SPECIAL NOTICE
Q -- Evidence-Based Bioinformatic Interpretation of New Generation Sequencing Data For Precision Cancer Diagnostics
- Notice Date
- 5/28/2024 2:08:27 PM
- Notice Type
- Special Notice
- NAICS
- 541990
— All Other Professional, Scientific, and Technical Services
- Contracting Office
- NATIONAL INSTITUTES OF HEALTH Bethesda MD 20892 US
- ZIP Code
- 20892
- Solicitation Number
- 75N91024NOI6913951
- Response Due
- 6/4/2024 9:00:00 AM
- Archive Date
- 06/19/2024
- Description
- The Department of Health and Human Services (DHHS), National Institutes of Health (NIH), National Cancer Institute (NCI), Center for Cancer Research (CCR) plans to procure laboratory testing, on a sole source basis, from Qiagen LLC of 19300 Germantown Road, Germantown MD 20874-1415. 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)(1); and is exempt from the requirements of FAR Part 6. The response close date of this notice for this requirement is in accordance with FAR 5.203(a)(1). The North American Industry Classification System (NAICS) codes and size standard is 541990 - $19.5M. 1.0�� �TITLE Evidence-Based Bioinformatic Interpretation of New Generation Sequencing Data For Precision Cancer Diagnostics 2.0�� �BACKGROUND The Clinical Oncologic Molecular Pathology Sequencing Service (NCI-COMPASS) at the Laboratory of Pathology (LP), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), develops and uses large New Generation Sequencing (NGS) panels for its Clinical Laboratory Improvement Amendments (CLIA)-certified and College of American Pathologists (CAP)-accredited program for precision cancer diagnostics. NGS is a high-throughput technology which can integrate molecular tumor profiles into clinical decision-making. NCI-COMPASS conducts NGS with whole-genome, whole-exome, whole-transcriptome, and targeted gene sequencing panels as part of its precision oncology. Since more than six years, NCI-COMPASS utilizes a commercial software platform, QIAGEN Clinical Insight Interpret (QCII), for the subsequent comprehensive bioinformatic profiling of its NGS data. This automated data analysis platform provides prognostic, diagnostic, and predictive insights needed to inform research or treatment decisions for cancer patients at the NIH Clinical Center. Patient sign-out by LP pathologists is supported through QCII-generated NGS reports. The interpretation of the clinical impact of tumor variants in the context of a specific cancer and for individual patients is enabled by QIAGEN�s Biomedical Knowledge Base. This knowledgebase integrates up-to-date information from public and priority databases on genes, variants, clinical significance, available supporting evidence, biomarker class, diseases, matched drugs, therapeutic effects, and clinical trials in a single space. In clinical oncology, the number of data variants generated is high because of the inherent genomic instability associated with biological carcinogenesis. standardized guidelines for pretherapy diagnostic assessment increasingly mandate the use of molecular biomarkers to guide therapies in newly diagnosed cancer patients. Many NIH cancer patients are being treated with drugs directed against specific genomic alterations or based on the determination of complex biomarkers. Reliable and reproducible bioinformatics tools are essential to obtain information on the molecular characteristics of each patient's tumor from the NGS data. The QCII platform collects biological and functional data for translational research applications to the most updated evidence on the clinical benefit obtained from matched drugs that can be used to drive variant-specific treatment recommendations. The current solution has been successfully customized and configured to fit all aspects of the clinical workflow at the NCI. 2.1�� �OBJECTIVE The NCI-COMPASS program requires comprehensive, evidence-based, customizable clinical reports on NGS data for NIH cancer patient sign out procedures. Variant classifications must be based on the professional guidelines published by the American College of Medical Genetics (ACMG) and the Association for Molecular Pathology (AMP). The content of these reports must be based upon up-to-date curated genomic data, clinical practice guidelines, drug labels, published clinical research results, and recruiting clinical trials. In addition, the resulting data must integrate with the program�s Laboratory Information Management System (LIMS). 3.0�� �SCOPE The NCI-COMPASS program will produce de-identified next-generation sequencing (NGS) data from patient cases on commercial and customized panels and upload NGS data through the Contractor�s secure online portal into the Contractor�s cloud-based bioinformatics analysis platform. The Contractor�s platform shall then automatically compute variant classifications, based on an evidence-based, curated, up-to-date knowledgebase. The computed results shall be provided to the Government through the bioinformatics platform as customizable, patient-specific clinical reports. Furthermore, the Contractor shall integrate the bioinformatics platform with the program�s LIMS to allow the documentation of the NGS report results. 4.0�� �CONTRACT REQUIREMENTS All data generated shall be the sole property of the U.S. Government. All data shall be retained throughout each period of performance unless otherwise instructed by the Contracting Officer Representative (COR). Independently and not as an agent of the Government, the Contractor shall provide all labor, materials, and equipment required to perform the following tasks: 4.1�� �TASK 1: INFORMATION SECURITY The data and IT information for this requirement fall into the category of Controlled Unclassified Information [CUI] in the Non-Federal Systems and needs to follow NIST 800-171 (final), see: https://csrc.nist.gov/pubs/sp/800/171/a/final. 4.1.1�� �DELIVERABLES Deliverable #1. System Security Plan (SSP) Within 60 calendar days of award, the Contractor shall provide a System Security Plan (SSP) to give an overview of the system environment and security requirements to protect the information system as well as to describe all applicable security controls in place, or to include the plan for meeting those requirements. The SSP shall provide a structured process for planning adequate, cost?effective security protection for the system. ��� �The SSP shall comply with NIST 800-171 (final), Protecting Controlled Unclassified Information in Non?Federal Systems and Organizations. ��� �The SSP shall address all questions in the SSP template, see: https://csrc.nist.gov/files/pubs/sp/800/171/r2/upd1/final/docs/cui-ssp-template-final.docx.� ��� �The Contractor shall update the SSP at least annually thereafter. Deliverable #2. Security Assessment Plan of Action Within 90 calendar days of award, the Contractor shall provide a security assessment plan of action to provide an overview of identified weaknessess and remediations for the protection of controlled uncassified information (CUI). The Contractor shall use the NIST CUI Plan of Action template available at: https://csrc.nist.gov/CSRC/media//Publications/sp/800-171/rev-1/final/documents/CUI-Plan-of-Action-Template-final.docx. 4.2�� �TASK 2: VARIANT CLASSIFICATION The Contractor shall provide the Government access to the automated bioinformatics data analysis platform QIAGEN Clinical Insight Interpret (QCII) through the secure online portal QIAGEN Ingenuity. Access shall be restricted through password-protected, secured user accounts. The Government will upload genomic data files (i.e., patient cases) from the NCI-COMPASS program for downstream analysis. Depending on the NGS panel used by the NCI to generate the genomic data, the subsequent data analysis by the Contractor shall either follow an analysis pipeline for somatic cancer, or an analysis pipeline for hereditary diseases. 4.2.1�� �QIAGEN CLINICAL INSIGHT INTERPRET (QCII) BIOINFORMATICS PLATFORM� The cloud based NGS bioinformatics analysis platform must fulfill the following requirements: 1)�� �Health Insurance Portability and Accountability Act (HIPAA) Safe Harbor compliant 2)�� �Authorized for laboratory and clinical use. 3)�� �Allows automated variant reporting, drug and clinical trial selection from targeted NGS panels. 4)�� �Secured though Application Programming Interface (API) and HL7 interface. 5)�� �Accepts NGS data in Variant Call Format (VCF) file format. 6)�� �Automatically generates comprehensive, patient-specific clinical reports in pdf format. Reports shall include biomarker results summary; biological and clinical relevance; clinical evidence in tumor types; sample therapies; matching trials; and bibliographic references. 7)�� �Allows the customization by NIH staff of resulting reports, including configuring final classification, comments, and recommendations. 8)�� �Integrates results in Extensible Markup Language (XML) format with NCI/LP�s LIMS. 9)�� �Computed variant classifications must be in compliance with ACMG/AMP guidelines. 10)�� �The computed variant classifications shall be tiered for therapeutic, diagnostic, and prognostic actionability. 11)�� �The classifications shall configurable, i.e., the automated platform shall enable NCI staff to classify alterations in accordance with ACMG/AMP guidelines. 4.2.2�� �BIOINFORMATICS PLATFORM KNOWLEDGEBASE REQUIREMENTS The Contractor shall have a knowledgebase (i.e., databank) for the NGS bioinformatics analysis platform in place. This knowledgebase shall incorporate up-to-date, curated information from biomedical literature and biomedical databases. The content shall include human phenotype-associated findings, therapeutic, prognostic, and diagnostic evidence, drug labels, clinical case counts, recruiting clinical trials, clinical studies, and functional studies. It shall also include and clinical practice guidelines by the Federal Drug Administration (FDA), the American Society of Clinical Oncology (ASCO), CAP, ACMG, and AMP. The Contractor shall curate this knowledgebase under a stringent quality review program to integrate clinically relevant information. The knowledgebase shall be updated weekly with new therapeutic, prognostic, and diagnostic evidence. The knowledgebase shall incorporate information from the following online databases and websites: 1)�� �For inherited and somatic mutations, genomic variations: o�� �Exome Sequencing Project (ESP), by the NIH National Heart, Lung, and Blood Institute (NHLBI) o�� �ClinVar, by the NIH National Center for Biotechnology Infirmation (NCBI) o�� �Breast Cancer Information Core (BIC), by the NIH National Human Genome Research Institute (NHGRI) o�� �Encyclopedia of DNA Elements (ENCODE), by the NHGRI and the Standford University o�� �VISTA Tools for Comparative Genomics, by the Lawrence Berkeley National Laboratory (LBL) o�� �Exome Variant Server Project, by the University of Washington o�� �Allele Frequency Community o�� �Exome Aggregation Consortium (ExAC) / Genome Aggregation Database (gnomAD), by the Global Core Biodata Resouce (GCBR) o�� �1000 Genomes, by the European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI) o�� �JASPAR CORE, by an international collaboration o�� �Catalogue of Somatic Mutations in Cancer (COSMIC) by Qiagen o�� �Online Mendelian Inheritance in Man (OMIM; by Qiagen) o�� �Human Gene Mutation Database (HGMD; by Qiagen) 2)�� �For biological impact of mutations and variations: o�� �Polyphormism Phenotyping (PolyPhen) o�� �SIFT o�� �PhyloP o�� �Blosum o�� �MaxEntScan 3)�� �For pharmacological impact of mutations and variations: o�� �PharmacoGenomic Mutation Database (PGMD; by Qiagen) 4)�� �For matching active clinical studies: o�� �ClinicalTrials.gov, by the NIH National Library of Medicine 5)�� �For matching drug labels: o�� �FDA.gov/Drugs, by the Food and Drug Administration (FDA) o�� �ema.europa.eu/en/medicines, by the European Medicines Agency (EMA) 6)�� �For evidence-based literature: o�� �pubmed.ncbi.nlm.nih.gov, by the NIH National Library of Medicine (NLM) The following QIAGEN product fulfill the requirements under this task: Product #�� �Product Name�� �Analysis Type�� �NCI Panel 830716�� �151-200 Genes�� �HereditaryGenome�� �NCI Germline 830900�� �One PreCur 1-50 Genes�� �RapidInsight�� �NCI RNA exome fusion 830901�� �One PreCur 51-150 Genes�� �RapidInsight�� �56 gene Custom Neuro Solid Tumor 830902�� �One PreCur 151 � 200 Genes�� �RapidInsight�� �161 gene Thermo Fisher Oncomine v3 830904�� �One PreCur 301 � 600 Genes�� �RapidInsight�� �523 gene TSO500; and 523 TSO500 ctDNA 830905�� �One Curation 1-50 Genes�� �RapidInsight�� �NCI RNA exome fusion 830910�� �One Precur Exome�� �RapidInsight�� �NCI Whole Exome Sequencing 4.2.3�� �DELIVERABLES Deliverable #3. Monthly Reports The Contractor shall deliver monthly Usage Report in Excel file format to the LP Clinical Manager/Bioinformatics Unit. Deliverable #4. Annual Reports The Contractor shall deliver one annual Usage Report in pdf file and in Excel file format to to the LP Clinical Manager/Bioinformatics Unit. 5.0�� �PERIOD OF PERFORMANCE The Period of Performance shall be twelve months, followed by two (2) twelve-month Option Periods, as follows: Base Period:�� �July 29, 2024 � July 28, 2025 Option Period 1:�� �July 29, 2025 � July 28, 2026 Option Period 2:�� �July 29, 2026 � July 28, 2027 6.0�� �PLACE OF PERFORMANCE All work shall be performed at the Contractors facilities. 7.0�� �TYPE OF ORDER This is a severable Firm-Fixed-Unit-Price purchase order. The services acquired under this contract are severable services. Funds are only available for use for the contract line item (CLIN) to which they are obligated. Unused funds from one CLIN may not roll over for use in other periods. 7.1�� �CEILING PRICE (a)�� �The parties estimate that performance of this contract will not cost the Government more than the Ceiling Price specified in the Price Schedule.� (b)�� �The Government is not obligated to reimburse the Contractor for costs incurred in excess of the Ceiling Price; and the Contractor is not obligated to continue performance under this contract in excess of the Ceiling Price specified in the Price Schedule until the Contracting Officer (i) notifies the Contractor in writing that the Ceiling Price has been increased and (ii) provides a revised Ceiling Price of performing this contract.� (c)�� �No notice, communication, or representation in any form other than that specified in paragraph (b) of this clause, or from any person other than the Contracting Officer, shall affect this contract�s Ceiling Price to the Government. In the absence of the specified notice, the Government is not obligated to reimburse the Contractor for any costs in excess of the Ceiling Price. (d)�� �Change Orders/Modifications shall not be considered an authorization by the Government to exceed the Ceiling Price specified in the Price Schedule unless the action explicitly contains a statement increasing the Ceiling Price. (e)�� �Funds remaining following receipt of the Final Invoice may be unilaterally de-obligated by the Government. (f)�� �This contract is divisible. In the case of default, the Contractor shall be paid for units delivered and accepted. The Contractor�s responsibility for default shall only be with respect to uncompleted work. 7.2�� �PRICE SCHEDULE The following price schedule is for estimated quantities to establish the price per analysis of clinical datasets and the overall Ceiling Price for line items. Actual quantities purchased may vary. � 8.0�� �TECHNICAL POINT OF CONTACT The Technical Point of Contact (TPOC) will serve as the Governments primary point of contact for coordination of all required efforts covered under the scope of the purchase order. Additionally, all services shall be delivered to the TPOC for final inspection and acceptance upon completion. All deliverables will have been deemed accepted fifteen (15) calendar days after date of delivery, except as otherwise specified in this purchase order if written approval or disapproval has not been given within such period. The TPOC role is limited to the authorities specified herein. The TPOC does not have the authority to issue directions that: ��� �Constitutes a change of assignment or additional work outside the statement of work. ��� �Constitutes a change as defined in clause 52.212-4 (c) ""Changes�. ��� �In any manner causes an increase or decrease in the purchase order price, or the time required for performance. ��� �Changes any of the terms, conditions, or requirements of the purchase order. ��� �Interferes with the Contractor's right to perform under the terms and conditions of the purchase order; or ��� �Directs, supervises, or otherwise controls the actions of the Contractor's employees. If at any time the Contractor feels that such direction listed above has been given, they must contact the Contracting Officer immediately. 9.0�� �INSPECTION AND ACCEPTANCE Pursuant to FAR clause 52.212-4, all work described in the SOW to be delivered under this purchase order is subject to final inspection and acceptance by an authorized representative of the Government. The authorized representative of the Government is the NCI Technical Point of Contact (TPOC) who is responsible for inspection and acceptance of all services, materials, or supplies to be provided by the Contractor. Regardless of format, all digital content or communications materials produced as a deliverable under this purchase order, shall conform to applicable Section 508 Standards to allow Federal employees and members of the public with disabilities to have access to and use of information and data that is comparable to the access to and use of information and data by Federal employees or by members of the public who are not individuals with disabilities. Remediation of any materials that do not comply with the applicable Section 508 requirements as set forth below, shall be the responsibility of the Contractor. HHS guidance regarding accessibility of documents can be found at: https://www.hhs.gov/web/section-508/making-files-accessible/create-accessiblepdfs/index.html. Federal Government-wide guidance regarding accessibility of documents can be found at https://www.section508.gov/, including the documents describing the preferred method of authoring and testing documents produced in Microsoft Word 2013 or later, Microsoft Excel, and files formatted as PDF. All written drafts and final deliverable products shall be submitted as an electronic copy in draft format for review, comment, and approval by the TPOC. Final copies of approved drafts shall be delivered to the TPOC within 3 business days after receipt of the Government�s comments. If requested, final deliverable products shall be submitted in an electronic format. Other quantities and formats may be submitted after prior approval from the TPOC. 9.1�� �DELIVERABLES AND DELIVERY SCHEDULE The below table outlines the deliverables which the Contractor is responsible for fulfilling throughout the requirement. All submittals shall be submitted electronically to the Technical Point of Contact (TPOC) for inspection and acceptance. #�� �Section�� �Deliverable�� �Due Date� 1�� �4.1.1 System Security Plan (SSP); as pdf file.�� �Within 60 calendar days of award 2�� �4.1.1 System Assessment Plan of Action (SSP; as pdf file.�� �Within 90 calendar days of award 3�� �4.1.1 Access to the Contractor�s cloud-based software portal for NGS data submission and for retrieving reports�� �Immediately upon award 4�� �4.2.3 QCI reports with ACMG/AMP Guideline Compliance�� �Within three (3) business days of receipt 5�� �4.2.3 Monthly Usage Report, indicating the number of cases run by NGS panel type and by product, during the past month; to be submitted to the COR via email as Excel file.�� �Within the first seven calendar days of the following month. 6�� �4.2.3 Annual Usage Report, indicating the number of cases run by NGS panel type and by product throughout the Period of Performance; to be submitted to the COR via email as PDF file.�� �30 business days prior to the end of the Period of Performance. This notice is not a request for competitive quotation. However, if any interested party, especially small business believes it can meet the above requirement, 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 sufficient detail to allow NCI to determine if the party can perform the requirement. �Responses must be received in the contracting office by 12:00 PM ET, on May 31, 2024. �All responses and questions must be via email to Miguel Diaz, Contracting Officer at miguel.diaz@nih.gov. �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 the purpose of determining whether to conduct a competitive procurement. �To receive an award, contractors must be registered and have valid certification through SAM.GOV with Representations and Certifications completed. Reference: 75N91024NOI6913951�� �on all correspondence.
- Web Link
-
SAM.gov Permalink
(https://sam.gov/opp/4293c66975a548f298c39829bf14f1ae/view)
- Place of Performance
- Address: Bethesda, MD, USA
- Country: USA
- Country: USA
- Record
- SN07077653-F 20240530/240529051339 (samdaily.us)
- Source
-
SAM.gov Link to This Notice
(may not be valid after Archive Date)
| FSG Index | This Issue's Index | Today's SAM Daily Index Page |