Specs.docx

STATEMENT OF WORK FOR A DROPLET DIGITAL PCR MACHINE

I: GENERAL INFORMATION

A. Introduction: The U.S. Geological Survey, Leetown Science Center, National Fish Health Research Laboratory needs to purchase a Droplet Digital PCR System to advance our environmental DNA research. This machine should be a Bio-Rad QX200 Droplet Digital PCR System OR EQUAL and be able to partition a 20uL PCR reaction into 20,000 nanoliter-sized droplets, taking no more than 3 minutes and analyze a full 96-well plate in less than 3 hours. This system must deliver an absolute count of the number of target DNA sequences for applications that include copy number variation, mutation detection, and gene expression analysis.

B. Background: The National Fish Health Research Laboratory (NFHRL) is a part of the U.S. Geological Survey’s Leetown Science Center (LSC), located at 11649 Leetown Road, Kearneysville, WV 25430. The NFHRL conducts research on fish and wildlife for Department of the Interior bureaus and other Federal and State agencies. This research spans animal health, early detection of new and reemerging pathogens, early arrival and colonization of invasive species and determination of the presence of threatened and endangered species or cryptic animals. Research has grown and expanded from the basics of determining a gene sequence of a bacterial pathogen to the genome of a virus to which genes are expressed under identifiable conditions whether it be changes in temperature regime or exposure to a biological or chemical contaminant. Given our expertise in genetics and genomics is well recognized we are Increasingly being requested to engage in environmental DNA research (eDNA). These projects can range from screening an environment for aquatic pathogens, source tracking of E. coli and other bacterial pathogens associated with human or animal feces contamination or early detection of invading aquatic fish, invertebrates or plants. New chemistry has been developed to quickly and more accurately detect and analyze eDNA. The U.S. Geological Survey, Leetown Science Center, National Fish Health Research Laboratory requires this new technology to meet the growing needs of our partners in fish and aquatic animal health.

Estimated Dollar Value C. Definitions:

Environmental DNA (eDNA): DNA that is collected from a variety of environmental samples such as water, sediment or air, that is not directly sampled from an individual organism. Vertebrates, invertebrates, plants and microbes shed their DNA into their habitats becoming environmental DNA.

Droplet digital PCR: method for performing digital PCR based on water-oil emulsion droplet technology that can be used to directly quantify and clonally amplify nucleic acids strand including DNA, cDNA and RNA. A "digital" measurement quantitatively and discretely measures a certain variable. The droplet digital PCR method also carries out a single reaction within a sample, however the sample is separated into a large number of partitions and the reaction is carried out in each partition individually. This separation allows a more reliable collection and sensitive measurement of nucleic acid amounts. The massive sample partitioning is a key aspect of the droplet digital PCR technique.

D. Scope: The purpose is to obtain a droplet digital PCR system that includes a specialized laptop with proprietary operation and analysis software, PCR Plate Sealer and a thermal cycler with a 96 deep reaction module. The system must be able to partition samples into thousands of nanoliter-sized droplets, each of which is an independent PCR reactor. After PCR droplets are streamed on a droplet reader, must be able to count positive and negative reactions and deliver an absolute quantification of target DNA or RNA molecules without the use of standard curves. This includes count of the number of target DNA sequences for applications including copy number variation, mutation detection and gene expression analysis.

Bio-Rad QX200 Droplet Digital PCR System OR EQUAL Salient Characteristics:

· Droplet Digital PCR system with an associated customized laptop containing proprietary software so the system will function

· PCR Plate Sealer

· Thermal cycler with a 96 deep well reaction module

· System must be able to partition a 20 ul PCR reaction into 20,000 nanoliter-sized droplets

· Droplet generation should take no more than 3 minutes

· System must be able to accurately count target copies when multiple target copies are distributed in a droplet

· Droplets must be able to be PCR amplified in bulk on a thermal cycler

· Droplet reader must be able to analyze a full 96 well plate in less than 3 hours

· Droplet reader must be able to perform excitation and detection of up to two fluorescent dyes per droplet.

· Droplet reader must be able to illuminate and detect fluorescence from each individual droplet and automatically detect fluorescence from both channels during reading process.

· The system must have a linear dynamic range of 5 orders of magnitude for detection of input samples. And be able to distinguish between four and five copies of input target nucleic acid between samples.

· One 96 well plate must be able to be used to analyze approximately 1,500,000 droplets

· DNA from unread droplets can be recovered for downstream applications

II. WORK REQUIREMENTS

A. Technical Requirements:

· Contractor shall deliver the System and set it up in ready to use conditions

· Contractor must provide 1 year of Technical Support

· Contractor shall provide a one year standard warranty covering parts, labor, service and technical support

· Contractor shall provide an in-house training to on-site researchers on the system upon completion of set up by the contractor’s engineer

· Contractor will provide all warranties, operation instruction guide and maintenance program documentation to Leetown Science Center B. Criteria for Acceptance of Product or Service: N/A C. Deliverables: The contractor shall provide deliverables in accordance with the Reporting Requirements Checklist.

III. SUPPORTING INFORMATION:

A. Place of Performance: Droplet Digital PCR System will be delivered to the U.S. Geological Survey, Leetown Science Center, NFHRL located at 11649 Leetown Road, Kearneysville, WV 25430.

B. Period of Performance: The contractor shall deliver the Droplet Digital PCR System within 60 days of award.

C. Government Furnished Property: N/A