A16_Sole_Source_JOFOC_-_Sequencer_redacted_1.pdf

SOLE SOURCE JUSTIFICATION AND APPROVAL FOR ACQUISITION UNDER

THE SIMPLIFIED ACQUISITION THRESHOLD

1. Contracting Agency and Activity. The Department of the Interior, United States Geological Survey (USGS), Eastern Ecological Science Center (EESC), intends to acquire a MiSeq i100 Plus next-generation sequencing system on a sole source basis. This justification is prepared in accordance with FAR 13.106‑1(b)(1), “Only One Source Reasonably Available.”

2. Nature of Action Being Approved. The EESC requires a benchtop next-generation DNA sequencing instrument capable of performing integrated sequencing, primary analysis, and hardware‑accelerated DRAGEN Bio‑IT secondary analysis to support ongoing ecological genomics, fisheries biology, and environmental DNA (eDNA) research programs.

3. Description of Supplies or Services. This acquisition is for one (1) Illumina MiSeq i100 Plus System (Catalog No. 20115695), including onboard touchscreen interface, integrated computing, DRAGEN secondary analysis pipelines, and 12‑month warranty (parts and labor).

Freight and applicable surcharges are also included. Total investment: USD 119,473.68.

4. Statutory Authority. This procurement is authorized under FAR 13.106‑1(b)(1), “Only One Source Reasonably Available.”

5. Rationale Supporting Use of Citation in No. 5. Illumina is the sole manufacturer of the MiSeq i100 Plus System and retains proprietary control over its software (including DRAGEN pipelines), hardware, consumables, and all associated sequencing chemistry. These components are not cross-compatible with instruments or consumables manufactured by any other company.

The MiSeq platform is the only system that provides:

• Fully integrated primary and hardware-accelerated DRAGEN secondary analysis

• Workflow compatibility with Illumina-formatted genomic libraries already used heavily in USGS EESC research

• Established utility with EESC laboratory network and DOI/USGS IMT support

• Established calibration and quality systems that are required for EESC’s multi-year funded research programs

No third-party manufacturer can legally or technically provide a sequencing instrument compatible with Illumina’s proprietary sequencing-by-synthesis (SBS) workflows. Therefore, Illumina is the only reasonable source for the required instrumentation.

6. Other Information. This instrument will be used to support eDNA, population genetics, and ecological monitoring projects across multiple campuses and requiring continuity with Illumina sequencing data generated across previous USGS studies.

7. The Efforts to Identify Additional Sources Including the Market Research Conducted.

a. The program office conducted online market research to identify other potential vendors capable of providing a sequencing platform compatible with existing Illumina library prep workflows and DRAGEN‑integrated pipelines. No alternative manufacturer offers a system that provides these capabilities.

b. The acquisition will be synopsized per FAR 5.202 when required.

c. No responses have been received from prior synopses for similar Illumina sequencing system purchases.

8. Future Plans to Permit Competition. This is a one‑time acquisition. Should additional instruments or upgrades be needed in the future, EESC will conduct new market research to determine whether other manufacturers have developed compatible or equivalent sequencing chemistries, workflows, or data‑processing architectures.

9. Recommendation Program Office

Based on the facts above, I recommend approval of this sole source acquisition and certify that the statements in this justification are true and complete to the best of my knowledge and belief.