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This notice announces the intent by the U.S. Army Medical Acquisition Activity (USAMRAA), 820 Chandler St, Fort Detrick, Maryland, 21702, to award a sole source Firm-Fixed-Price (FFP) Blanket Purchase Agreement (BPA) to Illumina under the statutory authority 13.501(a). This contract is for the purchase of Two (2) NextSeq 550 Sequencing Systems and associated software, for the Armed Forces Medical Examiner Systems (AFMES).

The AFMES DoD DNA Operations (AFMES-DNAOps) is requiring the purchase, maintenance, and installation of Two NextSeq 550 Sequencing Systems and associated software, to replace one existing MiSeq FGX Sequencing Systems that is past its defined End of Life (EOL) cycle replacement and to purchase one new NextSeq to meet increased training and mission requirements. The required instrumentation, computers and software are used to support AFMES-DNAOps mission of assisting AFMES and the Defense POW/MIA Accounting Agency (DPAA) with human remains DNA testing for the identification of U.S. Service members as mandated under title 10 USC, chapter 75, 1471 and 10 USC, Chapter 76, 1501-1513; NDAA 2010, Section 541 (d)(2) and DODI 5154.30. AFMES-DNAOPS requires this instrument to provide optimal performance for next generation whole mtDNA genome sequencing and nuclear Single Nucleotide Polymorphism analysis of human remains. To minimize the variation between NextSeq 550 Sequencing Systems Illumina instruments are made using Good Laboratory Practices (GLP) / Good Manufacturing Practices (GMP) process as well as following and being International Organization Standards (ISO) 18385 compliant.

Illumina Inc. is the sole manufacturer and reseller of the Forensic NextSeq 550 Sequencing System listed in this document. AFMES-DNAOps is a forensic DNA testing laboratory that is accredited by the ANSI National Accreditation Board (ANAB) to the ISO-17025 and FBI-QAS standards for DNA Forensic Laboratories. Based on accreditation adherence (Volume III of the Quality Manual and the FBI's QAS document), all equipment and software must be developmentally validated by the manufacturer and internally validated by the laboratory to all reagents used for DNA testing as well as pass a stringent quality control before being released for casework. Furthermore, forensic accreditation standards say that manufactures who supply DNA forensic instruments and reagents must have established GLP/GMP processes as well as being ISO 18385 Forensic DNA grade accredited. Illumina Inc. is ISO 18385 compliant.

AFMES-DNAOps is the only DoD human remains DNA testing laboratory, which under title 10 USC, chapter 75, 1471 and 10 USC, Chapter 76, 1501-1513; NDAA 2010, Section 541 (d)(2) and DODI 5154.30 is charged with providing human remains DNA testing in support of current day operations (AFMES), past accounting operations (Defense POW/MIA Accounting Agency (DPAA), other DoD Agencies missions, and other Bureaus of the Federal Government, and civilian medical institutions. The NextSeq 550 Sequencing System’s platform accuracy and read time (turnaround time) are critical for AFMES-DNAOps to supporting DPAA with the capability to annually make 200 identifications (NDAA 2010) and to maintaining 100 NGS samples per month.

At the end of the Korean War as part of Operation Glory, 4000 sets of unidentified remains of U.S. service members were returned to the United States. Eight hundred and fifty of these service members could not be identified and they were chemically treated prior to burial. Between 1998 and 2007, DPAA disinterred 100 of these chemically treated unknown service members, and using Sanger based mtDNA sequencing method, success rates were 6% (6 samples). This differed from non-chemically treated samples where Sanger based mtDNA sequencing methods generated results 93% of the time. In 2013, AFMES-DNAOps started to develop an NGS whole genome mtDNA sequencing method for chemically treated samples. After 2 years of research and development the NGS mtDNA capture assay was developed and in accordance with the sequencing method, the Illumina MiSeq FGx Next Generation Sequencing system was compared against other commercial equivalents; was deemed optimal for use with chemically treated and highly degraded human remains samples. The MiSeq FGx was then validated for use following accreditation standards, which took 12 months to perform. In 2016, the MiSeq FGx coupled with the NGS mtDNA capture assay was published and brought on-line for human remains testing. AFMES-DNAOps was the first and only DNA forensic laboratory with the capability to process human remains that have been chemically treated. AFMES has 6 MiSeq FGX systems forensic validated with a monthly through put of 21 samples.

In 2017, the Defense POWMIA Accounting Agency under DoDI 1300.29 was authorized to disinter unknown service members buried in American Battle Monument Cemeteries. There are over 8000 unknown service members buried in American Battle Monument Cemeteries and most of the World War II unknowns were chemically treated prior to burial. This has led to a 200% increase in the number of specimens requiring NGS testing and AFMES has exceeded the through-put of the MiSeq®’s. To meet the increased demands, AFMES-DoD DNA Operations assessed the market for other higher through-put instruments that could run the existing diagnostic technology and reagents. The only instrument that could support the existing validated sequencing plates and chemistries was the Illumina NextSeq 550, which was a medical diagnostic instrument not meant for DNA forensic assays. After meeting with Illumina and having them review our validated NGS sequencing methods using Illumina reagents, Illumina determined they could support AFMES purchasing the NextSeq 550. Initially, their concern was their ability to support the instrument if there were issues and once it was determined we were utilizing reagents and consumables supported by the NextSeq 550 they were willing to sell them to AFMES. In 2018 three NextSeq 550 Sequencing Systems were purchased. The Illumina NextSeq® 550 Sequencing System utilizes the same diagnostic technology as the currently validated MiSeq FGX Sequencing System. This will allow the seamless integration of the currently forensically validated mtDNA whole genome sequencing methods by preventing the need to perform a full forensic developmental validation as well as preventing the need to reprogram existing LIMS and CLC software workflows. These systems were validated for use with the whole mitochondrial genome and nuclear Single Nucleotide Polymorphism (SNP) assay according to the ANSI National Accreditation Board (ANAB) to the ISO-17025 and FBI-QAS standards for DNA Forensic. These instruments have allowed AFMES-DoD DNA Operations to increase NGS sample throughput from 21 samples per month to over 100 samples per month and increasing sample success rates from 25% to over 65%. The NGS method has led to 175 new identifications that could not be accomplished using traditional forensic methods.

A cost analysis was conducted to determine the cost of validating a different NGS sequencing instrument and data collection software with the currently validated mtDNA NGS and nuclear SNP capture sequencing chemistries and through-put employed by AFMES-DNAOPS. Validation of a new NGS sequencing instrument and data collection software with the currently validated mtDNA and nuclear SNP NGS sequencing chemistries would take 24-36 months to accomplish. In addition, the new high through-put instrument would need to be purchased prior to the validation and will include custom programing of the data collection software. The validation will require initial product testing and optimization, data analysis, and the development of the final running conditions. Once a final procedure has been developed the formal FBI-QAS validation will be initiated that requires the laboratory to perform sensitivity, reproducibility, mixture, precision, contamination, casework sample, injection parameter and sequencing cassettes studies. All of the data will need to be analyzed, written up, reviewed by senior scientific staff and then signed off by the Director, AFMES-DNAOps. After the validation is completed, Standard Operating Procedures (SOP) would need to be generated, the casework Laboratory Information Management system and the CLC AFDIL-Qiagen-mtDNA Analysis module would need custom programing. Once signed off the 45 scientific staff currently trained, and proficiency tested per accreditation standards will need to be trained and given written and oral competency exams prior to using it for casework. The total time for training and validation period would be 24-36 months.

Illumina is the only Contractor that can supply the required NextSeq 550 Sequencing Systems AFMES needs in order to meet these standards.

The North American Industry Classification System (NAICS) for this requirement is 334516 and the size standard is 1,000.

This announcement fulfills the synopsis requirements under FAR 5.102(a)(6) and 5.203(a). USAMRAA intends to award a contract no sooner than 15 days after publishing this synopsis. This Special Request for Information is not a request for competitive quotes. Information received in response to this notice will be considered solely for the purpose of determining whether a competitive procurement is in the best interest of the Government. If no written responses are received by the expiration date listed in this notice, which reflects at least fifteen (15) days after the publication of this notice, the award will be issued as sole source. All questions and responses concerning this notice shall be emailed to Mr. Christopher L. Cook at christopher.l.cook68.civ@health.mil.