JA_Qiagen_Redacted.pdf

that the software is completely functional, which shall require license delivery on the existing implementations of laboratory reporting policies, validations, training, quality control, and final approval of a functioning system that is authorized for laboratory and clinical (Health Insurance Portability and Accountability Act [HIPAA] compliant) use.

b. Project background.

The Clinical Oncologic Molecular Pathology Sequencing Service (COMPASS) program in the LP is committed to advancing genomic research and offering genomic testing so that new treatments, therapies, and therapeutics against cancer can be developed. The COMPASS program is developing large NGS panels, whole exome sequencing and whole transcriptome sequencing assays to identify genetic changes in clinical specimens from cancer patients who are being evaluated and/or treated by the intramural program of the National Cancer Institute. These genetic changes include mutations, copy number changes and gene rearrangements. Given the massive amount of genetic data generated from NGS assays and rapidly changing information on clinical trials, professional guidelines, and public databases, it is challenging for the Laboratory of Pathology to accurately survey and compile all sources of evidence that are necessary to interpret and report patient test results. Therefore, software supported variant clinical interpretation services are greatly needed to become an integral part of the COMPASS program workflow.

In addition, such services help in keeping track of the cases signed out by the LP and creates a knowledge base of the variants that has been observed earlier, bringing efficiency during the sign out process.

3. Description of the supplies or services required to meet the agency’s needs (including the estimated value).

a. Project title.

Clinical Interpretation of Genomic Variants from Large Next Generation Panel (NGS), Whole Exome Sequencing and Whole Transcriptome Sequencing

b. Project description.

See the attached Statement of Work (SOW).

Requirement type.

Research & development (R&D)

R & D support services Support services (non R&D) Supplies/equipment Information technology (IT) Construction Architect engineer (A & E) services Design build Other (specify): ____________________

Type of action.

New requirement Follow on Other (specify): ______________________

Proposed contract/order type.

Firm fixed price Other fixed price (specify, e.g., fixed price award fee, fixed price incentive fee): Firm Fixed Unit Price Cost plus fixed fee Other cost reimbursement (specify, e.g., cost plus award fee, cost plus incentive fee): ___________ Time and materials Indefinite delivery (specify whether indefinite quantity, definite quantity, or requirements): ___________ Other (specify): ___________ Completion Form Term form

Acquisition identification number.

c. Total estimated dollar value and performance/delivery period.

The anticipated period of performance shall be for one (1) 12 month base period, plus one (1) 12 month option period as follows:

Base Period: July 29, 2022 to July 28, 2023 Option Period 1: July 29, 2023 to July 28, 2024

See the attached IGE for additional information.

4. Identification of the statutory authority permitting other than full and open competition.

This acquisition is conducted under the authority of 41 United States Code (U.S.C.) 253(c)(__) as set forth in Federal Acquisition Regulation (FAR) 6.302 __modified to reflect that the procedures in FAR subpart 13.5.

This acquisition is conducted under the authority of FAR subpart

13.5 in accordance with 41 U.S.C. 1901 or 1903.

5. 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).

Qiagen LLC 19300 Germantown Road, Germantown, MD 20874

b. Nature of the acquisition and proposed unique qualifications of the contractor(s).

Qiagen Clinical Insight (QCI) Interpret One is a clinical decision support tool that combines flexible and automatable software, powered by the structured content in the QIAGEN Clinical Knowledge Base, with interpretation services of N of One, a wholly owned QIAGEN Company.

The QCI is updated weekly with therapeutic, prognostic, and diagnostic evidence, including drug labels, recruiting clinical trials, practice guidelines (FDA, ASCO, CAP, AMP, ACMG), and clinical/functional studies.

The software allows customization of the LP’s specific reporting policies to automate variant reporting and drug and trial selection. It leverages a feature rich Application Programming Interface (API) to integrate with the Laboratory Information Management System (LIMS) to scale up case processing. QCI Interpret One is designed to augment in house expertise and enhance decision making in clinical workflow by providing all the content necessary to generate a comprehensive, patient specific report, while giving molecular pathologists full control over final classifications, comments, and five recommendations.

This Purchase Order is a continuation of the clinical report services under Purchase Order # 75N91020P00551 with Qiagen LLC to provide a software system and gene panel analysis that meets the requirements and needs for LP’s clinical reporting. The customized implementation and improvement of the current system have been ongoing for over 3 years with LP molecular pathologists and scientists. As a result, Qiagen QCI software has helped analyze and produce reports for over 3000 cases from six (6) Clinical Laboratory Improvement Amendments (CLIA) certified NGS panels. The reports are currently in use for over 100 clinical trial protocols of cancer treatment and research at the NIH Clinical Center. In meeting LP’s clinical needs, Qiagen’s Knowledge Base (database) has provided a breadth of the biology and chemical knowledge, accuracy, and structure of content. The Qiagen Knowledge Base also curates’ drug labels, clinical case counts, and clinical trials and currently has over 4,100,000 human phenotype associated findings.

The knowledge acquisition and extraction process for the Qiagen Knowledge Base is protected by multiple US Patents and is recognized as an industry standard.

Continued support by Qiagen is required to tailor reporting to clinical needs and shorten reporting turnaround times. If the laboratory were to switch to a different vendor, there would be a complete breakdown of the reporting workflow currently in place, leading to negative clinical effects. The existing tools and user interface have been customized by Qiagen to fit into the laboratory’s pipeline. This allows staff to upload genomic data files from the LP directly into the Qiagen database and then securely download PDF reports and results in XML format to NCI’s information infrastructure. Additionally, any change in CLIA tests from wet lab/dry lab to interpretation and reporting would be required to have extensive validations and a reapproval process. This logical follow on requirement will be facilitated using the same methodology and expertise to ensure consistency with reporting and timely delivery. In summary, any efforts to identify a different vendor and tool would pose additional costs to the Government (e.g., initial setup, custom reporting policy, difference in variant classification rules, setting up of IT infrastructure to upload and download results, revalidation process and training of multiple doctors and scientists in the lab), significant delays in the workflow, and risk the overall work performed by NCI, CCR, LP.

6. Description of the efforts made to ensure that offers are solicited from as many potential sources as practicable. Indicate whether a FedBizOpps notice was or will be publicized as required by FAR Subpart 5.2 and, if not, which exception under FAR 5.202 applies.

A SAM.gov sole source notice of intent will be published in accordance with FAR Part 5.2. Any quotes, proposals and/or capability statements received shall be considered solely to determine whether to conduct a competitive procurement.

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

The Project Officer completed the Independent Government Estimate (IGE) by referencing the informal pricing table submitted by Qiagen and past contract pricing. The Contracting Officer has considered the Independent Government Estimate (IGE) and will consider any capability statements and/or quotes received from the sole source notice of intent. The contract file will be documented to support the Contracting Officer’s fair and reasonable price determination.

8. Description of the market research conducted (see FAR Part 10) and the results, or a statement of the reasons market research was not conducted.

The NCI Office of Acquisitions (OA) reviewed the informal pricing requested and received by the LP. The Contracting Officer considered the LP’s technical knowledge of the requested services, as the staff frequently carry out these services with industry. This logical follow on requirement will be facilitated using the same methodology and expertise by Qiagen to ensure consistency with reporting and timely delivery. Any efforts to identify a different vendor and tool would pose additional costs to the government, significant delays in the workflow, and risk the overall work performed by NCI, CCR, LP. Additional market research efforts shall include posting the sole source notice of intent via SAM.gov. Any quotes, proposals and/or capability statements received shall be considered solely for determining whether to conduct a competitive procurement.

9. Any other facts supporting the use of other than full and open competition.

All facts have been previously detailed.

10. Listing of sources, if any, that expressed, in writing, an interest in the acquisition.

No sources expressed interest in writing.

11. Statement of the actions, if any, the agency may take to remove or overcome any barriers to competition before any subsequent acquisition for the required supplies or services.

NCI anticipates their needs will successfully be met in this Purchase Order. If upon completion of the anticipated Purchase Order, additional services are required, the NCI program office, LP, and the Contracting Officer will conduct market research to determine if there are other sources available that can provide the required services. This market research will include a SAM.gov announcement, an inquiry into whether additional vendors are available that would allow a competitive procurement, and consideration to whether the use of new solutions to the requirement are available, if applicable.