caBIG^® Product Inventory

caBIG^® offers a suite of software development toolkits, applications, database technologies, and Web-based applications to meet a wide range of needs for the cancer research community. Below is a partial list of such caBIG^® tools. For a more complete list, or to access these tools, please visit https://caBIG.nci.nih.gov/inventory.

CLINICAL TRIAL MANAGEMENT SYSTEMS

Challenge
The most expensive and time-consuming part of the development of new therapeutics is clinical development. The development process costs an estimated $800 million or more per product, and clinical trials take many years to design, implement, compile results, and submit to regulators. At present, there is no standardized, uniform system for clinical trial management, and no central registry of all cancer-related clinical trials. Moreover, only a small number of cancer patients actually participate in clinical trials of experimental therapies. "Legacy," or paper-based, information systems for clinical trials are slow and inefficient for the collection, analysis and sharing of data, resulting in unnecessary work delays, duplication of effort, human errors in data entry, and missed opportunities for data mining and secondary use of the data.

The Role of caBIG^®
Partnering with organizations that design and run clinical trials, regulatory bodies, pharmaceutical companies and the patient advocacy community, caBIG^® has delivered the capabilities described below. In the aggregate, they comprise the building blocks of a system for end-to-end collection, management, and exchange of information from the electronic medical record through regulatory submission.

The caBIG^® Clinical Trials Compatibility Framework
This modular open-source suite of tools is designed to lower the barriers to clinical trial conduct at NCI-designated Cancer Centers and other trial sites. The Suite includes software that provides a central repository for the management of research participants management and reporting of adverse events encountered during trials, the automatic generation of calendars for participants and the automatic transfer of laboratory and other data between clinical care systems and clinical research systems.

Clinical Data Management System (CDMS)
NCI has made strategic procurements of two generations of clinical data management system (CDMS), available to the entire NCI-supported clinical research enterprise. The first generation, the Cancer Central Clinical Database, provides the infrastructure to collect and manage clinical trial data in a manner that supports reuse and efficiency in building studies. caBIG^® is in the final stages of the second CDMS procurement, which will unify the NCI Cooperative Groups, responsible for over 1,700 trial sites, over 30,000 new accruals per year and more than 100,000 patients in active follow-up, with a common, paperless standards-based infrastructure. These systems deliver full-function clinical data management capability to the entire NCI-supported clinical research community, irrespective of ability to pay, and will integrate with the caBIG^® Clinical Trials Compatibility Framework, allowing researchers to share information with other caBIG^® compatible systems and tools, within and between research organizations, as well as with NCI.

Regulatory Submission of Clinical Data
caBIG^® has delivered the first two components of a standards-based electronic infrastructure for submission of regulatory information, developed in association with the Food and Drug Administration (FDA). The first component, FIREBIRD, allows electronic submission of investigator accreditation investigation, previously a cumbersome paper-based process. The second component, Janus, provides a standards-based data repository for clinical information required in regulatory submission. The Janus standard will integrate with another current caBIG^® initiative, which is delivering through broad consensus a series of standard case report forms consisting of common data elements.

caBIG^® Clinical Trials Product Inventory

Cancer Central Clinical Participant Registry (C3PR)
Patient Study Calendar (PSC)
Cancer Adverse Event Reporting System (caAERS)
Cancer Data Exchange (caXchange)

Benefits

• Reduced human error
• Consistent format, language, and structure throughout the entire life cycle of the trial, enabling reliability and comparability of results, particularly for multi-site trials
• Better molecular sub-grouping of patients to improve clinical outcomes
• More efficient and systemized administrative process, reducing costs
• Greater potential accessibility to larger population of patients for faster enrollment

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LIFE SCIENCES

Challenge
Modern molecular-based research is generating vast amounts of complex data that must be collected, aggregated, and correlated in order to identify biological pathways and genetic signatures. Currently, there is no centralized or easy to use informatics infrastructure in place to handle this huge and growing tidal wave of information. Tools that can synthesize large amounts of data from disparate sources and present it in a visual format are enabling cancer researchers to spend more time innovating and less time collating numbers and connecting data sources.

The Role of caBIG^®

An integrated caBIG^®-enabled software system has been developed that includes an analytical pipeline, a data management system, data access portals and visualization tools for analyzing and disseminating the integrated cancer genomic data to the research community. As a result, researchers can correlate key observations from diverse collections of genomic data, such as SNPs and copy number changes, with clinical information to help prioritize research activities.

Cancer Molecular Analysis (CMA) Portal

The caBIG^®–enabled Cancer Molecular Analysis (CMA) Portal (http://cma.nci.nih.gov) provides tools and resources that enable cancer researchers to explore, visualize, and integrate genomic characterization, sequencing, and clinical data from a variety of data sets.

For example, the Portal allows researchers to use analysis programs developed at three different organizations, and to access data produced by more than 10 different institutions, all by a unified web interface. Portal tools allow researchers to access clinical characteristics such as survival data and tumor staging, and correlate those with mutation and other genomic data. This capability enables researchers to conduct cross-platform queries, helping them to find correlations between research and clinical data that would be difficult, if not impossible, to find using conventional means.

Cancer Genome Wide Association Studies (caGWAS)

In Genome Wide Association Studies (GWAS), DNA markers are scanned across the genomes of many individuals to find genetic variations associated with a particular disease. But researchers need sophisticated tools in order to make sense of the potentially millions of data points generated in a single GWAS study.

Cancer Genome-Wide Association Studies (caGWAS) is a data management system that allows researchers to integrate, query, report, and analyze significant associations between genetic variations and disease, drug response or other clinical outcomes, helping researchers to find the “needle in a haystack”. caGWAS accelerates the process of analyzing results from whole genome association studies and allows researchers and bioinformaticians to access and analyze clinical and experimental data across multiple clinical studies.

The Cancer Genetic Markers for Susceptibility (CGEMS) project represents the first public release of a GWAS study for cancer. Accessible by the caBIG^®-enabled CGEMS data portal (http://cgems.cancer.gov), over 500,000 SNPs have been analyzed so far, facilitated by caGWAS to produce and upload pre-computed results tables rapidly. The data generated as part of the CGEMS program has already helped identify variations in Fibroblast Growth Factor Receptor 2 (FGFR2), associated with increased risk for breast cancer, and multiple novel loci associated with increased risk for prostate cancer.

caBIG^® Life Sciences Product Inventory

caArray
Cancer Genome-Wide Association Studies (caGWAS)
Cancer Molecular Analysis Portal (CMA)
Cancer Genetic Markers for Susceptibility (CGEMS)

Benefits

• Access to, and integrated analysis of, data from diverse genomic and clinical sources
• Ability to find novel correlations across data sets
• Accelerated discovery of molecular signatures

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IN VIVO IMAGING

Challenge
There is currently no system in place to share or archive images among clinicians and researchers, to validate clinical research hypotheses, or to facilitate development of new diagnostics, prognostics, or therapeutic algorithms. As a result, there is no "reference source" that embodies the community’s collective experience and knowledge.

The Role of caBIG^®

• National Cancer Imaging Archive: This in vivo image repository provides the cancer research community, industry, and academia with access to image archives that can store and manage a variety of medical images. Additional imaging tools including Annotation Imaging Markup (AIM) and the eXtensible Imaging Platform (XIP), aid the development and validation of analytical software tools supporting lesion detection and classification, accelerated diagnostic imaging evaluation, and quantitative imaging assessment of drug response. The Imaging Middleware tools provide services and extensions to caGrid enabling the exchange and analysis of DICOM-format medical images.

caBIG^® Imaging Product Inventory

National Cancer Imaging Archive (NCIA)

Annotation Imaging Markup (AIM)

eXtensible Imaging Platform (XIP)

Imaging Middleware/Virtual PACS

Benefits

• Digitized format enables information to be merged with other data sources
• Tools provide the ability to capture standardized image annotation and markup that can be exchanged between sites
• Improved clinical decision support: researchers can see a patient’s response to treatment more quickly, accurately, and objectively

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TISSUE BANKS AND PATHOLOGY TOOLS

Challenge
It is widely known that access to large quantities of high-quality, clinically annotated human biospecimens is critical to genomics-based research. Yet, at present, there is a lack of standardized, integrated systems for collecting, processing, archiving, and disseminating biospecimens and associated clinical data, either within or across multiple institutions. As a result, discovery research does not progress as rapidly as possible. While polices, conflicting regulations, and other non-technical issues contribute to this problem, creating readily available software supporting the highest standards of biospecimen and data collection is considered one of the biggest hurdles, and thus a key focus for caBIG^®.

The Role of caBIG^®

NCI’s Best Practices for Biospecimen Resources¹ identify the importance of software interoperability to manage biospecimens, with the dual goals of integrating the repository with other research functions and with other biospecimen resources. Towards those goals, caBIG® has delivered:

caTissue Suite

This suite integrates biospecimen management (caTissue Core), annotation with clinical data and data extracted from pathology reports (caTIES). caTissue Core provides browser-based and programmatic access to biospecimen data, provides a means for collecting, processing, storing, and distributing specimens for correlative science cancer research, manages tissue, fluid, cell and molecular biospecimen information, and allows users to find and request specimens needed for use in molecular correlative studies.

caBIG^® Tissue Banks and Pathology Tools Product Inventory

caTissue Core

caTissue Suite

caTIES

Benefits

• Expanded access to sets containing statistically significant numbers of high-quality, clinically annotated specimens for molecular research available from a network of connected research facilities
• Ethically-based chain of trust that ensures patient privacy and confidentiality, in compliance with human research subject and patient protection regulations

caGrid

caGrid is the enabling infrastructure, which allows researchers to be able to share biomedical research data and the community to use their expertise to add value to that data. caGrid is an example of a “service oriented architecture” (SOA) that simplifies connecting software tools and data collections so large groups of users can access the information. It is similar to a power grid, but without the wires. caGrid itself provides no real "data" or "analysis" to caBIG^®. Rather it provides core “services”, software tools and common interfaces so that the community can access these data collections for their own use. Some of these services are “analytical services” that perform a function on the data. Other services are “data services” which is another term for a collection of data that is accessible on the grid.

Benefits

• The “power grid” of caBIG^® that serves as the framework that enables data sharing and collaboration between researchers at diverse sites.

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¹   “NCI Office of Biorepositories and Biospecimen Research, http://biospecimens.cancer.gov.