FBO_J A.pdf

Justification and Approval (J&A) for Other Than Full and Open Competition

I. Contracting Activity.

This justification is executed by the Air Force Medical Operations Office (AFMOA)PMO, Fort Detrick, MD, on behalf of the Wright Patterson Air Force Base Hospital. The contracting agency for this request is 10 CONS/LGCB located at the United States Air Force Academy (USAFA).

II. Nature and/or description of the action being processed.

The action being requested is the sole source acquisition of a Digital Polymerase Chain Reaction System

(dPCR) and a Next-Generation Sequencing (NGS) content enrichment system from one responsible source. The Government intends to procure this requirement through other than full and open competition IAW FAR 13.500(a). FAR Parts 12 and 13 procedures will be used and a new firm fixed price contract will be awarded.

A notice of intent will be posted on www.fbo.gov. An opportunity to quote this requirement will be afforded to any company that can provide evidence of like product and qualifications.

III. Description of supplies/services required to meet agency needs.

The current needs are for a Digital Polymerase Chain Reaction System (dPCR) and a Next-Generation

Sequencing (NGS) DNA content enrichment system meeting the following salient characteristics:

A next generation sequencing enrichment system consisting of an intergratable digital PCR and liquid handling systems

The digital PCR system shall perform multiplex analysis with the ability to detect 1 mutation in

1,000,000 base pairs.

The digital PCR system shall do single molecule PCR to provide for copy number variation and point mutations.

The digital PCR system must use the multi-color and intensity per marker methods for use in quantification of nucleic acids (qPCR).

The digital PCR system must produce amplicon samples for use in Next Generation sequencing systems to include Ion Torrent PGM, Ion Torrent Proton, Illumina MiSeq DX, Illumina HiSeq

2500 and Roche 454 Junior.

The digital PCR system shall be 100-240 VAC/50-60 Hz/600W and be capable of being set on a standard 30” deep laboratory bench.

The integratable high throughput liquid handling sample preparation system shall automate all next generation sequence sample preparation steps from digital PCR-based amplification through sequencing adapter ligation with no intermediate user input.

The liquid handling system shall allow the preparation of up to 48 next generation sequence-ready samples in less than 24 hours with no more than 15 minutes technician hands-on time.

The liquid handling system shall allow the preparation of at least two specimens at a time without use of excess reagent or consumables.

The liquid handling system shall be compatible with the following next generation sequencing platforms: Illumina HiSeq, Illumina MiSeq, Ion Torren PGM, and the Roche GS Junior.

The liquid handling system shall be able to integrate with the digital PCR system, so that the amplicon gleaned from the digital PCR process can be transferred to the system.

The liquid handling system shall include thermal control for samples and reagents at 10° C.

The liquid handling system shall be 100-240 V AC/50-60 Hz/600W and be capable of being set on http://www.fbo.gov/ a standard 30” deep laboratory bench.

The combined system shall include a Windows 7 or higher workstation with a minimum 17” monitor.

The combined system shall include installation of hardware and software complete with 12 month warranty and software dongle(s).

The combined system shall include consumables sufficient for installation (testing of 12 chips) and customer evaluation (testing of an additional 60 chips).

IV. Statutory authority permitting Other than Full and Open Competition.

41 U.S.C. 1901, as implemented by FAR 13.501(a)(1)(ii)

V. Demonstration that the contractor's unique qualifications or nature of the acquisition requires the use of the authority cited above (applicability of authority).

Digital PCR (dPCR) enables reliable, absolute quantification or rare gene sequences in very small quantities of sample, fast. The RainDance instrumentation is capable of separating into samples into 10 million partitions per sample, making it by far the instrument with the largest dynamic range and sensitivity currently on the market. It can detect targets over a much wider concentration range than competing instruments. This ability could be critical for detecting targets in clinical specimens, especially when only a small amount of sample is available. More partitions result in greater sensitivity.

The RainDrop digital System includes both RainDrop Source instrument (Creates and collects up to 10 million Pico droplets per lane) and RainDrop Sense instrument (Identifies and counts each Pico droplet following PCR amplification) with dedicated control computer and instrument control software. This approach increases sensitivity by generating between 1 million and 10 million-pico-liter sized droplets per lane, which is a 500-10,000x improvement over existing methods. Since each droplet encapsulates a single molecule, researchers can quickly determine the absolute number of droplets containing specific target

DNA. The system offers superior sensitivity to detect 1 mutant among 250,000 wild-type molecules with a lower limit of detection of 1 in more than 1,000,000. It has unprecedented multiplexing to conduct up to 10 tests on the same sample using the single molecule multi-color detection technique. In addition, the closed-tube design ensures the highest quality data by eliminating contamination or carryover.

The Thunderstorm system enables researchers to apply the RainDance PCR more cost-effectively and at higher throughput. The system leverages RainDance's single molecule PCR technology that generates millions of unique picodroplet PCR reactions and enables scientists to target up to 20,000 PCR amplicons in a single sample. The system also features true walkaway capabilities that will automatically process up to 96 samples in a single run and access up to eight difference primer panels with minimal hands-on-time.

The RainDance RainStorm technology is generally covered by patents as listed below. There are no licensed systems or products offered by third party providers that are able to use any components or methods of the RainDance RainStorm technology.

- RainDance ThunderStorm systems allow the simultaneous thermocycling of millions of individual

PCR reactions by encapsulating each reaction in a separate aqueous microdroplet. This "massive parallelization" of PCR reactions is unique to RainDance and covered by USPTO patent No. 7,041,481.

- RainDance ThunderStorm system initiates millions of individual PCR reactions by combining individual microdroplets containing DNA template with microdroplets containing oligonucleotide primers.

The capability to merge droplets without the need to impart an electric charge onto each droplet is unique to RainDance and covered by USPTO patent application serial No. 13/759,660.

- RainDance can produce custom libraries of oligonucleotide primers for any portion of the genome where sequence is available. These libraries are covered by USPTO patent application serial Nos.

12/504,764 and 14/226,482.

RainDrop/Thunderstorm will be used as a combination for detection and absolute quantitation of low abundance pathogens, rare genetic mutations, copy number variations, and gene expression quantitation prior to next generation sequencing for emergent disease detection. Digital PCR (the technology underlying the RainDrop) is the only method of amplification capable of providing absolute quantitation and has a higher sensitivity than standard PCR reactions, giving us the necessary power to observe low abundance infectious diseases and rare (1 in 1,000,00+) genetic mutations responsible for human performance and personalized medicine. As an integrated solution, the RainDrop/Thunderstorm package provides a single-platform interface for sample-to-sequence processing. There are no other systems on the market capable of providing both the high sensitivity of digital PCR and automated, integrated library preparation.

VI. Description of efforts made to ensure that offers are solicited from as many potential sources as practicable.

A sources sought notice was posted to FedBizOps on 29 September 2015. The notice invited interested concerns to provide capability packages to 10 CONS/LGCB on 19 October 2015. This posting resulted in no responses, outside of the proposed vendor identified by the customer.

AFMOA's market research found Quant Studio 3D and Bio Rad QX200 provided similar dPCR systems but were limited with the ability to separate samples to 20,000 partitions per sample whereas the

RainDance system partitii0ons 10 ,million partitions per sample.

A notice of Intent to Sole Source will be posted on fbo.gov. An opportunity to quote this requirement will be afforded to any company that can provide evidence of like product and qualifications.

VII. Determination by the Contracting Officer that the anticipated cost to the Government will be fair and reasonable.

The Contracting Officer will determine the dPCR and NGS systems to be fair and reasonable in accordance with FAR 13.106-3. Since only one response is anticipated the Contracting Officer will utilize price analysis techniques to evaluate the RainDance quote.

VIII. Description of the market research conducted and the results, or a statement of the reasons market research was not conducted.

Market research, in accordance with FAR Part 10, was conducted to the maximum extent practicable, and supports that this is a commercial type commodity sold to the general public. dPCR and NGS systems are used by hospitals and laboratories across the country and as such the equipment and reagents are widely available.

The dPCR and NGS equipment is not unique to military medical facilities and is not being modified to meet military requirements. Internet searches were conducted and Sources Sought Solicitation was posted to FedBizOps in search for other manufacturers, but no other source could meet the required qualifications.

IX. Any other facts supporting the use of Other Than Full and Open Competition.

A notice of Intent for Sole Source purchase announcement will be posted on FedBizOps and any challenges will be evaluated.

X. List of sources, if any, that expressed interest in the acquisition.

No other source has express an interest in this acquisition.

XI. A statement of the actions, if any, the agency may take to remove or overcome any barriers to competition before making subsequent acquisitions for the supplies or services required.

In this case, every effort was made to allow competition for this purchase. Since RainDance

Technologies, Inc. is the sole authorized supplier of the equipment needed and it is the only product that will meet the needs of the government, there were no opportunities for competition. Should the government need to purchase a dPCR and NGS equipment in the future, competition will depend on the government's requirement and the market conditions at the time of the need.

XII. Certification by the Contracting Officer.

As evidenced by my signature above, I have determined this document to be both accurate and complete to the best of my knowledge and belief.

XIII. Certification by the technical/requirements personnel.

As evidenced by my (our) signature(s) above, I (we) certify that any supporting data contained herein, which is my (our) responsibility, is both accurate and complete.