SAM SOLE SOURCE JUSTIFICATION 2024-87888 Redacted.pdf

JUSTIFICATION FOR SOLE SOURCE PROCUREMENT (OPEN MARKET OR GSA)

UNDER $250,000

Sole source acquisitions may be used on a limited basis and only when the Contracting Officer’s Representative (COR)/Program Official has provided sufficient justification and the Contracting Officer has determined that the circumstances warrant such action. The content for a justification must contain detailed facts and rationale to justify the sole source acquisition. Soliciting from a single source must be done in accordance with FAR 13.106-1(b) or 8.405-6. At a minimum, the following information must be included:

Identification of Program Office, Contracting Activity, and Proposed Requirement, Justification and Program Office Certification:

A. Program Office:

Chronic Viral Diseases branch (CVDB) Division of High Consequence Pathogens and Pathology (DHCPP) National Center for Emerging and Zoonotic Infectious Diseases (NCEZID) Roybal Campus Building 23. Room 4-430, H23-4 Centers for Disease Control and Prevention Atlanta, GA 30329

B. Contracting Activity:

Centers for Disease Control and Prevention Office of Financial Resources Acquisition Branch II

C. Identification of Requirement:

1. Nature of Action to be Approved by Contracting Officer:

a. Sole source acquisition of: Georgia Tech Center for Bioinformatics & Computational Genomics, Georgia Tech Research Corporation for the custom analysis of Human Papillomavirus (HPV) sequence data generated by target enrichment and next-generation sequencing technologies at CVDB

b. Procurement Request (PR) Number (if available): Click here to enter text.

2. Proposed Vendor and Estimated Procurement Amount (if available):

a. Proposed Vendor: Georgia Tech Research

b. Estimated Procurement Amount: ___________

3. Is the requirement on GSA Schedule? ☐ Yes ☒ No

If yes, provide schedule number: Click here to enter text.

Rev. 5/14/19

D. Justification:

1. The justification for this non-competitive action is:

CVDB has on-going project titled “baited Single Molecule Sequencing of HPV genotyping test (baited HPV-SMS genotyping test)” to explore the feasibility of determining HPV genotypes using target enrichment and next generation sequencing technologies (NGS) for all known HPV types. This project needs scientific personnel with expertise in both the laboratory for generating the massive sequence data and for its analyses using the state of the knowledge and expertise in computational science and bioinformatics fields. CVDB is expanding its application of NGS, and generated HPV whole genome sequence data using several sets of samples, but CVDB has no scientific personnel with expertise in bioinformatics for the custom analysis of the currently generated sequence data to enable HPV type and variant determination and assessment of the physical status (integration of HPV genome into human genome) of the dominant HPV types in each clinical sample. Georgia Tech Research Corporation has unique expertise in genome analysis and genome annotation. It has also developed the proprietary software tools used in pioneering genome projects. Georgia Tech Center for Bioinformatics & Computational Genomics has been able to solve several long-standing programs, particularly the one of automatic gene prediction in eukaryotic genomes by come-up with “unique in the filed” automatic software tools. It also has unique “know-how” or expertise in developing custom built pipelines for genome annotation where their original algorithms play a central role. Based on these unique experience, Ga Tech Center for Bioinformatics and Computational Genomics has been participating with CDC-DHCPP/CVDB’s HPV whole genome sequencing project through CDC contract # 200-2017-M-95197 starting from 09/24/2016. During these contract periods, Ga Tech collaborated with CVDB on developing algorithm, and development and implementation of softwares for automated calling of HPV types, and determination of variant and integration status of HPV using data generated employing an enriched HPV whole genome sequencing (eWGS) developed by CVDB. CVDB improved the eWGS technology recently for successful production of sequencing data from formalin-fixed-paraffin embedded tissues (FFPE).

HPV detection and typing methods rely on genomic assays that are increasingly based on NGS.

HPV typing information continues to be critical to demonstrate the impact of HPV vaccination and guide public health decisions. Monitoring type-specific HPV prevalence in the general population and in HPV-associated cancers and pre-cancers is required to verify HPV vaccine impact and monitor for potential HPV type replacement. Increased laboratory efficiency through enhanced NGS methods will shorten the time to results and reduce costs. This in turn will allow expanded sentinel surveillance for HPV testing-associated cancers and pre-cancers. Currently national surveillance of HPV in general US population is conducted through NHANES and sentinel surveillance of HPV in cervical cancer and precancer is conducted through HPV-IMPACT. NGS assays are being introduced – TypeSeq (sequences amplicons of 51 types) and enriched whole genome sequencing (eWGS) detecting all HPVs including types not previously identified. Automated and validated procedures developed for HPV will serve as a blueprint for other pathogens.

This current contract will end on 9/23/2024, and CDC DHCPP/CVDB needs to continue the bioinformatics services from this contractor for another year to expand the application of pipeline for determination of variant and integration status, in addition to genotyping HPV. The already conducted research opened new horizons in terms of additional avenues of research that would make the outcomes more precise with respect to changing technology and new volumes of accumulated data on HPV whole genome sequencing at CDC. As part of the statement of work (SOW) during the renewal period of consultancy, the contractor will continue to provide expertise and direction to develop work-flows, and novel algorithms to automate determination of HPV types, variants and its physical status (integration of HPV genome into human genome) using whole genome sequence data from multiple sources including challenging materials like FFPE; generating multiple levels of information from the sequence data which is not dependent on the library preparation or sequencing platforms (HiSeq vs MiSeq vs Nextseq 2000).

Workflows and algorithm development will take into consideration of evaluating multiple parts of the whole genome and single and multiple infections of HPV types in a clinical sample. A main thrust and outcome of this consultancy will be to continue development of the customized bioinformatics pipeline that automates determination of genotype, variant and integration status of HPV in each sample. We expect several bioinformatics challenges in developing reliable algorithms for HPV genotyping, variant assignment, and determination of integration status in a single pipeline. However, CVDB expects these challenges within the expertise of the contractor and thus their continued participation as a consultant through the GA Tech Research Corporation is highly recommended to make continued progress on this project.

☒ In accordance with FAR 13.106-1(b)(1), “only one source [is] reasonably available” which states that, “For purchases not exceeding the simplified acquisition threshold. (i) Contracting officers may solicit from one source if the contracting officer determines that the circumstances of the contract action deem only one source reasonably available (e.g., urgency, exclusive licensing agreements, brand-name or industrial mobilization). (ii) Where a single source is identified to provide a portion of a purchase because that portion of the purchase specifies a particular brand-name item, the documentation in paragraph (b)(1)(i) of this section only applies to the portion of the purchase requiring brand-name item. The documentation should state it is covering only the portion of the acquisition which is brand- name.”

☐ Urgency

☐ Exclusive licensing agreements/Proprietary data

☒ Brand name required

☐ Industrial mobilization

☒ Other (e.g., compatibility, space issues, continuity, compatibility, etc.)

☐ In accordance with FAR 8.405-6 “Limiting Sources” which states that, “the only circumstances that may justify the action are – (A) An urgent and compelling need exists, and following the procedures would result in unacceptable delays; (B) Only one source is capable of providing the supplies or services required at the level of quality required because the supplies or services are unique or highly specialized; or (C) In the interest of economy and efficiency, the new work is a logical follow-up to an original Federal Supply Schedule order provided that the original order was placed in accordance with the applicable Federal Supply Schedule ordering procedures. The original BPA must not have been previously issued under sole-source or limited-sources procedures.”

☐ Urgency ☐ Only One Source

☐ Logical Follow Up

☐ Brand name required

2. Other facts supporting sole source procurement:

a. What can this product/service do that other products/services cannot do?

Georgia Tech Research Corporation has unique expertise in genome analysis and genome annotation. It has also developed the proprietary software tools used in pioneering genome projects. Georgia Tech Center for Bioinformatics & Computational Genomics has been able to solve a number of long standing programs, particularly the one of automatic gene prediction in eukaryotic genomes by come-up with “unique in the filed” automatic software tools. It also has unique “know-how” or expertise in developing custom built pipelines for genome annotation where their original algorithms play a central role. The bioinformatics component of the HPV project includes a number of bioinformatics tasks that require development of novel algorithms to automate determination of varied characteristics of HPV. The Georgia Tech Center for Bioinformatics & Computational Genomics has the capacity to apply it proprietary GeneMark software to new genome data sets and to customize the software as the additional data (both genome sequences and RNA-Seq data) is produced. Georgia Tech Research Corporation has the required experience and expertise in genome analysis and genome annotation in a portable format and access to the proprietary GeneMark software for its application to eukaryotic genome sequence data. CDC-DHCPP/CVDB and Georgia Tech Center for Bioinformatics and Computational Genomics group collaborated on the HPV whole genome sequencing project, and substantial progress made during this past collaboration under is a foundation for the continued progress on HPV whole genome sequencing efforts at

CDC.

b. What other products/services were considered and why did they not meet the need?

No other products/services were considered because of the need for continuity and urgency that can be provided by The Georgia Tech Center for Bioinformatics & Computational Genomics.

3. Program Office efforts to seek potential offerors:

Program did not consider other potential services because of the need for continuity and urgency that can be provided by The Georgia Tech Center for Bioinformatics & Computational Genomics.

E. Program Office Certification:

I have reviewed this sole source justification and certify the justification is true and accurate to the best of my knowledge and adequate to support other than full and open competition.

Center/Institute/Office COR/Program Official Name/Title: NCEZID/DHCPP/CVDB/ Niyai Johnson COR/ Mangalathu Rajeevan Molecular Team Lead

Center/Institute/Office COR/Program Official Signature:

Certification Date: June 6, 2024

F. Contracting Office Certification:

I have fully relied on the information provided herein and hereby certify that this justification is accurate and complete to the best of my knowledge and belief:

Contracting Officer Name: Click here to enter text.

Contracting Officer Signature:

Certification Date: Click here to enter a date.