Justification consolidated - redacted.pdf

Justification for Other than Full and Open Competition at or Below the Simplified Acquisition Threshold

Project Title: Pacific Biosciences SMRT Sequencing for High-Throughput, Single-Genome Amplification and Sequencing (HT-SGS) of HIV, SARS-CoV-2, influenza, and other viruses

I . Identification of the agency and contracting activity

II. Description of the project, and supplies or services required to meet the agency’s needs (including the estimated value)

A. Type of action. Check the appropriate box:

☐ New requirement

☒ Follow-on

• Name of the previous contractor(s): ________________________________

• Sequence number(s), if available: ____________________________________

• Was the initial and any subsequent awards competed? ☐ Yes ☐ No

B. AMBIS Sequence number for this requirement:

C. Total estimated dollar value of the requirement (including options, if applicable):

D. Period of performance, inclusive of options:

The Vaccine Research Center Virus Persistence and Dynamics Section (VPDS) works to elucidate mechanisms of virus persistence in vivo, with the aim of informing development of vaccines, immune-based therapies, and other medical countermeasures for virus-mediated diseases. A central mechanism of virus persistence is mutational variation, which can lead to antigenic variation and escape from naturally-acquired, vaccine-elicited, or passively-administered immunity. VPDS has developed technology termed high-throughput, single-genome amplification and sequencing (HT- SGS), which uses long-read deep sequencing to describe genetic variation among virus genomes within individual samples. Applied to longitudinal samples across multiple people, experimental animals, or other infection models, HT- SGS can reveal important patterns of virus mutational variation and evolution. The Pacific Bioscience SMRT sequencing platform is the only commercially-available technology capable of generating multi-kilobase single-molecular reads with circular consensus sequencing correction. Thus, no other available technology can generate the data required in the HT-SGS analysis process. The requested supplies are proprietary to Pacific Biosciences and are not available from other manufacturers.

III. Identification of the statutory authority permitting other than full and open competition (SELECT ONE) 41 USC 253(c)(1) a n d F A R P a r t 6 . 3 0 2 - 1 : Only one responsible source

☐ 41 USC 501 a n d F A R P a r t 8 . 4 0 5 - 6 : Federal Supply Schedule (FSS), limited competition Important Note: The statutory authorities listed below will rarely ever be used in NIH. Before selecting one of these authorities, please ensure that you have read and understood the citation and discussed it with the cognizant Contracting Officer.

☐ 41 USC 253(c)(2) a n d F A R P a r t 6 . 3 0 2 - 2 : Unusual & compelling urgency

☐ 41 USC 253(c)(3) a n d F A R P a r t 6 . 3 0 2 - 3 : Industrial mobilization; or engineering, developmental, or research capability; or expert services

☐ 41 USC 253(c)(4) a n d F A R P a r t 6 . 3 0 2 - 4 : International agreement

☐ 41 USC 253(c)(5) a n d F A R P a r t 6 . 3 0 2 - 5 : Authorized or required by statute

☐ 41 USC 253(c)(6) a n d F A R P a r t 6 . 3 0 2 - 6 : National security

☐ 41 USC 253(c)(7) a n d F A R P a r t 6 . 3 0 2 - 7 : Public interest

IV. Demonstration that the proposed contractor(s) unique qualifications or the nature of the acquisition requires use of the authority cited.

A. Name and address of the proposed contractor(s): Pacific Biosciences B. Describe why only the requested supply/service will meet the government’s needs: The HT-SGS process requires highly accurate single-molecule sequence data, with a read length of multiple kilobases. Only two commercial technologies are capable of generating single-molecule sequences of this length. The other, Oxford Nanopore, lacks circular consensus sequencing capability and thus has an excessively high error rate for the government’s needs in this case. Pacific Biosciences is the only manufacturer of the supplies that are required to run their sequencing platform.

C. Describe why only the proposed contractor is capable of providing the requested supply/service: Pacific Biosciences is the only manufacturer of the needed supplies and is the only vendor from which they can be purchased.

V . Determination by the Contracting Officer that the anticipated cost/price to the Government will be fair and reasonable.

The price is determined to be fair and reasonable based on (provide a narrative describing how the determination was made and the rational for the determination):

VI. Certification

This is to certify that the justification for the proposed acquisition has been reviewed and that to the best of my knowledge and belief the information and/or data provided to support my request (for the requestor) and approval (for the CO) of is accurate and complete.

Additional Justification for Brand Name

There are technical requirements that are unique to this equipment that justify its Brand Name limitations. Pacific Bioscience SMRT sequencing platform’s is the only commercially-available technology capable of generating multi-kilobase single-molecular reads with circular consensus sequencing correction. No other available technology can generate the data required in the HT-SGS analysis process. More specifically, only 2 commercial technologies are capable of generating single molecule sequences of this length: PacBio technology and Oxford Nanopore technology. The entire foundation of Program’s research is that their sequencing is highly accurate, which allows biological conclusions to be drawn that require high accuracy. Program would not be able to do their experiments using Oxford Nanopore tech due to its lower accuracy. For example, Program requires 99.99% single‐molecule sequence accuracy which can be achieved with PacBio tech. This cannot be achieved with Oxford Nanopore’s tech because its accuracy is down to around 90% accuracy.

Furthermore, compatibility is another requirement. Program’s laboratory currently uses PacBio equipment, including this same assays, reagents, and sequencing items that are designed for compatibility with other PacBio equipment. To use equipment from another manufacturer would 1) jeopardize the compatibility of the existing reagents and assays, and 2) threaten Program’s research results that have already been done with PacBio equipment due to inconsistent methods and parameters from using a different branded items & equipment. Specifically, these reagents are required based on intended experimental design, compatibility with current lab equipment/assays, and the proven ability of the product to produce consistent and reliable data. Use of alternate products could negatively impact the manner in which samples are processed and analyzed. Additionally, use of a different product from the one requested may introduce unacceptable variables during research trials. To have successful research results, methods and parameters must be consistent. Furthermore, these reagents & kits will be utilized to analyze, store, and manipulate samples. Some of these samples are rare and difficult to replace/obtain. Utilizing any alternative items that have not been repeatedly tested and verified for compatibility by the lab may jeopardize these rare samples and/or cause our research/data to be corrupted/destroyed. Thus, the changes in research variables caused by using a different product would involve unacceptably high risks to the research being conducted.