FAR 13 Justification NovaSeq 6000 Redacted.pdf

JUSTIFICATION FOR OTHER THAN FULL AND OPEN COMPETITION (IAW FAR PART 13)

In accordance with FAR 13.106-1(b), Contracting Officers may solicit from one source if the Contracting Officer determines that the circumstances of the contract action deem only one source reasonably available.

Per FAR 13.106-1(b)(2), this requirement is for supplies and services and exceeds the Simplified Acquisition Threshold (SAT) but is not greater than $7 million and the Contracting Officer reasonably expects, based on the nature of the supplies or services sought and on market research, that offers will only include commercial items.

1. Identification of the agency and the contracting activity:

Uniformed Services University of the Health Sciences, Acquisitions Directorate

2. Nature and/or description of the action being approved:

The Collaborative Health Initiative Research Program (CHIRP) is implementing the flexibility and efficiency of the Laboratory Core for precision medicine studies with the acquisition of two (2) additional genomic sequencing platforms. CHIRP currently utilizes three of the exact genomic sequencing platforms, that were purchased in FY18. The purpose of this acquisition is to provide a resource for consistent performance of precision medicine workflows unavailable from other academic resources at this university. This will ensure that USU maintains throughput and expands existing capability for the CHIRP Laboratory Core to facilitate precision medicine studies and initiatives for DoD investigators. This platform will increase precision and reproducibility of multiplex sequencing, which is a requirement for population genomics studies critical to CHIRP studies. For this action, two

(2) additional genomic sequencing platforms are requested for addition to the Laboratory Core platforms within the common unified infrastructure currently operating.

No other companies offer similar sequencing platforms with comparable functions. Furthermore, if other platforms for whole genome sequencing at throughput sufficient for population research existed, their procurement would require extensive development and validation for comparative outcomes with the existing standard operating procedures and infrastructure. This development and validation would have a greater cost burden, due to the time and personnel required for these activities, than the cost of the desired sequencing platforms indicated in this action.

3. Description of the supplies or services required to meet the agency’s needs (including estimated value):

The equipment being requested for purchase is two (2) Illumina NovaSeq 6000 Sequencing Systems for next-generation sequencing of whole human genomes, to include installation, training, and 12 months warranty (including parts and labor). The estimated value for each system is $985,000.00. The NovaSeq 6000 Sequencing System consists of a sequencing-by-synthesis module, an instrument control computer and an instrument touch screen display. The technical specifications required are capability for up to 10 billion reads passing filter and up to 3000 gigabases of data output with quality scores > 75% and run time < 48 hr. for PCR-free TruSeq genome sequencing libraries of 2 x 150 bp read length. The platform is required to process patterned flow cell of at least 4 output types.

Additionally, the base quality scores from the platform is requested to be binned quality scores for reduction of data storage and analysis burden. The platform must also perform 100-cycle, 200-cycle as well as 300-cycle sequencing by synthesis run parameters under 17, 26 and 48 hours per run duration, respectively. For sequencing library types, the platform must be compatible for transcriptome, exome and genome targetspace projects. The system will also perform cluster generation onboard and has the ability to use BaseSpace Clarity Laboratory Information Management System for run tracking.

4. Demonstration that the proposed contractor’s unique certifications or the nature of the acquisition requires use of the authority cited:

Illumina is the global leader in innovative genome sequencing technologies and is the only supplier of next generation sequencing platforms for human whole genome sequencing at population scale.

Illumina holds several patents for their proprietary technology, which are posted in public domain, used with the NovaSeq 6000 Sequencing System; including their patented reversible terminator chemistry to generate consistent, reliable data. The Genome Centers and Core Facilities across the world all utilize Illumina platforms. Illumina has numerous collaborative interactions and solutions for population genomics research and clinical diagnostics. Illumina also provides Field Service Engineering and Field Application Specialists that currently support operations at USU for the CHIRP Laboratory Core. No other vendor has certified and trained Service Engineers or Application Specialists for the Illumina sequencing platforms such as the HiSeq X or NovaSeq 6000.

Consistency and stability is critical to the success of this program. Implementation of another methodology would be detrimental to the programmatic goals of CHIRP due to an estimated delay time of eighteen (18) months resulting from the implementation and validation of a new methodology.

Additionally, a new methodology would result in the generation of different types of data, producing confounding variables to the analysis. Further, USU would experience significant research delays due to required re-training on new systems and platforms.

5. Procedures of FAR 13.5 were or will be used in accordance with 41 USC 1901 or the authority of 41 USC 1903 (including publicizing required justifications): X Yes No

6. Description of market research conducted and the results, or a statement of the reason market research was not conducted:

Market research was conducted to determine if any other products or sources were available as an alternative to the Illumina NovaSeq 6000 Sequencing Platform. Through the market research, it was determined that no other products were capable of meeting the Government’s requirements for a human genome sequencing platform in accomplishing large-scale population research and clinical applications.

As part of the system’s unique functionality and capabilities, the system contains proprietary technology, unique to Illumina, Inc. The Government’s market research confirmed that Illumina, Inc. is the only supplier of this system.

IAW FAR 10.002(b)(2)(vi) and (vii), this was assessed by reviewing and evaluating all new next generation sequencing methodologies and sequencing systems, attending international and national conferences for genomics technologies to be aware of new genomics methodologies and products, and reviewing results of recent methodology research used to identify competing and disruptive technologies.

7. Any other facts supporting the use of other than full and open competition (see FAR 6.303-2(b)(9) for examples):

CHIRP now possesses three critical performance tasks for population scale genomics studies. The current performance tasks for these multi-year activities have already generated large-scale data from existing Illumina platforms at USU.

8. Listing of the sources, if any, that expressed, in writing, an interest in the acquisition:

A sole source notice was posted on Contract Opportunities, to give other potential sources the opportunity to express an interest in the acquisition. No other sources expressed interest in the proposed acquisition.

9. Statement of the actions, if any, the agency may take to remove or overcome any barrier to competition before any subsequent acquisition for the supplies or services required:

The American Genome Center (AGC) and CHIRP perform bi-annual reviews of emerging sequencing platforms, technologies, and methodologies from other potential vendors and monitor innovation at international conferences. AGC and CHIRP will utilize these resources to maximize the opportunity for competition in future acquisitions.

Customer:

Signature Date

Contracting Officer: I hereby certify that the justification is accurate and complete to the best of my knowledge and belief, and I have determined that the anticipated cost to the Government will be fair and reasonable.

Signature Date

Competition Advocate: Ms. Victoria Cunningham

Signature Date

8 AUG 20

8/10/2020

8/8/2020