NCI Genomic Characterization Centers

Synopsis: Small Business Sources Sought Notice Number: HHS-NIH-NCI-SBSS-TSB-87001-94 Title: NCI Genomic Characterization Centers This is a Small Business Sources Sought notice. This is NOT a solicitation for proposals, proposal abstracts, or quotations. The purpose of this notice is to obtain information regarding: (1) the availability and capability of qualified small business sources; (2) whether they are small businesses; HUBZone small businesses; service-disabled, veteran-owned small businesses; 8(a) small businesses; veteran-owned small businesses; woman-owned small businesses; or small disadvantaged businesses; and (3) their size classification relative to the North American Industry Classification System (NAICS) code for the proposed acquisition. Your responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. An organization that is not considered a small business under the applicable NAICS code should not submit a response to this notice. This requirement is assigned a code of 541990 in the North American Industry Classification System (NAICS), and the size standard for such requirements is $15.0 million. Your response to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. An organization that is not considered a small business under the applicable NAICS code should not submit a response to this notice. A determination by the Government not to compete this requirement as a set-aside based upon responses to this Notice is solely within the discretion of the Government. Interested parties are expected to review this Notice and the draft Statement of Work to familiarize themselves with the requirements of this project; failure to do so will be at your firm's own risk. Background: Cancer is a complex and heterogeneous disease in which mutations and other genomic and epigenomic abnormalities play a role in both its initiation and progression. Accumulated research data implicate numerous somatic mutations and a more limited number of inherited mutations in carcinogenesis. Understanding cancer-specific somatic mutations can provide important clues regarding the molecular processes underlying the development and progression of certain tumors. Given cancer's complexity, it is generally believed that only a fraction of alterations that may be useful as characteristic markers of specific tumor types and/or potential molecular targets have been identified to date. Therefore, to be successful, comprehensive genomic analyses of cancer must overcome a broad range of challenges stemming from the biological complexity and heterogeneity of human tumors and subtypes. An important role in tumor heterogeneity is played by the genomic instability, which is inherent to the progression of cancer. The dynamic changes in tumor genomes are influenced by the cellular and biological context, genetic characteristics of individual persons, and environmental factors. Certain similarities exist across tumor types, however any effort to characterize the genomes of tumors in a comprehensive, systematic manner must address the heterogeneity across distinct cancer types and subtypes. In 2006, the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI) initiated a collaboration to pursue a project to determine the feasibility of more comprehensively cataloging the genomic alterations associated with a number of different human cancers. The project demonstrated that cancer-associated genes and genomic regions can be identified by combining diverse information from genome analyses (as defined in the previous paragraph), with tumor biology and clinical data, and that the sequencing of selected regions can be conducted efficiently and cost-effectively. The comprehensiveness and rate of progress of The Cancer Genome Atlas (TCGA) depended on both optimization of technical issues and resource availability. The strength of TCGA was to produce unprecedented multi-dimensional data sets using an appropriate number of samples to provide statistically robust results that sets the stage for a new era in the discovery of new cancer interventions. The integrative analyses leading to the formulation of an unanticipated hypothesis on a potential mechanism of resistance highlights precisely the value and power of such project design, demonstrating how unbiased and systematic cancer genome analyses of large sample cohorts can lead to important discoveries. Three key "lessons learned" during the TCGA Program were that, to be able to interpret the results generated by the various characterization platforms, the Centers had to a) utilize high quality molecular analytes isolated from well characterized tissue specimens, b) perform experiments utilizing strictly standardized protocols and c) deposit the results in structured and well-described formats. The last lesson strongly impacted on the ability of the various analytical groups to extract meaningful results from the genomic data generated. The unique aspect of TCGA Project was the development and function of an integrated research network. The intent of TCGA was to conduct a coordinated and comprehensive, genome-wide analysis of cancer-relevant alterations by simultaneously applying several technologies to interrogate the genome, epigenome or transcriptome in large collections of quality controlled cancer biospecimens derived from specific cancer types. To accomplish this goal, TCGA included multidisciplinary teams of investigators and associated institutions that collectively provided biological data, as well as informed strategies for sequencing. The progress in understanding some cancer-associated molecular alterations and the accompanying advances in technology suggest that it was now possible to obtain comprehensive genomic information from multiple tumor types to catalog most, if not all, of the genomic changes associated with cancer. The TCGA Project Research Network demonstrated that a coordinated pipeline approach to investigation of cancer is the best way to avoid biases in the datasets, thus allowing for interoperability of the different projects. The Center for Cancer Genomics (CCG) conducts and collaborates on genomic studies on biospecimens from cancer patients for whom clinical characteristics and treatment outcome data are also available using many of the components in the existing CCG infrastructure. This is a non-R&D requirement for severable services. In view of the extensive experience gained through the TCGA project, the leadership of the CCG has decided that all of its in-process genomic characterization projects will proceed using the same operational model through a coordinated pipeline to receive tissues accrued to the different projects, process analytes, generate and analyze data and present the results to the community. Components of this pipeline are: - Biospecimen Core Resource (BCR): The BCR serves as the tissue processing center and provides the biomolecules for GCCs. - Genome Characterization Centers (GCCs) (current acquisition): As a part of any CCG project, the GCCs will produce high quality genomic, transcriptomic, proteomic, and epigenomic data using validated technologies (e.g., DNA and RNA sequencing, methylation arrays, etc.) to reveal the spectrum of alterations that exist in human tumors. - Genome Data Analysis Centers (GDACs): The Genome Data Analysis Centers (GDACs) work hand-in-hand with the Genome Characterization Centers (GCCs) to perform "higher level" analyses of the data produced by the GCC and to develop state-of-the-art tools that assist researchers with processing and integrating data analyses across the entire genome. - Data Management, Bioinformatics, and Computational Analysis: Data generated by CCG Projects will be deposited into the Genomic Data Commons (GDC) for use by the cancer research community. The end goal of CCG's programs is to make cancer genomic data available to the research community via the GDC. This requirement will be for the award of up to ten Indefinite Delivery Indefinite Quantity (IDIQ) type contracts, with firm fixed price type task orders for Non-R&D services. The task orders will be for severable services. The base IDIQ contracts will have a five-year ordering period and period of performance estimated to be begin on 4/1/2019 and continue through 3/31/2024. It is anticipated that more than one award will be made in each of the following categories listed below: - DNA sequencing - RNA sequencing - Protein sequencing - ATAC-seq CCG requires the ability to add additional task order awards to the contract as new sequencing technologies are developed by the research community over the course of the period of performance. Purpose and Objectives: This request for proposal (RFP) is designed to support the Center for Cancer Genomics' (CCG) large-scale generation of high-throughput genomic data. Under this RFP, the NCI is soliciting proposals for Genome Characterization Centers (GCCs) that must be capable of completing comprehensive genomic characterizations of different tumor types in a timely manner and with high quality standards. Prior contribution to large scale genomics projects such as The Cancer Genome Atlas (TCGA) Project is not required and all qualified institutions and individuals are encouraged to apply to this RFP. The purpose of this Small Business Sources Sought Notice (SBSS) is to identify qualified small business concerns that are interested in and capable of performing the work described herein. On behalf of the Division of Cancer Prevention, the NCI does not intend to award a contract on the basis of responses received nor otherwise pay for the preparation of any information submitted. As a result of this SBSS Notice, the NCI may issue a Request for Quote (RFQ). THERE IS NO SOLICITATION AVAILABLE AT THIS TIME. However, should such a requirement materialize, no basis for claims against NCI shall arise as a result of a response to this Small Business Sources Sought Notice or the NCI's use of such information as either part of our evaluation process or in developing specifications for any subsequent requirement. Project Requirements: The overarching goal for the GCCs is to perform high-resolution, systematic and comprehensive characterization of cancer-related genomic alterations in multiple types of cancers for an expanding list of National Cancer Institute (NCI)-supported genomics projects. These genome-wide characterizations should be conducted with validated methods using high-throughput and quality controlled pipelines. The GCCs will receive cancer biomaterials (DNA, RNA, protein or other types of molecular analyte) and associated data from a centralized Biospecimen Processing Center (funded by NCI separately). The aim is to have all molecular characterizations conducted on biomolecules from the same biospecimens for optimal analytical integration and for data comparability. The specific or mandatory requirements for characterization platforms will be identified in a separate Task Order Statement of Work. All Contractors shall perform the following tasks in general: 1. Receive molecular analytes from BCR 2. Operate genome characterization pipelines 3. Perform Quality Control 4. Improve performance of characterizations 5. Informatics and Data Delivery 6. Conduct Transition Activities Delivery: Public availability of data/information generated by GCCs will be critical to facilitate disease-relevant discoveries of clinical significance. Data generated by GCCs shall be transmitted into NCI Genomic Data Commons (GDC) as soon as they are validated, in general within four weeks of generation. GCCs will submit primary data and metadata to GDC by adapting their submission process to meet the submission requirements of GDC. Contractors are required to submit a Data Sharing Plan documenting how data will be released and shared. The Data Sharing Plan must be consistent with the goals of CCG and NCI genomic programs, with adherence to NIH data sharing policies for the protection of human subjects. Other Important Considerations: A copy of the Draft Statement of Work (SOW), which is subject to revisions, is attached. Capability Statement/Information Sought: Respondents must be qualified and prepare tailored capability statements for all areas in the attached draft Statement of Work. The capability statements will be evaluated based on the information provided in relation to the project requirement and current capability. Information Submission Instructions: 1. Page Limitations: Interested qualified small business organizations should submit a tailored capability statement for this requirement not to exceed ten (10) single sided pages including all attachments, resumes, charts, etc. (single spaced, 12 point font minimum) that clearly details the firm's ability to perform the aspects of the notice described above and in the draft SOW. Statements should also include an indication of current certified small business status; this indication should be clearly marked on the first page of your capability statement, as well as the eligible small business concern's name, point of contact, address and DUNS number. 2. Number of Copies: One (1) electronic copy of the capability statement submitted electronically (via e-mail) to Alexis Hudak, Contracting Officer at alexis.hudak@nih.gov. 3. Delivery Point: All capability statements sent in response to this SOURCES SOUGHT notice must be submitted electronically (via email) to Alexis Hudak, Contracting Officer, at alexis.hudak@nih.gov in MS Word or Adobe Portable Document Format (PDF), by January 31, 2018 at 2:00 PM, EST. All responses must be received by the specified due date and time in order to be considered. No calls or facsimile transmissions will be accepted. CAPABILITY STATEMENTS RECEIVED AFTER THIS DATE AND TIME WILL NOT BE CONSIDERED. DISCLAIMER AND IMPORTANT NOTES: This notice does not obligate the Government to award a contract or otherwise pay for the information provided in this response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization's qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a pre-solicitation synopsis and solicitation may be published in Federal Business Opportunities. However, responses to this notice will not be considered adequate responses to a solicitation. CONFIDENTIALITY: No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s). Contracting Office Address: 8490 Progress Drive, Suite 400 Riverside Five Frederick, MD 21701 Primary Point of Contact: Alexis Hudak Contracting Officer alexis.hudak@nih.gov Phone: 301-624-8753