JA Illumina brand redacted.pdf

Illumina Brand Genomics Analysis System CONTROL NUMBER VA-25-00056640

JUSTIFICATION FOR A SOLE SOURCE AWARD

FOR CERTAIN COMMERCIAL ITEMS

1. Contracting Activity: Department of Veterans Affairs (VA) Office of Procurement, Acquisition, and Logistics

Technology Acquisition Center 23 Christopher Way

Eatontown, NJ 07724

2. Description of Action: The proposed action is for a firm-fixed-price contract with Illumina, INC for Illumina brand name Dynamic Read Analysis for GENomics (DRAGEN) genomic analysis appliances, Informatics Professional Services, DRAGEN Server Licenses and DRAGEN Server Advanced Exchange Support Plans

3. Description of Supplies or Services:

The Center for Data and Computational Sciences (C-DACS) requires the procurement of a high-throughput genomic analysis appliance, including integrated software and hardware as a complete unit (i.e. an appliance), capable of performing whole genome sequencing (WGS) and variant calling to meet specific MVP research requirements.

The system will be an all-in-one, turnkey, commercial off-the-shelf solution, delivering ultra-rapid, highly accurate, and comprehensive secondary analysis of sequencing data out-of-the-box. Such a system is fundamental to supporting C-DACS's mission to advance genomic research and enable precision medicine for Veterans.

This solution will be validated and not require further scientific validation, nor will it necessitate secondary or external multistep workflows that would require validation by C-DACS. Leveraging the most advanced sequencing technology, this system will deliver exceptional accuracy, scalability, and automation, seamlessly integrating with existing bioinformatics pipelines. The appliance must be capable of handling high sample volumes, averaging 175,000+ WGS per year. Robust variant detection is essential for both clinical and research applications. To meet these demands, the appliance must include several key features.

First, it should have dedicated FPGA hardware with integrated genomic workflows, where both the hardware and software components, including the FPGA, are validated at scale (175,000+ WGS) as a complete unit, ready to use out-of-the-box. It must also include PGx star allele callers that can identify the genotypes of Tier-1 PGx genes such as CACNA1S, CFTR, CYP2C19, CYP2C9, CYP3A5, CYP4F2, IFNL3, RYR1, NUDT15, SLCO1B1, TPMT, UGT1A1, VKORC1, DPYD, G6PD, MT-RNR1, BCHE, ABCG2, NAT2, F5, and UGT2B17.

Additionally, the genomic analysis software should demonstrate variant calling performance with greater than 99% accuracy on clinically relevant but challenging genomic regions, particularly CYP2D6 CNV and allele calling. The appliance should also have transcriptomic RNA analysis capability with RNA-seq (splice-aware) aligners and optional rRNA filtering during alignment. A robust pipeline for epigenetics analysis is necessary to rapidly analyze the whole genome and targeted bisulfite DNA methylation data. Furthermore, oncology sequencing workflows should be equipped with a variant calling pipeline capable of identifying low-allele frequency somatic variants from both tumor-only and tumor-normal paired samples. The software solution must be unified, capable of performing the variant calling process internally and automatically, thereby eliminating the need for multistep processes. Finally, it should have efficient processing capabilities, enabling the analysis of one WGS in approximately 30 minutes for the full suite of analyses.

The contractor shall provide Illumina DRAGEN solution appliance, including one year of DRAGEN Advance Exchange Support Plan, Informatics Professional Services, and DRAGEN appliance licenses. The period of performance shall be a one-year base period with 2 option years for maintenance and optional tasks that will allow the system to be scaled up to allow processing of more WGS. The total estimated value of the proposed action is $1,983,683.34 inclusive of options.

4. Statutory Authority: The statutory authority permitting other than full and open competition is 41 U.S.C. 1903 as implemented by the Federal Acquisition Regulation (FAR) 13.501, entitled “Special Documentation Requirements”.

5. Rationale Supporting Use of Authority Cited Above: The proposed source for this action is Illumina, Inc., located at 5200 Illumina Way, San Diego, CA 92122. Illumina, Inc. is the sole authorized seller of Illumina brand DRAGEN services, licenses, professional services, and support plans. This solution provides dedicated FPGA hardware with integrated key genomic workflows. The hardware and software components, including the FPGA, are validated at scale (175,000+ WGS) as a complete unit and are ready to use out-of-the-box in an all-in-one appliance. It also includes PGx star allele callers that identify, at a minimum, genotypes of Tier-1 PGx genes such as

CACNA1S, CFTR, CYP2C19, CYP2C9, CYP3A5, CYP4F2, IFNL3, RYR1, NUDT15,

SLCO1B1, TPMT, UGT1A1, VKORC1, DPYD, G6PD, MT-RNR1, BCHE, ABCG2,

NAT2, F5, and UGT2B17. Including challenging genomic regions like CYP2D6.

Additionally, it supports transcriptomic RNA analysis with an RNA-seq (splice-aware) aligner and optional rRNA filtering during alignment. For epigenetics analysis, there is a pipeline to rapidly analyze whole genome and targeted bisulfite DNA methylation data.

Oncology sequencing workflows are also included, featuring a variant calling pipeline capable of identifying low-allele frequency somatic variants from both tumor-only and tumor-normal paired samples.

Moreover, this unified software solution can perform the variant calling process internally and automatically without the need for multi-step processes. It is capable of processing one whole genome sequence (WGS) in approximately 30 minutes per WGS for the full suite of analyses. This integrated approach makes this solution capable of delivering all these requirements out-of-the-box.

6. Efforts to Obtain Competition: Market research was conducted, details of which are in the market research section of this document. This effort did not yield any additional sources that can meet the Government’s requirements. Additionally, the proposed action will be synopsized on the Contracting Opportunities Page in accordance with FAR 5.201. Any proposals that are received shall be evaluated.

7. Actions to Increase Competition: The Government will continue to conduct market research to ascertain if there are changes in the marketplace that would enable future actions to be competed.

8. Market Research: VA technical and scientific experts conducted market research from March of 2025 to July of 2025 via web-based searches, conferences, and direct communication with multiple vendors. VA technical and scientific experts reviewed QIAGEN and Dell who is in partnership with Falcon Computing. QIAGEN offered genomic server software but did not offer an appliance-based solution validated as a complete solution. Dell in partnership with Falcon Computing offers a solution, this solution is not an appliance supporting all genomic workflows out-of-the-box. In addition, this solution did not meet the requirement for being able to process one WGS in 30 minutes; and did not meet the requirement of validation at scale. Per research publications there were options for custom solutions, all of these did not meet the requirement of an appliance-based out-of-the-box solution with integrated and validated genomic workflows at scale. An RFI was posted June 3, 2025 thru June 6, 2025 besides Illumina, another vendor responded Government Scientific Source, INC. The vendor offered custom solution offerings. Custom offering do not meet the need for appliance-based solution that is out-of-the-box that do not require validation of the custom pipelines. Validation of a custom solution would not only exceed the required timeline, but also require additional resources and time to validate these pipelines. A validation effort like this would take a year or more to complete. This delays research that improves outcomes for conditions such as cancer, rare genetic disorders, and chronic diseases, providing Veterans with access to cutting-edge healthcare advancements.

Additionally cloud-based solutions were reviewed, AWS HealthOmics by Amazon, Microsoft Genomics, Broad institute of MIT and DNAnexus were reviewed. Microsoft Genomics does not have built-in star allele callers and does not offer an integrated on-premises solution. Broad institute of MIT is targeted more at generating primary genomic data, they do not offer comprehensive secondary analysis services. AWS HealthOmics and DNAnexus do not generate the secondary data directly; they are more geared toward managing and storing sequenced data. In addition, neither offered on-premises solutions. In addition, cloud solutions require extra time to migrate data and additional validation of a new cloud infrastructure. Validation of a new cloud infrastructure and data copy to the new environment would take 6-8 months on top of the time to validate the genomic pipelines.

Based on all of these market research efforts, the government’s technical experts have determined that only Illumina, INC is capable of meeting the VA’s technical requirements.

9. Other Facts: N/A

Technical/Requirements Certification I certify that the supporting data under my cognizance, which are included in this justification, are accurate and complete to the best of my knowledge and belief.

Brian T. Ibbison Date

Fair and Reasonable Cost Determination I hereby determine that the anticipated price to the Government for this contract action will be fair and reasonable. Price analysis in accordance with FAR 15.404 will be conducted.

Debra Clayton Date

Contracting Officer Certification/Approval I certify that this justification is accurate and complete to the best of my knowledge and belief.

Debra Clayton Date

Approval In my role as the procuring activity Advocate for Competition, based on the foregoing justification, I hereby approve the acquisition of Illumina DRAGEN Servers, Informatics Professional Services, DRAGEN Server Licenses and DRAGEN Server Advanced Exchange Support Plans on an other than full and open competition basis pursuant to the authority cited in Section 4 above, subject to availability of funds, and provided that the property and services herein described have otherwise been authorized for acquisition.

Jason Bullen Date Advocate for Competition Technology Acquisition Center Office of Procurement, Acquisition, and Logistics Department of Veterans Affairs