invasive sex determination for broodstock selection but also allow monitoring of effects of experimental manipulation (e.g. hormonal treatment) to manipulate sex ratios to improve growth rate. The identification of locally adapted traits will improve efficiencies of culture both through lowered costs for thermal manipulation of broodstock tanks (yearround spawning induction) as well as through optimizing growth and feed conversion rates through selection of individuals best adapted to local oceanographic conditions.
Developing genetic resources and tools are necessary steps for making broodstock-based aquaculture of S. lalandi sustainable and profitable. The genetic resources developed by the proposed project will be made available to aquaculture facilities to guide their broodstock selection. As such techniques have proven very useful in agriculture we feel there is great potential to rapidly improve culture practices for yellowtail through increased value and efficiency.
III. Description of Work and Services
Task 1. Next Generation DNA Sequencing
This task entails the sequencing of 90 Seriola lalandi male and female samples taken from three locations. The sequencing will utilize the Illumina platform, which was also used in the sequencing of the S. lalandi genome. Sequencing of these samples will include generation of 90 indices (one for each sample), and four lanes of HiSeq 100bp paired-end sequencing. Costs associated with the sequencing incorporate both materials and labor.
Task 2. Bioinformatics support
Under this task, bioinformatics support will be used to align sequencing data from the 90 fish to the existing S. lalandi genome. The support will also be used to identify variation among the samples (e.g., SNPs and InDels). Advanced bioinformatics analyses will help to identify molecular markers that may reveal (or are associated with) the sex-determining region in Seriola lalandi, and identify molecular markers that are strongly associated with and can discriminate between the 3 geographic locations and potentially identify locally important variation. Any markers or regions identified through these analyses will be incorporated into the Seriola lalandi Genome Browser.
IV. Deliverables
The contractor will complete the following projects and deliver them to the project leader no later than January 9, 2016. The duration of the contractor's performance period is based on: the availability of samples to submit for sequencing, the sequencing processing time, the number of hours of bioinformatics support, and availability of CPU processing time.
Task 1. Next generation sequencing of 90 S. lalandi samples.
Task 2. Alignment of the sequencing reads to the existing S. lalandi genome.
Task 3. Identification of molecular markers/regions related to variation in sex or geographic region.
Task 4. Marker development for sex-determination, traits of interest, and geographic variation.
Task 5. Incorporating these markers or elements into the Genome Browser for Seriola lalandi.
Task 6. Depositing the data into the appropriate public databases after submission of manuscripts.
V. Non-Personal Service Contract Statement
Contractor employees performing services under this order will be controlled, directed and supervised at all times by management personnel of the contractor. Contractor employees will perform independent of and without the supervision of any Government official. Actions of contractor employees may not be interpreted or implemented in any manner that results in any contractor employee creating or modifying Federal policy, obligating the appropriated funds of the U.S. Government, overseeing the work of Federal employees, providing direct personal services to any Federal employee or otherwise violating the prohibitions set forth in Parts 7.5 and 37.1 of the Federal Acquisition Regulations. The Government will perform the inspection and acceptance of the completed work.
Travel
Not applicable. Work will be performed offsite at vendor's address
Training
Not applicable
VI. Required Knowledge and Experience
Selected individuals must have the following qualifications:
• Expertise in next generation sequencing techniques (specifically with the Illumina platform)
• Expertise in processing next generation sequencing data (specifically with data generated with the Illumina platorm)
• Expertise in genomic and transcriptomic analyses (specifically with the work conducted for S. lalandi)
• Statistical and bioinformatics analytical expertise
Associated Travel costs shall be reimbursed for expenses incurred in accordance with the Government's standards.
Diana Romero, Purchasing Agent, Phone 303-497-3761, Fax 303-497-3163, Email [email protected]
