Bioinformatics: Biomarkers of early detection

NASA Jet Propulsion Laboratory, Pasadena, CA, USA.
Cancer biomarkers: section A of Disease markers (Impact Factor: 1.72). 01/2011; 9(1-6):511-30. DOI: 10.3233/CBM-2011-0180
Source: PubMed


Capturing, sharing, and publishing cancer biomarker research data are all fundamental challenges of enabling new opportunities to research and understand scientific data. Informatics experts from the National Cancer Institute's (NCI) Early Detection Research Network (EDRN) have pioneered a principled informatics infrastructure to capture and disseminate data from biomarker validation studies, in effect, providing a national-scale, real-world successful example of how to address these challenges. EDRN is a distributed, collaborative network and it requires its infrastructure to support research across cancer research institutions and across their individual laboratories. The EDRN informatics infrastructure is also referred to as the EDRN Knowledge Environment, or EKE. EKE connects information about biomarkers, studies, specimens and resulting scientific data, allowing users to search, download and compare each of these disparate sources of cancer research information. EKE's data is enriched by providing annotations that describe the research results (biomarkers, protocols, studies) and that link the research results to the captured information within EDRN (raw instrument datasets, specimens, etc.). In addition EKE provides external links to public resources related to the research results and captured data. EKE has leveraged and reused data management software technologies originally developed for planetary and earth science research results and has infused those capabilities into biomarker research. This paper will describe the EDRN Knowledge Environment, its deployment to the EDRN enterprise, and how a number of these challenges have been addressed through the capture and curation of biomarker data results.

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    ABSTRACT: Background: The National Cancer Institute's Early Detection Research Network (EDRN) has made significant progress in developing an organized effort for discovering and validating biomarkers, building resources to support this effort, demonstrating the capabilities of several genomic and proteomic platforms, identifying candidate biomarkers, and undertaking multicenter validation studies. In its first 10 years, the EDRN went from a groundbreaking concept to an operational success. Contents: The EDRN has established clear milestones for reaching a decision of "go" or "no go" during the biomarker development process. Milestones are established on the basis of statistical criteria, performance characteristics of biomarkers, and anticipated clinical use. More than 300 biomarkers have been stopped from further development. To date, the EDRN has prioritized more than 300 biomarkers and has completed more than 10 validation studies. The US Food and Drug Administration has now cleared 5 biomarkers for various clinical endpoints. Summary: The EDRN today combines numerous collaborative and multidisciplinary investigator-initiated projects with a strong national administrative and data infrastructure. The EDRN has created a rigorous peer-review system that ensures that preliminary data--analytical, clinical, and quantitative--are of excellent quality. The process begins with an internal review with clinical, biostatistical, and analytical expertise. The project then receives external peer review and, finally, National Cancer Institute program staff review, resulting in an exceptionally robust and high-quality validation trial.
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