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FBO DAILY - FEDBIZOPPS ISSUE OF SEPTEMBER 13, 2019 FBO #6501
DOCUMENT

66 -- Illumina NextSeq 550 System (Grant Funding) - Justification and Approval (J&A)

Notice Date

9/11/2019
 

Notice Type

Justification and Approval (J&A)
 

NAICS

334516 — Analytical Laboratory Instrument Manufacturing
 

Contracting Office

Department of Veterans Affairs;Network Contracting Office 2;James J. Peters VA Medical Center;130 West Kingsbridge Road;Bronx NY 10468-3904
 

ZIP Code

10468-3904
 

Archive Date

9/18/2019
 

Point of Contact

Aleta Jennette
 

E-Mail Address

737-4400
 

Small Business Set-Aside

N/A
 

Award Number

36C24219P1568
 

Award Date

9/4/2019
 

Description

Page 1 of 5 OFOC SOP Revision 08 Original Date: 03/22/11 Revision 08 Date: 04/18/2018 DEPARTMENT OF VETERANS AFFAIRS Justification and Approval (J&A) For Other Than Full and Open Competition (>SAT) Acquisition Plan Action ID: 36C24219-AP-3114 Contracting Activity: Department of Veterans Affairs, VISN 2, James J. Peters VA Medical Center 130 West Kingsbridge Road, Bronx, New York 10468. Organizational Acti vi ty;VA Medical Center Northport Campus 79 Middleville Road, Northport, New York 11768 seeks to purchase lllumina Nextseq 550 Sequencing system through 2237# 632-19-3-9136-0850 on a noncompetitive acquisition. Nature and/or Description of the Action Being Processed: The proposed action is to purchase as a sole source, firm-fixed priced award lllumina Nextseq 550 sequencing system for Northport Research Department with approved VA ORD ShEEP grant funding. The required Nextseq ® 550 sequecing system is needed to increase sample throughput of the currently forensically validated NGS DNA casework and family reference processing methods used to support Northport Research department. The nextseq system is a next generation sequencing system specifically designed for high-through-put sequencing and microarray scanning in an integrated benchtop unit. It's fast DNA- analysis workflow allows for the rapid sequencing exomes, targeted panels in a single run, and has the capability to switching to lower-thorough-put sequencing as needed. The unit has the flexibility to run high quality degraded samples and utilize both 75 cycle, 150 cycle and 300 cycle sequencing runs. This allows seamless integration of the currently forensically validated mtDNA whole genome sequencing methods for highly degraded casework samples and family reference specimen samples. FAR13.5 Simplified Procedures for Certain Commercial Items: This procurement is for the purchase of the lllumina NetSeq 550 sequencing system in accordance with FAR 13.5 Simplified Procedures for Certain Commercial Items and specifically FAR 13.501 Special Documentation Requirements, where acquisitions conducted under Simplified Acquisition Procedures are exempt from the requirements of FAR Part 6, but still require a justification using the format of FAR 6.303-2. Description of Supplies/Services Required to Meet the Agency's Needs: Northport Research department seeks to purchase an lllumina high throughput sequencing instrument, the NextSeq 550. This instrument will serve for sequencing analysis of the RNA and DNA libraries produced by the participating investigators using the Single Cell Core Facility that we will establish at the Northport VAMC research service, and of which this instrument will be one of the pillars. The system utilized dedicated library preparation kits, customized instrument control software, and an analytical software package to support reliable analysis of both routine and challenging (degraded) forensic samples. The system offers scalability (20-120 Gb) in a single run to Original Date: 03/22/11 Revision 08 Date: 04/18/2018 support a broad range of applications and study sizes, sequencing runs include on-board cluster generation complete In 12-30 hours, fully automated on-board cluster generation enables prepped libraries to be loaded directly onto the instrument, high accuracy using lllumina sequencing by Synthesis (SBS), proven SBS chemistry with single-base extension enables accurate sequencing of homopolymers, fully automated paired-end sequencing and automated beadchip array scanning and image file generation. The following technical specifications will meet the agency's need: ITEM#SY-415-1002-Nextseq 550 Sequencing System (1) EA ITEM#20024463-Nextseq 550 Reagent Replacement Add-on (1) EA ITEM#20024563-Nextseq 550Dx Bronze Support Plan (1) EA ITEM#20024906-Nextseq 500/ 550 High Output kit v2.5 (75 cycles) (3) EA ITEM#20024907-Nextseq 50 0/550 High Output kit v2.5 (150 cycles) (11) EA ITEM#20024908-Nextseq 50 0/550 High Output kit v2.5 (300 cycles) (1) EA ITEM#20024904-Nextseq 500/550 Mid Output kit v2.5 (150 cycles) (21) EA ITEM#20024905-Nextseq 500/ 550 Mid Output kit v2.5 (300 cycles) (1) EA ITEM#20020594-Truseq ® Stranded mRNA Library Prep (48 samples) (4) EA ITEM#20020596-Truseq ®Stranded Total RNA Library Prep Human/Mouse/Rat (48 Samples) (1) EA ITEM#20020598-Truseq ®Stranded Total RNA Library Prep Gold (48 Samples) (1) EA ITEM#20020492-TruSeq RNA Single set A (12 Indexes, 48 Samples) (3) EA ITEM#20020493-TruSeq RNA Single Indexes Set B (12 Indexes, 48 Samples) (3) EA ITEM#15027865- NX#TDE1,Tagment DNA ENZYME, 24 RXN finish Reag (5) EA The estimated amount for procurement: Statutory Authority Permitting Other than Full and Open Competition: Only lllumina Netseq 550 sequencing system will satisfy the agency's need at this time. (x ) (1) Only One Responsible Source and No Other Supplies or Services Will Satisfy Agency Requirements per FAR 6.302-1; ( ) (2) Unusual and Compelling Urgency per FAR 6.302-2; ( ) (3) Industrial Mobilization, Engineering, Developmental or Research Capability or Expert Services per FAR 6.302-3; ( ) (4) International Agreement per FAR 6.302-4 ( ) (5) Authorized or Required by Statute FAR 6.302-5; ( ) (6) National Security per FAR 6.302-6; ( ) (7) Public Interest per FAR 6.302-7; FAR13.5 Simplified Procedures for Certain Commercial Items: The Government intends to solicit under the authority of FAR 13.5 Simplified Procedures for Commerical Items and is restricting competition to Brand name only (lllumina Netseq ) as allowable under FAR 11.105-ltems Peculiar to One Manufacturer. Demonstration that the Contractor's Unique Qualifications or Nature of the Acquisition Requires the Use of the Authority Cited Above (applicability of authority lllumina is the world's leader in sequencing chemistries and instruments. They provide a large array of DNA sequencing instruments optimized for every possible application and sample volume. It is OFOC SOP Revision 08 Page 2 of 5 generally acknowledged that the lllumina technology is the gold standard for DNA sequencing and no other supplier can provide instruments with matching performance in every application. The lllumina NextSeq 550 System is the only desktop next-generation sequencing (NGS) system capable of sequencing a 3ox human genome in a single run. Two flow cell formats and multiple reagent configurations enable 20-120 Gb of data output in a single run, providing flexibility across the broadest range of applications and study sizes. Its simple workflow and quick run times enable fast desktop sequencing of exomes, transcriptomes, and whole genomes. Its high throughput is ideally suited to single cell sequencing applications. The NextSeq 550 System is an integrated platform that uses massively parallel sequencing technology for genetic analysis and functional genomics. Prepared libraries are loaded directly on the system. Integrated cluster generation provides automated clonal amplification of single molecules randomly distributed on a glass surface. Resulting DNA clusters are sequenced on the NextSeq 550 System using the lllumina sequencing by synthesis (SBS) method with patented reversible terminator chemistry. The system consists of the NextSeq 550 sequencer, which incorporates a suite of dedicated flow cell and reagent configurations to generate up to 400 million clusters passing filter (up to 120 Gb) in the High Output configuration and up to 130 million clusters passing filter (up to 40 Gb) in the Mid Output configuration. The system also includes an option to integrate with the BaseSpace genomics computing environment, an easy, secure, and cost-effective way to store, analyze, and share genomic data, available as either a cloud or an onsite deployment (BaseSpace Onsite system). In addition, the NextSeq 550 System is the only desktop system capable of both sequencing and BeadChip array scanning, transitioning seamlessly between the 2 technologies. For scanning, prepared BeadChips are loaded onto the array adapter and placed in the same position as a flow cell. After scanning, an image file is generated for off-instrument analysis. Currently, the NextSeq 550 System supports. The NextSeq 550 System offers: Scalability (20-120 Gb) in a single run to support a broad range of applications and study sizes Sequencing runs, including on-board cluster generation, complete in 12-30 hours Fully automated on-board cluster generation enables prepped libraries to be loaded directly onto the instrument High accuracy using lllumina Sequencing by synthesis (SBS) Proven SBS chemistry with single-base extension enables accurate sequencing of homopolymers Fully automated paired-end sequencing Automated BeadChip array scanning and image file generation Approximately 7000 peer-reviewed publications have been published using lllumina SBS sequence data, and more than 24,000 peer-reviewed publications have been published using lllumina array technology. No other instrument of equivalent output can offer the same level of performance, accuracy and reliability. OFOC SOP Revision 08 Page 3 of s OFOC SOP Revision 08 Original Date: 03/22/11 Revision 08 Date: 04/18/2018 Page 4 of 5 Accordingly, lllumina INC. is the only firm capable of providing the equipment described in Section Ill above without the Veteran's Health Administration experiencing unacceptable delays in fulfilling its requirements Description of Efforts Made to ensure that offers are solicited from as many potential sources as deemed practicable: Review of current scientific publications (PubMed, Google), technical bulletins, product catalogs, online technical articles and review articles and a product vision in the laboratory of a user. Also, attendance at Cold Spring Harbor Laboratories meetings where new developments in single cell sequencing techniques are regularly presented and discussed. Among the sequencers models offered by lllumina, we concluded that the NextSeq 550 was the most suitable for Northport VA's needs because of its combination of high sequencing depth and application range. No other desktop sequencer has adequate capacity to perform single cell sequencing, due the large number of reads required for complete analysis of large numbers of individual cells. At the same time, it has mid ­ throughput options that allow economical analysis of smaller scale experiments. It is, by a considerable margin, the most economical of the desktop sequencers in terms of cost per million reads. We also consulted known experts in the field of Genomics for input in this purchase and have determined that the lllumina NextSeq 550 is the only equipment capable of supplying the Veteran's Health Administration this standard. Determination by the CO that the Anticipated Cost to the Government will be Fair and Reasonable: This equipment was purchased using a VA ORD ShEEP grant. This is not subject to competition, but in determining the price for the grant the facility did research to find the cheapest system available. Description of the Market Research Conducted and the Results, or a Statement of the Reasons Market Research Was Not Conducted: See Section VI above. Any Other Facts Supporting the Use of Other than Full and Open Competition: N/A Listing of Sources that Expressed, in Writing, an Interest in the Acquisition: N/A 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: No barriers to overcone since this order is not subject to competitive range. 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, OFOC SOP Revision 08 Original Date: 03/22/11 Revision 08 Date: 04/18/2018 Page 5 of 5 which are included in the justification, are accurate and complete to the best of my knowledge and belief. Date Approvals in accordance with the VHAPM Part 806.3 OFOC SOP: 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. Date One Level Above the Contracting Officer (Required over SAT but not exceeding $700K): I certify the justification meets requirements for other than full and open competition. Date
 

Web Link

FBO.gov Permalink
(https://www.fbo.gov/notices/3ebc8bf29f968931758858e578ddc6a1)
 

Document(s)

Justification and Approval (J&A)
 

File Name: 36C24219P1568 36C24219P1568_1.docx (https://www.vendorportal.ecms.va.gov/FBODocumentServer/DocumentServer.aspx?DocumentId=5150292&FileName=-17973.docx)

Link: https://www.vendorportal.ecms.va.gov/FBODocumentServer/DocumentServer.aspx?DocumentId=5150292&FileName=-17973.docx

 

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Record

SN05439933-W 20190913/190912053424-3ebc8bf29f968931758858e578ddc6a1 (fbodaily.com)
 

Source

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