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SAMDAILY.US - ISSUE OF MAY 24, 2020 SAM #6751
SPECIAL NOTICE

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

Notice Date
5/22/2020 11:45:45 AM
 
Notice Type
Special Notice
 
NAICS
541990 — All Other Professional, Scientific, and Technical Services
 
Contracting Office
NIH National Cancer Institute Rockville MD 20850 USA
 
ZIP Code
20850
 
Solicitation Number
75N91020Q00029
 
Response Due
6/2/2020 6:00:00 AM
 
Archive Date
06/17/2020
 
Point of Contact
Adam Hernandez, Phone: 2402765633
 
E-Mail Address
adam.hernandez@nih.gov
(adam.hernandez@nih.gov)
 
Description
The U.S. Department of Health and Human Services (DHHS), 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 $16.5 million. 1.0 BACKGROUND The Clinical Oncologic Molecular Pathology Sequencing Service (COMPASS) program in the Laboratory of Pathology (LP) located in the Cancer Center for Research (CCR) at the National Cancer Institute (NCI) 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. 2.0 OBJECTIVE The purpose of this purchase order is to provide the Government with software-supported, evidence-based decision services to support the interpretation of variants observed in genomic sequencing data for cancer diagnostics and research. The objective of these services is to evaluate, classify and perform interpretation of the observed genomic variants in the context of published biomedical literature, professional association guidelines, publicly available databases and annotations, drug labels, and clinical trials. The user (i.e., NIH pathologists at LP) shall have the possibility to individually configure classifications by selecting and prioritizing rules for such classifications, based on medical expertise.� The services provided shall result in reports based on the genomic variations of patients that are ready for the NIH pathologists to sign out. These reports shall be fully configurable to (i) be able to select (i.e., sign out) variants below thresholds, and (ii) to be compliant to the different reporting policies set by the individual intramural programs. As software license is purchased and/or annual software license is renewed, the Contractor shall provide user access and complete implementation for the COMPASS program. The Contractor shall ensure that the software is completely functional, which shall require license delivery, 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. 3.0 CONTRACT REQUIREMENTS Independently, and not as an agent of the Government, the Contractor shall furnish all necessary labor, materials, supplies, equipment, and services not otherwise provided by the Government to perform the following tasks: 3.1 Task 1: Provide License for Software Application for Clinical Interpretation of Genomic Variants The Contractor shall provide a product license with user accounts for a cloud-based software application that supports high-accuracy clinical interpretation of genomic variants from scalable NGS panels and from whole-genome sequencing data. The software provided by the Contractor shall cover the period of performance identified in section 6.0 and shall have the following capabilities: 3.1.1 The software shall access all public genome data repositories (1000 Genomes, Complete Genomics, Exome Server Project, TCGA, ExAC, gnomAD and Allele Frequency Community (AFC)) and the non-public databases BioBase HGMD (Qiagen) and CentoMD� (Centogene). 3.1.2 The software shall be capable to accept sample data in Variant Call Format (VCF). 3.1.3 The software shall be capable to analyze data from targeted panels. 3.1.4 The software shall grant access to data from personal computers and provide account security via password. Variant classification shall be in compliance with ACMG/AMP guidelines: 3.1.5 The computed variant classification shall be based on the professional guidelines published by the American College of Medical Genetics (ACMG) and the Association for Molecular Pathology (AMP), i.e. focused on actionable content from drug labels and clinical trials. 3.16 The Contractor shall implement somatic alteration classification based on the AMP working group guidelines (tier-based) into the somatic variant workflow. Alterations classification shall be tiered for therapeutic, diagnostic, and prognostic actionability. 3.1.7� End users shall have the option to classify alterations according to ACMG and somatic guidelines (AMP). 3.1.8 The computed variant classification shall be fully configurable. Generation of reports: 3.1.9 The software shall generate draft reports that include bibliographic reference citations. 3.1.10 Reports shall be configurable for individual reporting policies. 3.1.11 Export of reports shall be available in industry standard formats. In addition, the contractor shall ensure the following data requirements: 3.1.12 Data security: The Contractor shall maintain data security by performing the clinical interpretation analysis on a secure server cluster maintained by the Contractor that is both HIPPA (CFR 45) and Safe Harbor compliant. The data shall be 256 bit encrypted in transit and at rest. 3.1.13 Data sharing: The sharing of data shall be at the discretion of the COR. 3.1.14 Data retaining: All data shall be retained until the COR deletes the data from the server. Software Training: 3.1.15 As part of the software ownership, the Contractor shall conduct introductory product training for all new COMPASS program staff (i.e., pathologists, data scientists, and technical review scientists) at no additional cost to the Government. This shall include training on standard reporting policy, on lab options for modification of criteria, and on weighting of evidence. The training sessions shall take place on the NIH main campus or at the Contractor�s facility via web-based conferencing.� Any virtual training shall allow participants to directly interact with the lecturer during the training session, and information shall be made accessible to the participants after the session is completed. 3.1 Task 2: Analyzing Gene Panels 3.2.1 Base Period: QCII One PreCur 51-150 Genes 1 u for 300 cases QCII One PreCur 151-200 Genes 1 u for 100 cases QCII One PreCur 301-600 Genes 1 u for 1200 cases QCII One PreCur Exome for 100 cases � 3.2.2 Base Period Optional Quantities: QCII One PreCur 51-150 Genes 1 u for 75 cases QCII One PreCur 151-200 Genes 1 u for 25 cases QCII One PreCur 301-600 Genes 1 u for 300 cases QCII One PreCur Exome for 25 cases 3.2.3 Option Period 1: QCII One PreCur 51-150 Genes 1 u for 300 cases QCII One PreCur 151-200 Genes 1 u for 100 cases QCII One PreCur 301-600 Genes 1 u for 1200 cases QCII One PreCur Exome for 100 cases 3.2.4 Option Period 1 Optional Quantities: QCII One PreCur 51-150 Genes 1 u for 75 cases QCII One PreCur 151-200 Genes 1 u for 25 cases QCII One PreCur 301-600 Genes 1 u for 300 cases QCII One PreCur Exome for 25 cases � 3.2.5 A monthly report shall be sent to the COR indicating the amount of cases run by case type. 3.2.6 A final report shall be sent to the COR indicating the amount of cases run throughout the period of performance and broken down by case type. 4.0 TYPE OF ORDER This is a severable firm-fixed-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 rollover for use in other periods. 5.0 PERIOD OF PERFORMANCE The period of performance shall be for one (1) 12-month base period, plus one (1) 12-month option period as follows: Base Period:���������������������� 12 months from the date of award (anticipated July 01, 2020) Option Period 1:� ������������ 12 months from exercise date (anticipated July 01, 2021) �6.0 PLACE OF PERFORMANCE All work shall be performed at the Contractor�s facility, with the following exception: Introductory product training; as requested by the COR, shall either be web-based or to performed at: Laboratory of Pathology, CCR, NCI COMPASS Program 10 Center Drive, Room 2S253 Bethesda, Maryland 20892-1500 7.0 CONTRACTING OFFICER�S REPRESENTATIVE AUTHORITY The following Contracting Officer's Representative (COR) will represent the Government for the purpose of this contract:� TBD at award The COR is responsible for: (1) monitoring the Contractor's technical progress, including the surveillance and assessment of performance and recommending to the Contracting Officer changes in requirements; (2) interpreting the statement of work and any other technical performance requirements; (3) performing technical evaluation as required; (4) performing technical inspections and acceptances required by this contract; and (5) assisting in the resolution of technical problems encountered during performance. The Government may unilaterally change its COR designation. 8.0 REPORT(S)/DELIVERABLES AND DELIVERY SCHEDULE The NCI COR shall review the contents of the deliverables. If no comments or requests for revisions are provided within 30 days, the deliverables shall be considered acceptable. Task 3.1: Software license and associated services as described in section 4.1 above. Due on the date of award (TBD). Task 3.1.15: Software training material, from training event as described in section 4.1.15 above, shall be submitted to the COR as a PDF file. Due within one (1) business day after training event. Task 3.2.2: Validation records as described in section 4.2.2 above shall be submitted to the COR as email memo file. Due within three (3) business days after receival of reference samples. Task 3.2.3: ACMG/AMP guideline compliance records as described in section 4.2.3 above, to be submitted to the COR as PDF file. Tasks 3.2.1, 3.2.2, 3.2.3, 3.2.4: Reports for the analysis of gene panels, not to exceed the quantities identified in section 3.3, shall be submitted to the COR as a PDF file. Due within 48 hours of request. Task 3.2.5: A monthly report indicating the amount of cases run by case type. Due the last business day of each month. Task 3.2.6: A final report indicating the amount of cases run throughout the period of performance and broken down by type, shall be submitted to the COR as a PDF file. Due 45 business days prior to the end of the period of performance. 9.0 INSPECTION AND ACCEPTANCE CRITERIA Pursuant to FAR clause 52.212-4, all work described in the SOW to be delivered under this contract is subject to final inspection and acceptance by an authorized representative of the Government. The authorized representative of the Government is the Contracting Officer�s Representative (COR), 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 contract, 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: http://www.hhs.gov/web/section-508/making-files-accessible/index.html; Federal Government-wide guidance regarding accessibility of documents can be found at: https://www.section508.gov/best-practices, 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. 10.0 UNIQUE QUALIFICATIONS OF THE CONTRACTOR This contract builds on prior purchase orders to N-of-One and then Qiagen, who acquired N-of-One in 2019. Qiagen is the primary name referred to throughout this justification. Under previous purchase orders, Qiagen, in collaboration with NCI, CCR, LP, provided a software system to meet the analysis requirements and needs for clinical reporting. Implementation of the current system has been ongoing for over a year and as a result, Qiagen has helped analyze and produce reports for over 289 cases. 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, has been operational for over 18 years, 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 data files from LP�s laboratory equipment directly into the Qiagen database. The new requirement will be facilitated using the same methodology and expertise 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. This notice is not a request for competitive quotations. However, if any interested party, especially a small business, believes it can meet the below 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 enough detail to allow NCI to determine if the party can perform the requirement. All responses and questions must be submitted via email to Adam Hernandez, Contract Specialist at adam.hernandez@nih.gov. Responses are due no later than 9:00 A.M. EST Tuesday, June 02, 2020 (06/02/2020). 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 75N91020Q00029 on all correspondence.
 
Web Link
SAM.gov Permalink
(https://beta.sam.gov/opp/554baa16a8a246d7b337fe1de7c6578f/view)
 
Record
SN05668774-F 20200524/200522230155 (samdaily.us)
 
Source
SAM.gov Link to This Notice
(may not be valid after Archive Date)

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