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

The U.S. Department of Health and Human Services (HHS), National Institutes of Health (NIH), National Cancer Institute (NCI), Center for Cancer Research (CCR), Laboratory of Pathology (LP) intends to procure, on a sole source basis, services for the clinical interpretation of genomic variants from large next-generation panel (NGS), whole exome sequencing and whole transcriptome sequencing from Qiagen, LLC, 19300 Germantown Road, Germantown, MD 20874-1415, United States.The response close date of the notice for this requirement is in accordance with FAR 5.203(b). This acquisition will be processed under FAR Part 12 – Acquisition for Commercial Items and will be made pursuant to the authority in FAR Part 13.106-1(b)(2); and is exempt from the requirements of FAR Part 6. The North American Industry Classification System (NAICS) code is 541990 and the business size standard is $17 million.The Statement of Work (SOW) is attached to this notice.UNIQUE QUALIFICATIONS OF THE CONTRACTORQiagen

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 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.RESPONSE INSTRUCTIONSThis notice is not a request for competitive quotations. However, if any interested party, especially a small business, believes it can meet the requirements found in the attached SOW, it may submit a proposal or quote for the Government to consider. The response and any other information furnished must be in writing and must contain material in enough detail to allow NCI to determine if the party can perform the requirement. All responses must be submitted via email to Adam Hernandez, Contracting Officer at adam.hernandez@nih.gov. Responses are due no later than 11:00 A.M. ET Monday, May 16, 2022 (05/16/2022). A determination by the Government not to compete this proposed requirement based upon responses to this notice is solely within the discretion of the Government. Information received will be considered solely for determining whether to conduct a competitive procurement. To receive an award, Contractors must be registered and have valid certification in the System for Award Management (SAM) through SAM.gov, and have Representations and Certifications filled out.Reference 75N91022Q00079 on all correspondence.