Presolicitation Notice - Illumina NextSeq 2000 Sequencing System

The Defense Health Agency Contracting Activity (DHACA) in Fort Detrick, MD intends to negotiate on a sole source basis (IAW RFO 12.201-1) with Illumina, Inc 5200 Illumina Way San Diego, CA 92122, as the only responsible source that can provide an Illumina NextSeq 2000 Sequencing System to replace the Illumina NextSeq 550 system that is approaching end-of-life status. This is a Presolicitation notice in accordance with RFO 5.101. To support the mission of the Armed Forces Medical Examiner System (AFMES) and the Defense POW/MIA Accounting Agency (DPAA), AFMES-DNA OPS with the identification of missing service members from World War II, Korea, Vietnam, and the cold war as part of DoD’s past accounting missions. To meet the National Defense Authorization Act (NDAA) 2010 mandate for 200 annual identifications, AFMES- DNA OPS has developed, validated Next-Generation Sequencing (NGS) methods on Illumina platforms. Due to the end-of-life status of the current NextSeq 550 systems and a significant increase in mission sample workload, a direct replacement is required. To maintain mission continuity, one (1) Illumina NextSeq 2000 Sequencing System is needed. This will allow for the seamless transfer of existing validated assays and provide the increased throughput necessary for identifying fallen service members. The NextSeq 2000 is the direct, next-generation replacement for the laboratory's current, end-of-life Illumina sequencers. It offers backward compatibility with the existing validated assays while providing increased throughput (up to 120 Gb), faster run times (approximately 8-42 hours), and higher data quality (2'90% of bases >Q30). This is critical as the NGS sample workload has increased. Furthermore, the NextSeq 2000 offers future scalability, as it can be upgraded to another NextSeq System if mission demands increase further. Switching to a different manufacturer's system would require complete re-development and re-validation of all sequencing assays, a process estimated to cost over $2.8 million and take 24-36 months. This would lead to mission stoppage, and unacceptable delays in identifying fallen service members, which would nullify years of government investment in developing these current, highly successful methods. The NextSeq 2000 is the only instrument that meets the technical requirements without incurring these prohibitive costs and mission delays. The following are the required minimum essential characteristics of the Sequencer: •           The system shall be compatible with the existing, forensically validated in-house custom Next Generation Sequencing (NGS) assays for whole mitochondrial DNA (mtDNA) genome and nuclear Single Nucleotide Polymorphism (SNP) analysis. •           Shall be a next-generation sequencing (NGS) based platform incorporating cluster generation and sequencing into a single, integrated workflow with onboard data analysis. •           Shall utilize XLEAP Sequencing by Synthesis (SBS) chemistry, which is 2.5x faster and provides higher fidelity than previous SBS versions. This is essential for compatibility with currently validated laboratory assays. •           Shall ensure superior data quality, achieving a metric of ≥90% of bases higher than Q30 for common read lengths. •           Shall support flexible read lengths, including 2x50 bp, 2x100 bp, 2x150 bp, and 2x300 bp, utilizing Illumina reagents. •           Shall provide a flexible output of up to 120 Gb per run to accommodate increasing sample throughput demands. •           Shall support a high read capacity of up to 400 million single reads per run. •           Shall have run times between approximately 8 and 42 hours, depending on the specific assay and read length configuration. •           Shall be designed with an integrated reagent cartridge that includes all fluidics and waste, eliminating the need for instrument wash cycles between runs. •           Shall incorporate a modern touchscreen interface and use RFID tracking for all consumables. •           Shall feature a direct, on-site architectural upgrade path to another NextSeq 2000 System to ensure future scalability without requiring a new instrument. •           Instrument Control Computer (Internal) shall be equivalent to or better than: o      &nbsp