C01-18-P-0156-_JA-Redacted.pdf

MCMR-AAP-AA

ENCLOSURE 1

Control No: JA-18-115

Sole Source Justification (SSJ) in accordance with FAR subparts 13.106 or 13.5 using Simplified Acquisitions Procedures (SAP)

1. Contracting Activity: Director of Contracting, U.S. Army Medical Research Acquisition Activity (USAMRAA). 820 Chandler Street, Fort Detrick, MD 21702-5014.

2. Requiring Activity: The Armed Forces Medical Examiner System (AFMES), Armed Forces DNA Identification Laboratory (AFDIL). 115 Purple Heart Drive, Dover AFB, DE. 19902.

3. Nature of Action:

Commercial Item Non-Commercial Item New Requirement Follow-on Requirement Mod to Existing Purchase Order/Contract Number

Pricing: Firm-Fixed Price* Time & Materials** Cost*

* See FAR 12.207(a) ** See FAR 12.207(b).

For Hybrid Contracts, list percentage of each type of pricing:

* Firm Fixed Price:

**Time & Materials:

* Cost:

Funds: RDT&E Operations and Maintenance, Army (OMA) Other Funds:

Fiscal Year of Funds: FY18

Estimated Total Dollar Value including Options: $ 1,004,678.63 _

Modification to Ceiling: $

4. Contractor Name:

Name of Proposed: Illumina, Inc Contractor(s):

Street Address: 5200 Ilumina Way City, State, Zip: San Diego, CA 92122-4616 Phone: 1-800-809-4566

DUNS:

Cage Code:

5. Description of Supplies/Services:

The required NextSeq® 550 Sequencing System is needed to increase sample throughput of the currently forensically validated NGS DNA casework and Family Reference processing methods used to support the Armed Forces Medical Examiner System (AFMES) and the Defense POW/MIA Accounting Agency (DPAA) with the identification of missing service members for World War II, Korea, Vietnam, and the cold war as part of DoD’s past accounting missions 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. The NextSeq® 550 Sequencing System is a next generation sequencing (NGS) system specifically designed for high-through-put sequencing and microarray scanning in an integrated benchtop unit. Its fast, integrated DNA-analysis workflow allows for the rapid sequencing of exomes, targeted panels in a single run, and has the capability of switching to a lower-through-put sequencing as needed. The unit has the flexibility to run high quality and degraded samples and utilize both 75 cycle, 150 cycle, and 300 cycle sequencing runs. The system utilizes dedicated library preparation kits, customized instrument control software, and an analytical software package to support the reliable analysis of both routine and challenging (degraded) forensic samples.

Currently, the Armed Forces Medical Examiner Systems Armed Forces DNA Identification Laboratory (AFMES-AFDIL) has purchased and forensically validated six Illumina MiSeq FGX Sequencing Systems. The Illumina MiSeq FGX Sequencing System is a lower throughput NGS system that utilizes the same diagnostic technology as the higher throughput NextSeq® 550 Sequencing System. This will allow seamless integration of the currently forensically validated mtDNA whole genome sequencing methods for highly degraded casework samples and family reference specimen samples.

6. Authority Cited: 41 U.S.C. 1901 OR 41 U.S.C. 1903

(a) FAR 13.106-1(b)(1)(i): Only one source reasonably available (e.g., urgency, exclusive licensing agreement, brand name or industrial mobilization); OR

(b) FAR 13.106-1(b)(1)(ii): Only one source can provide a portion of the purchase that is a particular brand-name item; OR

(c) FAR 13.501(a)(1)(i): Only one source reasonably available (including brand name); OR

(d) FAR 13.501(a)(1)(ii): Only one source can provide a portion of the purchase that is a particular brand-name item.

7. Reason for Authority Cited: The suggested source is Illumina, Inc.

a. AFMES-AFDIL is DoD only human remains DNA testing laboratory, which under

10 U.S.C. 1471 and 10 U.S.C. 1509 is charged with providing human remains DNA testing in support of current day operations (AFMES), past accounting operations (Defense POW/MIA Accounting Agency; DPAA) and other DoD Agencies missions. The required instrumentation, computers and software are needed to increase sample throughput of the currently forensically validated NGS DNA casework and Family Reference processing methods used to support the AFMES and DPAA with the identification of missing service members from World War II, Korea, Vietnam, and the cold war as part of DoD’s past accounting mission. The National Defense Authorization Act (NDAA) 2010 stipulates that the past accounting community needs to build the capability and capacity to annually make 200 identifications by 2015 and congress added additional requirements to the NDAA 2010 which stipulated that the Secretary of Defense should increase annual accounting to 350 identifications by 2020 (NDAA 2010 and H Report 111- 288). The Armed Forces Medical Examiner System’s - Armed Forces DNA Identification Laboratory (AFMES-AFDIL) met the NDAA 2010 by building the capability and capacity to support 200 identifications, this was accomplished by hiring additional staff and developing and implementing novel methods for recovering DNA data from the most difficult specimens. The newly developed Next Generation mtDNA captured assay for chemically modified samples has allowed for the first time ever the successful DNA processing of samples that for the last 20 years did not work with conventional methods. This has allowed DPAA to move forward with large-scale disinterments of unknown WWII and Korean service member gravesites whose remains were chemically treated (embalmed).

b. The Armed Forces Medical Examiner System’s-Armed Forces DNA Identification

Laboratory (AFMES-AFDIL) has validated new PCR amplification and sequencing techniques, specifically next generation sequencing (NGS), utilizing the Illumina MiSeq® instruments. Initially, this mtDNA Capture assay was developed for chemically treated samples associated with the Korean War, but recent disinterments associated with World War II losses have been chemically treated prior to burial. This has led to a 200% increase in the number of specimens requiring NGS testing and AFMES-AFDIL has exceeded the through-put of the MiSeq®’s. To support the increased NGS workload in the AFMES- AFDIL’s DNA identification and data basing activities, three NextSeq® 550 Sequencing Systems are needed for implementing and further developing novel methods for recovering DNA data from the most difficult specimens and to increase the number of samples analyzed per week.

c. The existing MiSeq® FGX sequencing system currently allows for the pooling of 5 samples per run and each run takes 36 hours, while the NextSeq® 550 sequencing system allows for the pooling of 16 or more samples per run and each run takes less than 29 hours. Since the MiSeq® FGX sequencing system utilizes the same diagnostic technology as the higher throughput NextSeq® 550 Sequencing System, will allow for seamless integration of the currently forensically validated mtDNA whole genome sequencing methods for highly degraded casework samples and family reference specimen samples.

Comparable equipment with even the very slightest differences would compromise the compatibility and consistency of DNA identification and lead to significant costs in reagents and man power hours to validate the a new platform.

Standardization of equipment and reagents is critical to ensure variances are mitigated. The equipment will be used to support their mandated missions as described above (7a-7b).

d. AFDIL is the operational element of the AFMES and is accredited by the

American National Standards Institute-American Society for Quality (ANSI-ASQ) National Accreditation Board (ANAB) to the International Standards Organization (ISO) 17025, ANAB supplemental and the FBI Quality Assurance Standards (FBI-QAS) for Forensic DNA Testing Laboratories. Based on accreditation adherence (Volume III of the Quality Manual and the FBI's Quality Assurance Surveillance (QAS) document), all reagents, procedures and equipment must be developmentally and internally validated by the laboratory as well as pass a stringent quality control before being released for casework. AFMES-AFDIL prior to implementing the current mtDNA whole genome NGS sequencing assay spent over one year forensically validating the procedure to meet accreditation standards, which included the development of seven standard operating procedures, custom Laboratory Information Management System programing to handle case workflow management, and a sole-source contract for the development of a custom analysis application to work on the previously purchased CLC software suite. 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. Validations are costly and AFMES-AFDIL does not possess the resources to carry out a developmental validation in order to change instrumentation or reagents.

8. Efforts to obtain Competition: Not applicable. No effort will be made to solicit offers from any other source as there is currently only one source capable of providing a complete system to include all components, software and licenses that is consistent with what has previously been validated for use by AFMES-AFDIL. An Request for Information (RFI) was posted to FBO for 7 days. Illumina responded and were the only source capable of meeting the customer’s needs. The only other instrument with similar characteristics has a diagnostic software that is based on the open source Umbutu operating system, which DoD has issued guidance as not being authorized for use on DoD NIPR systems. Additionally, the forensic validation and implementation of the Ilumina MiSeq FGX sequencing instrument for use in the identification of deceased and/or missing military individuals was completed in CY2015. If unable to purchase this instrument, AFMES-AFDIL current NGS sample backlog would increase, which would prevent the AFMES and DPAA from achieving mission requirements 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.

a. Effective competition. No effective competition is anticipated for this acquisition.

b. Subcontracting competition. Non Applicable: There is only one source capable of providing a complete instrument and software package.

9. Actions to remove or overcome barriers Competition: None. Because of the nature of the work performed at AFMES-AFDIL, using any other brand or substitute instruments would compromise the validity of future tests. Illumina, Inc. is the manufacturer and the only company that provides this instrument package. The only other company that can provide an NGS instrument with similar characteristics has a diagnostic software that is based on the open source Umbutu operating system, which DoD has issued guidance as not being authorized for use on DoD NIPR systems.

10. Market Survey:

Extensive market research was conducted from 2013-2015. The major players currently in the arena of benchtop next-generation DNA sequencing (NGS) are Illumina and Life Technologies. All vendors of the NGS platforms make quality instruments that have varying strengths and weaknesses. For the purposes of the AFDIL mission, the physical properties (bench-top), technical advantages, and capabilities of Illumina’s NextSeq® 550 Sequencing System is the only system that is consistent with the previously validated Illumina MiSeq® Sequencing System currently utilized at AFMES- AFDIL for samples that do not work with any traditional forensic testing method.

Additionally, Life Technologies instrument has a diagnostic software that is based on the open source Umbutu operating system, which DoD has issued guidance as not being authorized for use on DoD NIPR systems.

11. Interested Sources: A notice of intent to sole source as required by FAR 5.201 will be published on FedBizOps and any proposals received will be considered.

12. Procurement History and any other facts:

Previous Contract or Purchase Order Number:

a. W81XWH-14-P-0606 (software development CLC mtDNA plug-in)

b. W81XWH-15-P-0562 (5 MiSeq FGX)

c. W81XWH-15-P-0548 (CLC software maintenance contract)

Previously competed?

a. September 2014 (software development CLC mtDNA plug-in)

b. September 2015 (5 MiSeqFGX)

c. September 2015 (CLC software maintenance contract)

Previous authority for less than Full & Open Competition:

13. Technical / Requirements Certification: I certify that the support data under my cognizance which are included in this SSJ are accurate and complete to the best of my knowledge and belief.

25 14:24:54 -04'00'

E-Mail Address: Shairose.a.lalani.civ@mail.mil Date:

14. Contracting Officer Certification and Approval: I certify that this justification is accurate and complete to the best of my knowledge and belief. Based upon the facts described herein, I hereby determine that the anticipated price/ cost to the Government will be fair and reasonable, and a determination of price reasonableness will be documented and placed in the contract file.

Typed name

15. I hereby determine this SSJ to be Legally Sufficient.

Typed Name:

mailto:Shairose.a.lalani.civ@mail.mil

Approval

Based on the foregoing justification, I hereby approve the procurement of NextSeq® 550 Sequencing System on an other than full and open competition basis pursuant to the authority of 41 U.S.C. 1901 or 41 U.S.C. 1903, as implemented by FAR subpart 13.106- 1(b)(1) or FAR 13.501(a)(1)(ii), subject to availability of funds, and provided that the services and property herein described have otherwise been authorized for acquisition.

Typed Name