The Harvest Program: Integrated Research Databases

DBHi's Harvest program integrates data from multiple clinical and research-focused sources to generate a cohesive view of a patient relative to a therapeutic area.

  • Integration of genomic, imaging, research, and clinical endpoints
  • Dynamic querying engine with visualizations
  • Hypothesis-driven exploration of data

AudgenDB, the result of a collaboration with CHOP's Center for Childhood Communication, is DBHi's first developed iteration of the Harvest paradigm for a specific therapeutic or disease area. Audiologists and other researchers can dynamically query the data to return aggregate reports or individual cases, all within an interface that allows for seamless reconciliation of the integrated data types.

DBHi is currently seeking to apply its in-depth knowledge of CHOP's data systems, including the Epic EHR, genomic, imaging, and other research data sources into intuitive querying and reporting systems. Please contact Jeff Pennington, Director of DBHi's Translational Informatics Unit, to start a discussion.

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The Care Assistant Program: EHR Prompts, Interventions, and Decision Support

With some robust customizations and a governance model that allows for it, research interests can be represented in an EHR via our proprietary Care Assistant

  • Research recruitment prompts in EHR during patient visit
  • EHR-mediated interventions and alerts
  • EHR-mediated decision support
  • Complex decision support with advanced discovery engines and visualizations

Applications currently implemented within the Care Assistant program include those for:

DBHi also maintains language that can be inserted into protocols for regulatory and security purposes.

Please contact Marianne Chilutti to make a request for this language.

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Proband - Pedigrees Made Simple

Proband is an iPad(tm) application designed to capture a patient's genetic family history during the clinical encounter. Rapid data capture means pedigrees can be stored electronically during the interview, instead of transcribed later. The Department of Biomedical and Health Informatics at The Children’s Hospital of Philadelphia developed and tested the app with our genetic counselors in actual clinical settings. Proband has fully editable functionality and can capture any level of detail, without page size limitations. It stores information in a structured format for use by other software, computing systems, and clinical decision support algorithms. The app is available for download in the Apple iTunes store.

Click here to learn more about Proband.

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Biorepository Portal Toolkit

Designed with the modern biorepository in mind, the Biorepository Toolkit integrates key system components in a user-friendly interface to protect subject privacy, asynchronously collect data and deeply annotate growing institutional specimen, data and genomic repositories by integrating familiar tools.

The Biorepository Portal (BRP) is a federated web application originally designed to support longitudinal biospecimen collection activities. Using HTTP protocols, it interfaces with downstream data systems, including REDCap and Thermo Fisher Scientific's Nautilus LIMS, to provide a single unified interface for data collection and update activities. An electronic honest broker (eHB) ensures longitudinal data collection is performed in a manner compliant with NCI Best Practices for Biospecimen Resources.

The Children’s Hospital of Philadelphia (CHOP) Department of Biomedical and Health Informatics (DBHi) developed an open-source informatics infrastructure to support data-intensive longitudinal biorepository studies.

Benefits of using the BRP Toolkit include:

  • De-identification and re-identification of subjects on-the-fly.
  • Creation and addition of records in multiple research systems to ensure patient privacy.
  • A longitudinally updated specimen and data resource that enables more flexible non-human subjects research.

The design of this integrated application set serves a two-fold process: integrating data on the way in and on the way out. Therefore, the applications support study management/operations AND data query/scientific data integration. The toolkit integrates fully with REDCap and our enterprise LIMS for study data management. For data discovery, it integrates the Harvest Data Discovery Platform where the Portal and Honest Broker components of the toolkit broker data needs across systems and use cases.

Click here to link to the biorepository portal toolkit.

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CTCAE 4.0 Mobile Application

DBHi has converted the 190+ pages of the CTCAE v4.02 document into an intuitive iPhone application. With this application, healthcare providers can reference the full CTCAE v4.02 with an iPhone, allowing for bedside grading at the time of a visit and generally allowing the information to be accessed from anywhere at any time. The application contains all published grading standards for all 26 categories of adverse events as well as event definitions. It is available in the Apple iTunes App Store for download.

The application also offers a variety of advantages over the flat file CTCAE v4.02, including:

  • Hierarchical navigation of adverse event categories
  • Ability to bookmark adverse events and categories to quickly access frequently graded events
  • Search for events across names, definitions and grades

This application is one example of the many ways in which DBHi helps transform clinical care and research at our institution and across the industry. Have an idea for an mHealth application? This email address is being protected from spambots. You need JavaScript enabled to view it.

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Clinical Trial Management Systems

DBHi is working with CHOP's Center for Childhood Cancer Research (CCCR) to evaluate, implement, and optimize a comprehensive clinical trial management system, OnCore. The system, now in operation, manages over 200 CCCR clinical trials and has been instrumental in establishing a single source of data entry, archiving, and reporting for the disparate needs of each study. The system is now being extended to integrate with other CHOP databases and administrative resources such as eIRB.

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Laboratory Information Management Systems (LIMS)

DBHi has partnered with ThermoFisher Scientific to implement a unique protocol-centered LIMS to specifically support clinical and translational research. The resulting extension of ThermoFisher's Nautilus product allows researchers to accession and query samples within the context of a larger clinical protocol and is currently being used by CHOP's Clinical and Translational Resource Center to support ongoing research.

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CNV Workshop

CNV Workshop is a suite of open source tools that provides a comprehensive approach to CNV analysis for genome array data. The workshop's tools were compiled by the bioinformatics group within DBHi and include packages developed by the general open source community as well as custom modules developed by DBHi. Analysis activities supported by this application include CNV identification, annotation, visual representations and exports of the data, and limited project and account management.

Please click here to download this open source resource or click here to view the manuscript.

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CNV Database

The Copy Number Variation project at the Children's Hospital of Philadelphia (CHOP) represents an effort to identify all frequent copy number variations (CNVs) that exist in the human genome. Our ongoing research uses high-resolution genome-wide scanning and highly accurate computational approaches. CNV's found within this database have been identified from 2,026 healthy children recruited within CHOP's pediatric practice network. These efforts have yielded the first high resolution CNV map of the human genome, providing access to a data source that allows for effective assessment of the role of CNVs in human variation and disease susceptibility.

Please click here to access the database. You can also read the accompanying manuscript or read the OpenHelix blog about this highly accessed tool.

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updated 1/08/2015