IDIQ JOFOC -Final.pdf

JUSTIFICATION FOR OTHER THAN FULL AND OPEN COMPETITION

Contracting Activity U.S. Department of Agriculture, Agricultural Research Service Southeast Area, Area Administrative Office 2775 F&B Road College Station, TX 77845

260-9475 Nicholas.Langley@usda.gov

Nature/Description of Action Award a USDA wide Indefinite Quantity/Indefinite Delivery (IDIQ) contract for the purchase of Sequel- Sequel II product family equipment, reagents and services from Pacific Biosciences of California, Inc.

Description of Supplies/Services The IDIQ will include commercial pricelists for products and services related to the Sequel-Sequel II product family instruments, reagents, and services listed in the PacBio Requirements Document. Due to the expiration of the previous Blanket Purchase Agreement (BPA) presently each equipment, reagent and service requirements necessitates a Sole Source Justification and associated approvals/publication. The IDIQ will reduce the annual number of SSJs significantly and strengthen ARS’ and USDA’s Category Management. The actual value will fluctuate from year to year based on the number of Delivery/Task orders and their values. The annual ceiling will be $2.7 with an aggregate ceiling of $13.5M.

Statutory Authority 41 U.S.C. 3304(a)(1) as implemented by FAR 6.302-1, titled “Only one responsible source and no other supplies or services will satisfy agency requirements.” This procurement is also in accordance with FAR 13.5, Simplified Procedures for certain commercial items, In accordance with 41.U.S.C. 1901.

Demonstration of Contractor’s Unique Qualifications and/or Product’s Unique Features Pacific Biosciences is the sole manufacturer distributor, and servicer of the Pacific Biosciences Sequel- Sequel II Systems, and their associated library preparation, polymerase, sequencing reagents, software and related services. The systems are proprietary and protected by numerous patents owned by Pacific Biosciences.

Pacific Biosciences Sequel-Sequel II Systems sequences individual DNA molecules using a proprietary sequencing-by-synthesis approach. The instrument exclusively processes SMRT Cells and reagents, for sequencing with single-molecule resolution. The Sequel-Sequel II Systems are covered by numerous patents owned by or licensed to Pacific Biosciences. Pacific Biosciences is the sole manufacturer of the Sequel- Sequel II Systems and associated library preparation, polymerase, sequencing reagents and service.

The systems are unique in the following respects, critical to genome assembly and it is mission-critical for the USDA to have the most accurate and efficient tools available to them. Key features provided exclusively by the Pacific Biosciences Sequencing solutions include:

Unique template preparation of generating SMRTbells, allowing for repeated sequencing of the forward and reverse strand of individual DNA molecules.

Circularized sequencing of templates up to 20,000 (Sequel) and 25,000 (Sequel II) bases allow for multiple sequence passes of a single molecule, increasing the base accuracy of each molecule to >99%

(Q20) accuracy, thus generating a HiFi read. HiFi datasets have a median accuracy of >99.9% (Q30) with up to 500,000 (Sequel) and 4 million (Sequel II) reads depending upon the insert length

Unique kinetic information provides insight to base modifications such as DNA methylation and products of DNA damage using proprietary algorithms

High-quality genome assembly of organisms or regions regardless of genome size, repeat content or sequence complexity, including highly repetitive regions using a single data set source

Software pipelines specifically for analyzing HiFi read data provide accurate primary and secondary analysis

Low (Sequel and Sequel II) and Ultra-Low (Sequel II) DNA input protocols for high-quality sequencing of small organisms and samples with limited input DNA

Low compute, data storage and data transfer requirements for long-read sequencing technologies due to the compact nature of the HiFi sequence read format (Sequel II)

Sequencing time per SMRT Cell is adjustable per application needs, typically ranging from 30 minutes to 20 hours (Sequel) or 30 hours (Sequel II)

Need for proprietary PacBio Standard Services As highly advanced DNA sequencers, with robotics, high capacity informatics with specialized software, extremely sensitive detection equipment and micro liquid delivery systems, they require constant, specialized maintenance. Service contracts include software updates, offsite monitoring of the system, and onsite visits within a short time frame.

Technical assistance support is also provided. As the manufacturers, Pacific Biosciences is the only vendor that can provide the necessary services for the sequencers.

Any other service provider working on the equipment would void its warranty.

Additional services may include repair & maintenance to Sequel-Sequel II equipment with OEM parts by the Authorized PacBio Servicer.

Need for proprietary reagents (See Reagent Kits and SMRT Cells):

Due to the highly specialized nature of the experiments being conducted by USDA, only Pacific

Biosciences reagents can be used on Pacific Biosciences equipment. The reagents and related consumable supplies are patent-protected or license protected formulas, owned by Pacific Biosciences.

The Sequel-Sequel II instruments require Pacific Biosciences cells to operate properly. These disposable parts are manufactured and distributed solely by Pacific Biosciences.

Any other reagent product used on the equipment would void its warranty.

There are no resellers of these products.

In summary, the Pacific Biosciences reagents and equipment are not interchangeable with other systems.

The placement of any other sequencing reagent on the PacBio instruments would void any warranty or service issued under a PacBio maintenance agreement.

Continuation of existing work utilizing Pacific Biosciences equipment is required for scientific validity:

A significant number of USDA scientists are fluent in Pacific Biosciences products and equipment.

Several laboratories have invested a significant funding to equip and provide reagents for their systems:

it is important to maintain system consistency as well as continuity of research that allows for comparisons across years and projects due to the use of the same equipment, reagents, etc..

Beta.SAM.gov Announcement/Potential Sources In an effort to locate additional sources a sources sought announcement was advertised in the Government Point of Entry (GPE) beta.SAM.gov from December 14, 2020 – December 23, 2020. No responses from vendors other than Pacific Biosciences of California, the proposed sole source, were returned. In accordance with FAR publication requirements, the approved JOFOC will be posted to the GPE as a pre-solicitation notice.

Determination of Fair and Reasonable Cost Pricing will be evaluated according to “prices at which the same of similar items have previously been sold”, FAR 15.404-1(b)(1) and (2)(ii) “comparing the proposed prices to historical –prices paid”.

Pacific Biosciences will update their IDIQ with pricing and new products as needed via a modification to the IDIQ. Price reasonableness will be compared by utilizing costs paid for similar types of equipment and services on legacy contracts (including the expired BPA) for which pricing was already affirmed as fair and reasonable. Service contracts typically run between 10-20% of machine costs within the scientific equipment community and the prices of such services offered by Pacific Biosciences fall within that range.

Market Survey Sources a sources sought announcement was advertised in the Government Point of Entry (GPE) beta.SAM.gov from December 14, 2020 – December 23, 2020. No responses from vendors other than Pacific Biosciences of California, the proposed sole source, were returned

Additional Support None

Other Interested Sources No written responses from sources other than Pacific Biosciences of California, the proposed sole source, were received in response to the sources sought announcement.

Actions Taken to Remove Barriers to Future Competition USDA scientists routinely monitor emerging technology, considering new technology to support the research. When technology becomes available to satisfy research requirements, it is considered. The scientists continue to inquire, test and evaluate competitive manufactures’ equipment.

12. Certifications Requirements/Program Office:

I certify that facts and representations under my cognizance included in this justification form are complete and accurate basis for the justification.

Signature Date

Name Title Phone

Contracting Officer:

I certify that this justification is accurate and complete to the best of my knowledge and belief.

Signature Date

Name Title Phone

Chief of the Contracting Office:

I certify that this justification is accurate and complete to the best of my knowledge and belief.

Signature Date

Name Title Phone

Mission Area Senior Contracting Official (MASCO):

I certify that this justification is accurate and complete to the best of my knowledge and belief.

Signature Date

Name Title Phone

REVIEW/APPROVALS:

If approval is required at a higher level than that of the REE Acquisition Ombudsman, the Acquisition Ombudsman must still review the document, and a signature block should be included to indicate this.

Dr. Brian Scheffler Research Leader GBRU (662) 686-5454

Nicholas D. Langley Contract Specialist (979) 260-9475

Cindy J. Cose Section Head (979) 260-9447

1/25/2021BRIAN SCHEFFLER

Digitally signed by BRIAN

SCHEFFLER

Date: 2021.01.25 14:16:05 -06'00'

January 26, 2021

MASCOMichael L. Barnes

Digitally signed by NICHOLAS

LANGLEY

Date: 2021.01.26 16:37:31 -06'00'

Digitally signed by LUCINDA COSE Date: 2021.01.28 17:49:16 -06'00'

REE Acquisition Ombudsman:

I certify that this justification is accurate and complete to the best of my knowledge and belief.

Signature Date

Name Title Phone

Mission Area Senior Contracting Official (MASCO):

I certify that this justification is accurate and complete to the best of my knowledge and belief.

Signature Date

Name Title Phone

REVIEW/APPROVALS:

If approval is required at a higher level than that of the REE Acquisition Ombudsman, the Acquisition Ombudsman must still review the document, and a signature block should be included to indicate this.

KIRSTEN

PILKERTON

Digitally signed by KIRSTEN

PILKERTON

Date: 2021.02.12 15:58:31 -05'00'

Kirsten Pilkerton REE Acquisition Ombudsman & Deputy Director, Acquisition and Property Division

02/12/2021

MICHAEL BARNES

Digitally signed by MICHAEL

BARNES

Date: 2021.02.12 16:04:37 -05'00'

MASCO &

Director, Acquisition and Property DivisionMichael L. Barnes