SOURCES SOUGHT
A -- GenPort - Genomics Portal
- Notice Date
- 4/9/2015
- Notice Type
- Sources Sought
- NAICS
- 541712
— Research and Development in the Physical, Engineering, and Life Sciences (except Biotechnology)
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Heart, Lung and Blood Institute, Rockledge Dr. Bethesda, MD, Office of Acquisitions, 6701 Rockledge Dr RKL2/6100 MSC 7902, Bethesda, Maryland, 20892-7902
- ZIP Code
- 20892-7902
- Solicitation Number
- HHS-NIH-NHLBI-RDSS-HR-16-15
- Point of Contact
- Christopher Schaupp, Phone: 3014350364
- E-Mail Address
-
cschaupp@nhlbi.nih.gov
(cschaupp@nhlbi.nih.gov)
- Small Business Set-Aside
- N/A
- Description
- Introduction 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 NAICS code 541712 should not submit a response to this notice. Background Omics data from well phenotyped human cohorts are an invaluable window into the involvement of particular molecules and pathways in diseases. While much omics data has been made accessible through programs such as dbGaP, most investigators lack the bioinformatic expertise and computational tools that are required to analyze available data. Hence, there is widespread interest in developing tools that will provide non-informatic scientists, as well as informaticians, the opportunity to probe multi-platform, individual-level omics data. Providing wider access to omics data will help to focus basic science and human biomarker research on pathways and systems that are most relevant to human disease. Furthermore, the quantity of omics data is increasing at an explosive rate. For example, NHLBI has launched a Whole Genome Sequencing (WGS) project that is generating sequence data from approximately 20,000 well-phenotyped individuals in heart, lung, blood, and sleep (HLBS) cohorts. The WGS project defines a "high value" collection of cohorts and studies that will be used as the focus of the GenPort program, which will support development of a web-based portal for user-friendly access to and analysis of WGS-generated sequences, together with other omics and phenotypic data from these subjects. Purpose and Objectives The GenPort program is expected to leverage and be interoperable with NIH's NIH Big Data to Knowledge (BD2K) initiative http://bd2k.nih.gov/#sthash.AmaOgKKl.dpbs, which is currently developing tools for integration and analysis of large, multi-dimensional data sets. The GenPort contractor is expected to use general methods and approaches being developed through other efforts such as BD2K, to customize those tools to the data characteristics, scientific questions, and investigator capabilities of HLBS research. Project Requirements The NHLBI is seeking a small business with the ability to create and operate a genomics portal (GenPort) that will provide HLBS researchers access to genomic and phenotypic data from multiple cohort studies, together with tools for creating synthetic cohorts and performing statistical analyses. At a minimum, Offerors must document capabilities to develop, operate, and maintain a resource that facilitates investigators' access to and analysis of existing omics, molecular, and phenotypic data from a select group of cohorts of human subjects. In addition to developing and providing information technology systems needed for interfacing with users and for accessing individual level study data, the GenPort contractor will 1) harmonize data elements across studies and identify phenotypes of relevance to HLBS conditions that can be defined across multiple studies, 2) support the creation of synthetic cohorts by external users which may draw subject data from multiple primary studies, 3) provide web-based analytical tools for data visualization and analysis, 4) deliver individual level data to approved recipients for their advanced analyses, and 5) provide educational resources and/or links to educational resources that assist inexperienced users wishing to explore the datasets accessible through GenPort. The GenPort resource will incorporate and harmonize data from multiple studies. All software and tools developed for GenPort will be open source, transportable, and freely shared. To the extent practical, GenPort systems will be interoperable with informatics resources developed through the BD2K initiative (http://bd2k.nih.gov/#sthash.In0UiDjR.dpbs). The selected contractor must comply with the NIH Genomic Data Sharing (GDS) Policy (http://gds.nih.gov/) and adhere to NIH Security Best Practices for Controlled-Access Data Subject to the NIH Genomic Data Sharing (GDS) Policy (http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/GetPdf.cgi?document_name=dbgap_2b_security_procedures.pdf). Capability statements must document prior experience of the potential offeror for each of the activities detailed below. Capability statements must also identify available personnel with appropriate expertise, which must include information systems technology, bioinformatics, genomics, phenotype harmonization among human research studies with cardiopulmonary measures, and biomedical education. Contract activities included but are not limited to the following: 1. Create a Database and Catalogue of Studies. Obtain access to phenotype and whole genome data from approximately 10 studies per year related to HLBS conditions, together with permission to re-distribute those data to secondary users as an "NIH Trusted Partner" (http://gds.nih.gov/02dr2.html). Studies must be chosen from among those selected by NHLBI for whole genome sequencing and must include at least one study with phenotypic data related to each of heart, lung, blood, and sleep research. Create a GenPort database including study data, available omics data, and genome-wide genetic variant data for these studies. Develop a tabulation of key information from these studies (e.g., sample size, inclusion/exclusion criteria, cohort demographics, data collected, methods, data quality, data use restrictions) needed by investigators to evaluate the value of study data for contemplated secondary analyses. Maintain the confidentiality of the data received, produced, and distributed. Maintain a secure, off-site backup of GenPort data and software. In accordance with HHSAR Clause 352.239-72, Security Requirements For Federal Information Technology Resources, the contractor shall be required to submit an IT-Security Plan. 2. Provide Logistical Management of an External Advisory Committee. Nominate members and arrange for meetings of an External Advisory Committee which shall provide advice to the GenPort contractor on scientific issues relevant to GenPort development and operations. 3. Create a Dictionary of Common Data Elements. For each pair of studies selected for inclusion in the GenPort database, identify data elements for which the study designs are sufficiently similar to allow combined analyses of those data elements. Document any differences in study designs that would limit the reliability of combined analyses or could generate systematic errors in those analyses. Incorporate within the GenPort database annotations that indicate the comparability of data elements between studies. 4. Curate Harmonized Phenotypes. Define at least 20 discrete or quantitative phenotypes that can be specified using the data elements or combinations of the data elements available in the GenPort database. Incorporate these phenotypes as computed variables in the GenPort database. 5. Develop a Tool for Creating Synthetic Cohorts. Develop a data query system that permits users to define synthetic cohorts by selection of individuals from multiple studies in the GenPort database through specification of phenotypes or custom ranges of data values. Users shall be able to specify inclusion and exclusion criteria as Boolean combinations of at least six data elements, computed variables, and/or defined phenotypes. Develop interactive analytical and informatics tools for identifying research subjects meeting specified criteria, for performing basic analyses of subject data within these synthetic cohorts, and for reporting and visualizing the analytical results. Analyses shall include statistical characteristics of single data elements (distribution, mean, standard deviation, etc.), measures of relationship between pairs of data elements within a cohort (e.g., correlation coefficients, scatter plots, etc.), and statistical comparisons of data elements between or among cohorts (e.g., case-control design). 6. Develop Tools for Downloading Individual Level Data. Develop or adapt existing software utilities to allow approved users to download selected individual level data elements from synthetic cohorts defined through the GenPort system. Data shall be provided to users in standard formats appropriate to the data content and file size, which may include tab-delimited text, SAS, PLINK, and VCF. For datasets that may be too large for practical storage within the GenPort system (e.g., whole genome sequence data), develop web service application programming interfaces (APIs) for analyzing and/or downloading "big data" (e.g., whole genome sequence data) that are linked to subjects in the GenPort database but are stored remotely (e.g., in enterprise-level cloud data storage). 7. Develop or Adapt Tools for Omics Data Visualization and Analysis. Develop or adapt existing software utilities for visualization of and statistical analyses of transcriptomic and genetic data within the GenPort database. Analytical and informatics capabilities shall include data quality assessment and control, preprocessing and scaling, univariate and bivariate statistics, multivariate regression, identification of differentially expressed genes, principle components analysis, unsupervised clustering, allelic association testing, and logistic regression. Visualization capabilities shall include volcano plots, heat maps, and Manhattan plots. Develop interfaces that allow web-based specification of analyses as well as visualization and downloading of results. 8. Provide Educational Resources. Develop or link to existing reference materials that are appropriate for self-study by biologically trained scientists and that provide sufficient information to allow individuals without prior experience in omics or genetics research to 1) understand the objectives, approaches, and limitations of omics and genetics research, 2) utilize GenPort to conduct preliminary analyses of existing omic and genetic data, and 3) effectively communicate regarding questions and hypotheses relevant to their own research with experts in omics and informatics. 9. Design and Implement Procedures for Registering Users and Processing Data Requests. Develop and implement a web-based process for online registration of external GenPort users, for controlling their access to data and analyses, and for tracking their use of the portal. Downloads of individual level data will be permitted only by individuals who have submitted a specific application through a procedure analogous to that employed for access to data stored in dbGaP (see https://www.ncbi.nlm.nih.gov/gap), and whose application has been approved by the NHLBI. 10. Create and Operate a Web-based User Interface. Develop a public website that accepts registration requests from potential users and allows access to all of the GenPort features described in sub-tasks 1-9, above. The website shall provide an intuitive interface that allows users to readily understand the purpose and capabilities of GenPort and to access the resources available through it. Access to features and data that could compromise the confidentiality or privacy of human subjects shall be password-restricted to approved users (see subtask 9, above). The website shall track in a statistical manner user activities, data access by study, data downloads, and analyses performed. The website shall also include a description of GenPort organization and procedures, a link to the NHLBI public web site, GenPort contact information, and a means of collecting feedback from users. The website must acknowledge NHLBI as funding source for the study, provide a link to the NHLBI public website at http://www.nhlbi.nih.gov/, and be compliant with the standards of Section 508 of the Rehabilitation Act (see http://www.access-board.gov/508.htm) described in Subparts B 1194.21, 1194.22, 1194.31, and 1194.41. http://www.access-board.gov/508.htm) described in Subparts B 1194.21, 1194.22, 1194.31, and 1194.41. 11. Advertise the availability of GenPort through efficient media designed to reach heart, lung, blood, and sleep scientists whose research could be enhanced through omics analyses. Prepare and publish reports that describe GenPort datasets, capabilities, processes, and best practices. 12. Provide support to GenPort users, which shall include soliciting and responding to queries from individual users regarding GenPort capabilities and analytical tools, study protocols and data, harmonized data elements, and phenotypes. Track the number and nature of queries and the time between query submission and response. 13. Provide continuing administration of the GenPort program, which shall include annual ethical review of GenPort procedures, maintenance of access to study data, correction of any flaws in tools and errors in data elements that are recognized, updating of educational materials and links, and logistical management of GenPort committees and boards. 14. Solicit, receive, summarize and evaluate feedback from GenPort users regarding user satisfaction with the portal and its operation; validity of curated data, annotations, and phenotypes; accuracy and understandability of educational resources; contribution of GenPort usage to research planning, establishing collaborations, and applying for research funding; and users' research progress and publications enabled by GenPort. Anticipated Period of Performance: The Government intends to negotiate one Indefinite Quantity Indefinite Delivery (IDIQ) contract that may include cost-reimbursement and or fixed price task orders for a period of five years with an approximate award date of September 14, 2016. Capability Statement Small business concerns that believe they possess the capabilities necessary to undertake this work should submit complete documentation of their capabilities to the Contracting Officer. The capabilities statement must specifically address each project requirement separately. Additionally, the capability statement should include: 1. Evidence of ability to perform and experience in fulfilling GenPort functions, including methods for coordination, monitoring, and central management of all activities; 2. Evidence of ability to perform and experience in performing the project requirements described above; 3. Qualifications and availability of proposed personnel, with experience pertinent to the operation of GenPort, data collection and analysis, monitoring, standardization, quality assurance, quality control, preparation of scientific reports. Potential Offerors shall include information to support that it has the necessary staffing; 4. Evidence of the organizational and administrative structure capable of meeting the needs of the proposed program. Potential Offerors shall include information on: a) prior successful participation in similar programs, as well as experience in processing and analyzing human omics data; and b) facilities, equipment, and space; 5. Experience in administrative and scientific leadership and coordination necessary for exercising appropriate leadership in matters of data acquisition, management, and analysis. 6. Ability to recruit and engage scientific expertise in the areas of heart, lung, and blood diseases as required by products or services requested; 7. The firm's status as a small business under NAICS code 541712 8. The total number of employees; 9. A description of general and specific facilities and equipment available, including computer equipment and software; 10. An outline of previous research projects that are similar to the project requirements in which the organization and proposed personnel have participated, and 11. Any other information considered relevant to this program. The capability statement must not exceed 15 single sided or 7.5 double sided pages in length and using a 12-point font size minimum. Interested small business organizations are required to identify their size standards in accordance with the Small Business Administration. The government requests that no proprietary or confidential business data be submitted in a response to this notice. However, responses that indicate the information therein is proprietary will be properly safeguarded for Government use only. Capability statements must include the name and telephone numbers of a point of contact having authority and knowledge to discuss responses with Government representatives. Capability statements in response to this market survey that do not provide sufficient information for evaluation will be considered non-responsive. When submitting this information, please reference the solicitation notice number. All capability statements sent in response to this Sources Sought Notice must be submitted electronically (via email) to Christopher Schaupp, Contracting Officer, at mail to: cschaupp@nhlbi.nih.gov in MS Word or Adobe Portable Document Format (PDF), within 15 calendar days of the date of this announcement. All responses must be received by the specified due date and time in order to 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 the response. No proprietary, classified, confidential, or sensitive information should be included in your 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 review of the responses received, pre-solicitation and solicitation notices may be published in Federal Business Opportunities. However, responses to this notice will not be considered adequate responses to a solicitation. The solicitation release date is pending. Original Point of Contact Christopher Schaupp, Contracting Officer, NHLBI Extramural Contracts Branch, Phone (301) 435-0364, Email: cschaupp@nhlbi.nih.gov Department of Health and Human Services, National Institutes of Health, National Heart, Lung and Blood Institute, Rockledge Dr. Bethesda, MD, Office of Acquisitions 6701 Rockledge Dr RKL2/6016 MSC 7902, Bethesda, MD, 20892-7902, UNITED STATES
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