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249 System to Analyze and Support Biomarker Research and Development Strategies

Number of anticipated awards: 3-4
(Fast-Track proposals will be accepted.)
Budget (total costs): Phase I: $150,000;
Phase II: $750,000

The deadline for receipt of all contract proposals submitted in response to this solicitation is: 5:00 p.m. Eastern Standard Time Monday, November 5, 2007

Because of the rapid expansion of the worldwide biomarker research data in volume and breadth, there is a critical need for integrating all of these data within a knowledge management system that supports automated review and evaluation of current research and development efforts, particularly within the context of all cancer research and therapeutic and diagnostic product development. Such a system permits rapid identification and decision-making to allocate resources where they can most efficiently be used to enhance product development.

Thus, the objective of this project is to expand the present methodology of biomarker research data analysis and strategic planning using a system that allows review and analysis of biomarker research and development projects as they relate to available worldwide data. The system would permit rapid identification and correlations of parameters of interest to the users' senior scientific staff, while simultaneously providing high-efficiency development pathways for program areas of interest. The system should incorporate parameters allowing evaluation of methods/assays, tissue and disease specificities, clinical applications, and regulatory and clinical development status. The system when fully developed may be applied over a broad range of technologies such as genomics and proteomics, imaging modalities, immunohistochemistry, and histopathology. Also, when fully developed, the system should be usable by the private sector (e.g., pharma, biotech, diagnostics industries, etc.) and the public sector (e.g., NCI programs such as Developmental Therapeutics, SPOREs, EDRN, Cancer Imaging, OBQI, PACCT, NTROI, and intramural and extramural investigator-initiated research). Potential offerors can propose projects to comprehensively include all relevant cancer-related biomarkers or specific subsets (e.g., toxicity biomarkers) under a relational database system.

An example application would be selection of a biomarker of a molecular target (e.g., a mutated tyrosine kinase), all published drugs/chemicals that interact with the target, all cancer target organs that have the biomarker and in what incidence, stage(s) of cancer progression where the biomarker is found, existing assays to measure the biomarker and their states of development and use, toxicity associated with biomarker modulation, etc.

Project goals:

The core of the system will be a database cataloging and classifying the biomarker research projects with links to the original data sources. The remainder of the system will be tools (reports and algorithms) for summarizing, analyzing, and integrating the data with other sources. Multiple parameters describing the biomarkers cited shall be extracted into the database—e.g., biomarker name, clinical use, cancer target organ (clinical and non-clinical), specimen source, technology/assay methodology and/or assay target, biological process related to neoplastic progression (e.g., angiogenesis, proliferation, apoptosis), signaling pathway, drug or other intervention used in study (as appropriate), biomarker category (e.g., prognostic, predictive, risk, drug effect), disease stage, study population demographics, and phase of clinical study. The database shall be fully searchable (for individual records and categories of data) on all these parameters. The database shall be capable of supporting a large base of concurrent users via a user friendly, web-based user interface.

The database and other components of the system shall be built with open source code compatible with current industry and NCICB standards (e.g., J2EE, ANSI compliant SQL and Eclipse). Since NCI has invested substantially in developing informatics for cancer-specific uses, where possible, applications previously developed by NCICB should be leveraged. For example, applications developed for the Cancer Bioinformatics Grid™ (caBIG™) should be considered, and the system should be integrated with caBIG™ applications, if appropriate. The system should be fully integrated with the NCI Enterprise Vocabulary System (EVS) and should use EVS terminology (and should comply with NCI's Cancer Data Standards Repository (caDSR) metadata standards, using NCI approved Common Data Elements where appropriate). However, the system developed should be compatible with other users' specific requirements.

System and user documentation shall be provided, quality control procedures shall be developed and applied to maintenance of the system, and quality assurance audits shall be carried out periodically. The project shall also include organization and administration of technical and scientific advisory groups involved in the design and implementation of the system.

Phase I activities and expected deliverables:

  • Review a large, representative sample of relevant biomarker data and literature to develop an overall biomarker research program analysis and support model. Determine what, if any, algorithms exist to convert present research portfolio databases (electronic, manual, and hybrid) into an integrated automated knowledge management system that fulfills strategic research and business planning requirements for multiple users.
  • Determine what, if any commercial software products exist that may serve as a platform for the proposed research program analysis and support tool. For example, the proposed product might be best developed as an add-on to an existing portfolio management package.
  • Convene a focus group of senior scientists to solicit input on the scientific content and functionality required for the proposed product.
  • Evaluate the availability of research data in the world-wide scientific literature with respect to the desired selection and measurement parameters. Identify problems with comparability and availability of research and administrative data over time and as collected by different systems.
  • Develop a statement of functional requirements and user interface requirements for the product.
  • Develop a prototype of the system using a representative sample of biomarkers.
  • Include funds to present Phase I findings and system design.

Phase II activities and expected deliverables:

  • Conduct a formal usability study of the software with representative users to evaluate the prototype system developed in Phase I. Enhance and modify the prototype’s functionality and user interface based on this feedback.
  • Complete two iterations of the tracking program software, including technical documentation of the system and a training manual. Documentation of the system design, business procedures (SOPs), data sources, data extraction guidelines and evaluation criteria shall be prepared. An indexed/searchable User Guide describing data sources, data parameters, evaluation criteria, and system functionality (e.g., searching, report generation and linking to data sources) shall be prepared. SOPs shall include quality control procedures for data entry (e.g., data edit checks).
  • Develop and implement a project plan for populating, updating, and maintaining the biomarkers database.
  • Develop evaluation measures.
  • Demonstrate the flexibility of design that would permit updating the software as new biomarkers, research modalities, treatments, data formats, or other parameters of interest are added.
  • Documentation of the database design, business procedures (SOPs), data sources, data extraction guidelines and evaluation criteria shall be prepared upon implementation of the database and shall be updated annually. An indexed/searchable User Guide describing data sources, data parameters, evaluation criteria, and database functionality (e.g., searching, report generation and linking to data sources) shall be prepared and loaded on the database website. SOPs shall include quality control procedures for data entry (e.g., data edit checks).
  • Identify Phase II barriers to evaluating the impact of the software and resolutions to these barriers.
  • In the first six months of the first year of the contract, provide the program and contract officers with a letter of commercial interest to either purchase or subscribe to the system once it is created.
  • In the first six months of the second year of the contract, provide the program and contract officers with a letter of commercial commitment based on the successful outcome of the Phase II. It is anticipated that potential customers would be the NCI, NIH, and others in the public sector; and pharma, biotech, diagnostics industry, clinical laboratory industry, and others in the private sector.

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