JOFOC - Illumina - Redacted 2025 02 06.pdf

4. The statutory authority permitting other than full and open competition.

41 U.S.C. 3304(a)(1), as implemented by FAR 6.302-1, titled "Only one responsible source and no other supplies or services will satisfy agency requirements."

5. Supporting rationale demonstrating the unique qualifications of the proposed contractor or the nature of the action requiring the use of the authority.

USDA has a requirement for all product and service types listed in this justification which are only available from Illumina and no other supplies or services will satisfy agency requirements based on a need to maintain scientific research consistency.

Multiple locations throughout the USDA have an ongoing need for high-density marker assays, using Illumina's proprietary Infinium chemistry for SNP detection and decoding, which allows thousands of different genome locations (DNA markers) to be analyzed in multiple individuals in a single reaction assay, thus permitting a large amount of data to be generated in a short period of time. These markers are custom designed and fill integrated component of high-density SNP bead chip kits, along with other chemical reagents manufactured by Illumina. For those locations that have been utilizing Illumina technology; there is a need for continued use of the equipment, markers, and reagents to provide consistency that allows scientists to compare and share results with colleagues around the world. The chemistry and reagents are specific to Illumina products and are not compatible with any other manufacturer's equipment.

The HiSeq (various models), NextSeq500 and MiSeq are the main instruments used for sequencing, the HiScan and iScan are the main instruments used to scan iSelect BeadChip arrays which were developed by Illumina and are essential to USDA research. All the other items, kits and accessories are periphery items to make the instruments work. LJMS and AutoLoaders are for automation to process the assays using the bead chip arrays.

GenomeStudio is the software for analyzing the raw DNA marker data.

Due to the highly specialized nature of the experiments being conducted by USDA, Illumina reagents can only be used on Illumina equipment. The chemistries involved in assays run with this equipment were developed by Illumina and are proprietary and specific to the lllumina instrumentation. The MiSeq, NextSeq and HiSeq instruments require Illumina flowcells to operate properly. These disposable parts come in the cluster or sequencing kits and are manufactured solely by Illumina. The Illumina reagents and equipment are not interchangeable with any other system. The placement of any other sequencing reagent on the instruments would void any warranty or service issue under a service agreement with Illumina. Additionally, USDA staff is already trained on Illumina products and equipment.

Many laboratories have invested a large amount of funding equipping and providing reagents for their systems and it is important to maintain system consistency. If another brand system was available to be procured, USDA would realize substantial duplication of costs by purchasing new equipment, and training staff. These costs are not anticipated to be recovered through competition, further, Illumina is the only known source to utilize lnfinium (genotyping) and Sequence-by-Synthesis (SBS sequencing) technology which produces necessary and desired compatible results.