SPECIAL NOTICE
B -- Analysis Services for the Sherlock-Lung Genomic Epidemiologic Study
- Notice Date
- 5/2/2023 8:46:19 AM
- Notice Type
- Special Notice
- NAICS
- 541990
— All Other Professional, Scientific, and Technical Services
- Contracting Office
- NIH NCI Bethesda MD 20892 USA
- ZIP Code
- 20892
- Solicitation Number
- 75N91023Q00086
- Response Due
- 5/9/2023 12:00:00 PM
- Point of Contact
- Dana Summons, Contract Specialist, Phone: 2402765319
- E-Mail Address
-
dana.summons@nih.gov
(dana.summons@nih.gov)
- Description
- 1.0�� �DESCRIPTION The Division of Cancer Epidemiology and Genetics (DCEG) of the National Cancer Institute (NCI) plans to procure services, on a sole source basis, from the University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. The response 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)(1)(i); and is exempt from the requirements of FAR Part 6. The North American Industry Classification System code is 541990 and the small business size standard is $19.5 million. It has been determined there are no opportunities to acquire green products or services for this procurement. 2.0�� �BACKGROUND The NCI�s Sherlock-Lung study is analyzing cancerous and healthy tissue from up to 2,000 never-smoking lung cancer patients and ~500 smoking lung cancer patients from the EAGLE study and conducting multi-omics analyses to elucidate the etiology and evolutionary paths to progression in smokers and nonsmokers. Short-read, bulk whole-genome sequencing data, and long-read PacBio HiFi sequencing data will be analyzed in the studies to infer aspects of cancer evolution, intratumor heterogeneity, and cell-of-origin. Currently, there are no published genomic pipelines in the world to perform such analyses incorporating information from PacBio HiFi long-read sequencing. Therefore, the NCI�s Sherlock-Lung study is requesting expertise and services to develop novel algorithms and genomic pipelines for such analyses. 2.1�� �OBJECTIVE The Integrative Tumor Epidemiology Branch (ITEB), Trans-Divisional Research Program (TDRP), Division of Cancer Epidemiology and Genetics (DCEG), of the National Institutes of Health (NIH), National Cancer Institute (NCI) seeks to characterize the genomic landscape of lung cancer in never smokers, to identify mutational signatures of exogenous and endogenous processes involved in lung tumorigenesis in never smokers and order them along lung tumor evolutionary trajectories, and to develop an integrated molecular, histological, and radiological classification of lung cancer in never smokers. Integration of the genomic and evolutionary landscape with histological characterization of the tumors and the surrounding microenvironment coupled with radiological features in the Sherlock-Lung study should advance the understanding of underlying etiologic causes of lung cancer in never smokers. 3.0�� �SCOPE The Contractor shall provide analytical services and develop novel software as part of the bioinformatics pipeline required for the genomic study.� 4.0�� �PERFORMANCE OBJECTIVES The Contractor shall meet the following objectives: 4.1�� �Receive the following Human Data from the NCI (as already established in the attached Collaboration Agreement for the Transfer of Human Data) via encrypted data transfer platform such as Globus: Whole Genome Sequencing data from cancerous tissue and matched normal samples from never smoking and smoking lung cancer patients from the Sherlock-Lung and EAGLE studies. After award of the contract, the NCI will provide the Contractor access to the data, which have been de-identified. � 4.2�� �Develop software/methods/tools as part of the bioinformatics pipeline required for the study. Share the developed software/methods/tools and bioinformatics pipeline with the NCI. 4.3�� �Perform analyses as outlined above, guided by expertise in computational methods for studying tumor evolution and heterogeneity using Human Data. 4.4�� �Attend meetings/discussions related to this project and apply computational/ bioinformatics expertise. 4.5�� �Deliver preliminary and final results to the NCI Technical point of contact (TPOC) via encrypted email and/or data transfer platform such as Globus. �The data files and summary results shall be provided in appropriate formats (including but not limited BAM, CRAM, VCF, Excel, DOC, CSV, PDF, PNG, etc.). No personally identifiable information shall be included.� 4.6�� �Provide a manuscript draft after the delivery of final results. No personally identifiable information (PII) shall be included. 4.7�� �After successful completion of all objectives above, dispose of all raw genomic data received in objective 4.1. 5.0�� �TYPE OF ORDER This is a firm fixed-price purchase order. 6.0�� �NON-SEVERABLE SERVICES The services specified in each contract line item (CLIN) have been determined to be nonseverable services - a specific undertaking or entire job with a defined end product of value to the Government. 7.0�� �PERIOD OF PERFORMANCE The period of performance shall consist of 12 months, plus one (1) 12-month option period as follows: Base Period:�� ��� �TBD (12 months from award of contract) Option Period One:�� �TBD (12 months following the Base Period) 8.0�� �PLACE OF PERFORMANCE Services shall be performed at the Contractor�s facility. 9.0�� �GOVERNMENT INFORMATION The Collaboration Agreement for the Transfer of Human Data is attached. 10.0�� �REPORT(S)/DELIVERABLES AND DELIVERY SCHEDULE All written deliverables shall be sent electronically to the NCI Technical Point of Contact (TPOC), TBD at award, in appropriate formats (including but not limited BAM, CRAM, VCF, Excel, DOC, CSV, PDF, PNG, etc.) unless approved by the TPOC in accordance with the deliverable schedule below. The TPOC shall review the contents of all draft deliverables. If no comments or requests for revisions are provided to the Contractor within 30 business days, the deliverables shall be considered acceptable. If revisions are required, NCI shall respond to the Contractor within five (5) business days of receiving the deliverable, specifying the required changes/revisions. Final copies of approved drafts shall be delivered to the NCI TPOC within five (5) business days after receipt of the Government�s comments. The TPOC for this order is: (TBD) DELIVERABLE # 1�� � � � � � � � � � � � � � Base Period DESCRIPTION � Preliminary results for the analytical services and novel software, and bioinformatics pipeline development based on smokers samples. � ��� �The Contractor shall participate in monthly meetings and discussions related to the project.� DUE DATE Every 3 months from the date of award of the Base Period DELIVERABLE # 2 Option Period One DESCRIPTION � Results from the validation and extension onto additional non-smokers samples from the Base Period with quieter genome. ��� �The Contractor shall participate in monthly meetings and discussions related to the project.� DUE DATE Every 3 months from the date of award of the Option Period DELIVERABLE # 3 DESCRIPTION Final results for the analytical services, software, and bioinformatics pipelines as well as a manuscript draft DUE DATE No less than 30 days prior to the end of the Option Period 11.0�� �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 NCI TPOC, TBD, who is responsible for inspection and acceptance of all services, materials, or supplies to be provided by the Contractor. Section 508 of the Rehabilitation Act, as amended by the Workforce Investment Act of 1998 (P.L. 105-220) requires that when Federal agencies develop, procure, maintain, or use information and communication technology (ICT), it shall be accessible to people with disabilities. Federal employees and members of the public who have disabilities must have access to, and use of, information and data that is comparable to people without 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. Products, platforms and services delivered as part of this work statement that are ICT, or contain ICT, must conform to the Revised 508 Standards, which are located at 36 C.F.R. � 1194.1 & Apps. A, C & D, and available at https://www.access-board.gov/guidelines-and- standards/communications-and-it/about-the-ict-refresh/final-rule/text-of-the-standards- and- guidelines. Per Section 508 and as mandated under HHS Policy for Section 508 Compliance and Accessibility of Information and Communications Technology (ICT) (07/2020) all documents or electronic files provided to the NIH NCI under contract must be conformant with Section 508 standards and accessible to persons with disabilities. Conformance shall be confirmed by use of material provided at HHS OS Factsheets & Reference Guides and verified through the use of the HHS Checklist Documents (WCAG 2.0 Refresh); in addition, contractors and vendors are encouraged to make use of the instructional materials and checklists at GSA Section 508.gov�s Create Accessible Digital Products. 12.0�� �UNIQUE QUALIFICATIONS OF THE CONTRACTOR Dr. David Wedge at the University of Manchester is uniquely qualified to perform this work because he is the leading expert in the field of cancer genomics and tumor evolution. He was co-lead of the Evolution and Heterogeneity working group of the ICGC Pan- Cancer Analysis of Whole Genomes (PCAWG) project and is currently a leader of the Pan Prostate Cancer Group. Much of the research in the Dr. Wedge�s lab is focused on tumor evolution, from the initial transformation of normal cells to cancer, through the acquisition of treatment resistance and to the formation of metastatic lesions. Furthermore, Dr. David Wedge is in the unique position to identify the best samples for this project based on the results of his WGS analyses and will be able to develop the analytical pipelines for these analyses, which are currently completely lacking. The Wedge group has pioneered the development of computational methods to study heterogeneity in primary and metastatic cancers. Notably, Dr. Wedge has been involved in the genomics of lung cancer in non-smokers (LCINS) for several years. In this project, he analyzed short-read whole genome sequencing (WGS) data from over 1000 LCINS and will be able to integrate these WGS data with the data that will be generated from long-read sequencing of LCINS under this contract.. His enthusiasm in conducting research, expertise as a leader in field of cancer genomic research, and his quality of work have been well demonstrated by his numerous publications and he is highly respected in the field. In summary, Dr. David Wedge at The University of Manchester possesses unique expertise and resources to conduct this study. Moreover, he will be able to provide continuity in the analyses of LCINS in Sherlock-Lung, one of the most important NCI studies of cancer. 13.0�� �SUBMISSIONS INSTRUCTIONS This notice is not a request for competitive quotations. However, if any interested party believes it can meet the above requirements, 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. �All responses and questions must be sent via email to the Contract Specialist, Dana Summons, at dana.summons@nih.gov by no later than 3:00 PM EST on Tuesday, May 9, 2023, (5/9/23). 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. In order to receive an award, Contractors must be registered and have valid certification through SAM.gov. Reference: 75N91023Q00086 on all correspondence.� �
- Web Link
-
SAM.gov Permalink
(https://sam.gov/opp/7e9e4de8f153442aa989dd535071af5a/view)
- Record
- SN06668358-F 20230504/230502230111 (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 |