Informatics Infrastructure

The Informatics Infrastructure team designs, develops, implements, and maintains applications and databases for the collection, storage, and reporting of cancer research data to support scientific research. The team has successfully implemented Data Tracking Systems for use in the Clinical Breast Care Project (DTS-CBCP) and the Murtha Cancer Center Biobank program (DTS-MCC).  Most recently we are leading the efforts of the Informatics Infrastructure Task Force of the Applied Proteogenomics OrganizationaL Learning and Outcomes Consortium (APOLLO IITF). The main goals of the IITF are to develop and implement the Data Tracking System for the APOLLO project (DTS-APOLLO), as well as a Data Warehouse for Translational Research for APOLLO (DW4TR-APOLLO).

Each data tracking system was designed and implemented using a similar system architecture. The user interface and business logic were constructed using the Microsoft MVC framework. A harmonized data dictionary was created and the data design was established using an Oracle database. A role-based security system has been implemented to control access and functionality for the applications.

The Clinical Breast Care Project (CBCP) collects tissue and blood samples, as well as clinical, pathologic, treatment, and outcome data at three clinical facilities using a Case Report Form (CRF). The participant’s data is captured during initial and follow-up visits. The samples are shipped from the clinical facilities to our institute for long-term storage.  To facilitate the sample tracking and participant data collection, we developed a Data Tracking System for the Clinical Breast Care Project (DTS-CBCP).

The DTS-CBCP supports multiple data collection methods for initial and follow-up visits. Users may input data using desktop computers, laptops, or tablets.  The data may be entered in real-time or CRFs may be inputted at a later time. Copies of the data can also be printed when required. DTS-CBCP also has built in multiple levels of Quality Assurance/Quality Control (QA/QC) functions to improve data integrity within and between visits.

The John P. Murtha Cancer Center Biobank (MCCB) coordinates patient enrollment and biospecimen collection at the Walter Reed National Military Medical Center and a number of other military treatment facilities, medical centers of the Department of Veterans Affairs, and civilian medical centers. The collected biospecimens including blood, tissue, urine, and saliva are shipped to our biobank for long-term storage. Biospecimen annotations and patients’ clinical, pathologic, treatment, and outcome data are also collected. To manage all these activities, CSSIMMW and MCCB collaboratively developed a Data Tracking System for the John P. Murtha Cancer Center (DTS-MCC).

The system captures pathologic data by providing CAP eCC forms for completion, uploading of de-identified pathology reports, and the entry of histologic annotations.  Pathologists have the ability to view electronically scanned images of H&E slides using a link to the Aperio ImageScope from Leica. The DTS-MCC also includes data extraction and formatting for submission to the Oncology Research Information Exchange Network (ORIEN) Avatar program for research collaboration and identification of cases eligible for clinical trials.

Development of DTS-APOLLO is based on the successful implementation of DTS-CBCP and DTS-MCC. An APOLLO pathology queue was developed to allow the pathologists at the Joint Pathology Center (JPC) to view a list of cases that require expert review, along with functions to perform the review of the pathology reports and histologic annotations. A sample processing module will provide functions for the selection of samples for experiments, sample request and approval, sample tracking in laboratories, sample shipment and handling between laboratories and biobank, and experimental results handling.  Additional data, such as images and CLIA testing results, will be tracked.

Development of the DW4TR-APOLLO will be based on the successful implementation of the Data Warehouse for Translational Research (DW4TR).  It will provide a platform for researchers to view and analyze validated, harmonized data from disparate sources including Level 3 data integration.  It will include QA/QC of APOLLO data and provide for the export of harmonized data to current and future external data commons . Functionality will include tools for cohort selection and data queries.

The goal of the IITF is to produce secure, user-friendly, flexible, and reliable informatics infrastructure software products and utilities to support and facilitate APOLLO operations.  Tasks include:

  1. Manage the design and implementation of APOLLO clinicopathologic data collection and tracking (including CLIA testing, Images, and Patient-reported data) (DTS-APOLLO).
  2. Manage the design and implementation of APOLLO sample processing (blood samples, tumor blocks, QA, and shipment) in Windber (DTS-APOLLO).
  3. Manage the design and implementation of APOLLO data collection for genomics and proteomics labs (sample receiving, metadata, and status of samples in major steps of the pipeline for projection of data availability, and Level 3 data) (DTS-APOLLO).
  4. Manage the design and implementation of APOLLO Data Warehouse for Translational Research (DW4TR-APOLLO) including APOLLO data sharing and output for external research projects.

The task force kick-off meeting was held 10 August 2018, and weekly teleconferences are held to address the targeted tasks.