JA OVER SAT RNA Sequencing Duke final.pdf

DEPARTMENT OF VETERANS AFFAIRS

Justification and Approval (J&A) For

Other Than Full and Open Competition (>SAT)

Acquisition Plan Action ID: 36C246-23-AP-1289

1. Contracting Activity:

Department of Veterans Affairs Regional Procurement Office (RPO) – East 1010 Delafield Road. Bldg. 32, Suite 1A111 Pittsburgh, PA 15212 Requesting Activity:

Department of Veterans Affairs VA Durham Health Care System Research Office 508 Fulton Street Durham, NC 27705-3875 2237: 558-23-1-187-0112

2. Nature and/or Description of the Action Being Processed:

The Durham VA Medical Center Research Office intends to negotiate on a sole source basis a new firm fixed price contract with Duke University, its primary academic affiliate, to support the US Department of Veterans Affairs (VA) research office. This requirement is for Duke University Hospital System to provide RNA extraction, Sequencing, and data processing for sequencing of samples pursuant to the continued on-going research and scientific goals currently in process.

3. Description of Supplies/Services Required to Meet the Agency’s Needs:

RNA Sequencing is required from Duke University for operations relating to VA CSP #2028 Epidemiology, Immunology, and Clinical Characteristics of COVID-19 (EPIC3). Whole blood RNA Sequencing on RNA from blood for 800 samples and RNA extractions from whole blood on 1600 samples.

100 Each - NuGEN mRNA-Seq with AnyDeplete Globin up to 8 samples - $108,890.00 1600 Each - RNA extraction (PAXgene Blood Tube) - $82,624.00 4 Each - NovaSeq 6000 S4 gow cell 100bp PE - $60,158.80 Total Price: $251,672.80, Period of Performance: 04/01/2023 – 03/31/2024

4. Statutory Authority Permitting Other than Full and Open Competition:

( ) (1) Only One Responsible Source and No Other Supplies or Services Will Satisfy Agency Requirements per 41 USC §3304(a)(1) as implemented by FAR 6.302-1;

( ) (2) Unusual and Compelling Urgency per 41 USC §3304(a)(2) as implemented by FAR 6.302-2;( )

(3) Industrial Mobilization, Engineering, Developmental or Research Capability or Expert Services per 41 USC §3304(a)(3) as implemented by FAR 6.302-3;

( ) (4) International Agreement per 41 USC §3304(a)(4) as implemented by FAR 6.302-4

(X) (5) Authorized or Required by Statute per 41 USC §3304(a)(5) as implemented by FAR 6.302-5;

( ) (6) National Security per 41 USC §3304(a)(6) as implemented by FAR 6.302-6;

( ) (7) Public Interest per 41 USC §3304(a)(7) as implemented by FAR 6.302-7;

36C246-23-AP-1289 RNA Sequencing Duke University

5. Demonstration that the Contractor’s Unique Qualifications or Nature of the Acquisition Requires the Use of the Authority Cited Above (applicability of authority):

The Duke University provides high-throughput RNA Sequencing analysis of human gene expression necessitates batching expression runs together as much as possible. This is due to differences between discrete runs separated by time which must be accounted for statistically during the signature generation phase of this work. Essentially, in order to appropriately manage the massive scale of the datasets generated by RNA Sequencing analysis, we attempt to minimize any potential impact of ‘batch effect’ by running large numbers of samples simultaneously. This must of course be balanced with the need for generating new data throughout the course of the project period. These experiments are performed through our local Affiliate (Duke University) Sequencing Core facility, with the capability to perform these experiments and handle such complex datasets. Also critical to the success of the funded work is the fact that in order to leverage the existing data to support the completion of the Research, we will be combining new Sequencing Data generated herein with existing Sequencing data from our local and international sites. The Affiliate Sequencing Core has performed all of the prior and future experiments to which we will be comparing our current studies. This continuity is paramount for minimizing further issues relating to ‘batch effect’ and thus for interpreting the data with maximal impact - failure to maintain such continuity could be catastrophic. There is no other vendor that can supply the required sequencing data for these purposes. Due to the precise expertise required by the VA, proximity, and existing affiliate relationship, Duke University is the only vendor practical, without experiencing substantial duplication in costs or delays to VA research. Furthermore, since Duke University is an academic affiliate, the VA is authorized to procure these services pursuant to 38 U.S.C. 8153 described below in number 6.

6. Description of Efforts Made to ensure that offers are solicited from as many potential sources as deemed practicable:

FAR 6.302(a)(2)(i) states, Full and open competition need not be provided when a statue expressly authorized or requires that the acquisition be made through another agency or from a specified source. In accordance with 38 U.S.C. 8153 (a)(3)(A): “If the healthcare resource required is a commercial service, the use of medical equipment or space, or research, and is to be acquired from an institution affiliated with the Department in accordance with section 7302 of this title, including medical practice groups and other entities associated with affiliated institutions, blood banks, organ banks, or research centers, the Secretary may make arrangements for acquisition of the resource without regard to any law or regulation (including any Executive order, circular, or other administrative policy) that would otherwise require the use of competitive procedure for acquiring the resource."

7. Determination by the CO that the Anticipated Cost to the Government will be Fair and

Reasonable:

Duke University is a not-for- profit organization affiliated with the VA. Previous contracts have demonstrated that the anticipated cost to the government will be fair and reasonable. The established pricing is published within the University website and a quote was received for these services with the exact amounts the VA will pay. The Contracting Officer anticipates the price noted in #3 above to be fair and reasonable; however, price negotiations may be conducted if the CO determines this is necessary.

8. Description of the Market Research Conducted and the Results, or a Statement of the Reasons Market Research Was Not Conducted:

A search was conducted in the VA’s VIP database using NAICS code 541720, PSC code Q301, and keyword “Sequencing”, which resulted in 0 SDVOSB’s and no VOSB available to meet this requirement. A search was also conducted in the Small Business Administration Dynamic

Small Business Search (SBA DSBS) using NAICS code 541720 with keyword “sequencing”, which resulted in one small businesses, Stephanie C Martin available for this requirement. Although, they listed 541720 as a NAICS code, but their capability statement shows they are a Logistics Consulting Service.

The RNA sequencing is continuous and will be combining new Sequencing Data generated herein with existing Sequencing data research. The Affiliate Sequencing Core has performed all of the prior and future experiments to which we will be comparing our current studies. This continuity is paramount for minimizing further issues relating to ‘batch effect’ and thus for interpreting the data with maximal impact - failure to maintain such continuity could be catastrophic. To that end, there is no other vendor that can supply the required services for these purposes. There are no SDVOSBs/VOSBs or any small businesses that can meet the requirements for this procurement.

Based on the sole source affiliate U.S. Code 8153, I conclude that we move forward with the sole source. 38 U.S.C. 8153 allows for sole source awards related to research with VA academic affiliates.

In this case, Duke University is the primary academic affiliate for the VA Durham Health Care Systems research department.

9. Any Other Facts Supporting the Use of Other than Full and Open Competition:

The mission of the VA is to discover knowledge and create innovation that advances health care for our Veterans and the nation. VHA is the country’s largest integrated health care system and as such, it embraces close ties to its academic affiliates by partnering on common research interests and leveraging resources. The Durham VA Medical Center and Duke University are one of many examples of this strategic academic affiliate partnership recognized by the Secretary of the

VA.

10. Listing of Sources that Expressed, in Writing, an Interest in the Acquisition:

Duke GCB Sequencing and Genomic Technologies Shared Resource 701 W. Main St. (Chesterfield Building), Ste. 320 Durham, NC 27701

(919) 684-3359 [voice] | (919) 681-8973 [fax] | sequencing@duke.edu Lab phone: 919-613-7460 POC: Devjanee Swain Lenz (devjanee.swain.lenz@duke.edu)

11. A Statement of the Actions, if any, the Agency May Take to Remove or Overcome any Barriers to

Competition before Making subsequent acquisitions for the supplies or services required:

None, there are no other potential sources that can meet the specified requirement due to the highly specialized research services required for this procurement.

12. Requirements Certification: I certify that the requirement outlined in this justification is a Bona Fide Need of the Department of Veterans Affairs and that the supporting data under my cognizance, which are included in the justification, are accurate and complete to the best of my knowledge and belief.

Darin Dowdy Date R&D Budget Supervisor Durham VA Medical Center

DARIN D

DOWDY 131153

Digitally signed by

DARIN D DOWDY 131153

Date: 2023.03.02 15:11:21 -05'00' 03/02/2023

13. Approvals in accordance with the VHAPM Part 806.3 OFOC SOP:

a. Contracting Officer or Designee’s Certification (required): I certify that the foregoing justification is accurate and complete to the best of my knowledge and belief.

Ann Marie Stewart Date Contracting Officer Regional Procurement Office-East R&D

b. One Level Above the Contracting Officer (Required over SAT but not exceeding $750K): I certify the justification meets requirements for other than full and open competition.

Seth Custer Date Division Chief | VHA R&D Contracting Division Regional Procurement Office East

03/03/2023

ANN MARIE

STEWART

Digitally signed by ANN

MARIE STEWART

Date: 2023.03.03 07:11:19 -05'00'

VHALEBCUSTES

Typewritten Text 3/8/2023