InTouch Spring 2008 (Volume 5: Issue 1)
Children’s Memorial Research Center has entered into a multi-year agreement with Van Andel Research Institute (VARI) of Grand Rapids, Michigan, to license its XenoBase software and database system. This unique, advanced bio-informatics system integrates data analysis—from molecular to clinical—across the translational research work flow. Drug target and biomarker discovery and therapeutic
strategies are expedited.
Beginning in 1999, Craig Webb, PhD, and colleagues at VARI recognized the need to develop a computational system that allowed for the systematic management and analysis of pre-clinical, clinical, demographic, and biomedical information along with associated molecular data. The analysis engine needed to include vast data sets available from external sources for both hypothesis generation and validation. The team went on to design XB Bio-Integration Suite™ (XB-BIS) to store, manage, and retrieve this data; and to statistically analyze it, compile and test hypotheses, and identify viable strategies for accurate diagnoses and treatments. In partnership with numerous collaborators, they refined and tested the system using real clinical data to maximize its usefulness to clinicians and researchers.
XB-BIS is built for evidence-based discoveries. Other systems that may access a multitude of non-integrated data sets are less powerful in their abilities to facilitate decision-making. As an example, clinicians currently utilize patient charts, patient gene expression data, the published literature and other resources when making diagnoses and treatment decisions. The amount and variety of information they must consult is often difficult to manage. XB-BIS employs cross-mapping, data-based predictions and other analysis tools to easily generate hypotheses, troubleshoot and problem-solve.
VARI and the research center anticipate that collaborations with other institutions will be many. Currently, VARI is licensing XB-BIS only to the research center and one other party in order to test both the system’s current capabilities and its potential based on actual client needs. Children’s Memorial Hospital has recently embarked on several studies with the potential for significant diagnostic and therapeutic value that will be used as pilot projects.
The Projects
Falk Brain Tumor Center—Marcelo Bento Soares, PhD
Tumors of similar histopathology may differ significantly in growth potential and aggressiveness. This reality makes an oncologist’s decision to expose a child to the toxicities and long-term consequences of cytotoxic chemotherapy challenging. A major goal in the Soares laboratory is the identification of molecular signatures in pediatric brain tumors that are predictive of clinical behavior.
Changes in gene expression can be subtle, and depend on many things, including environment and the patient’s stage of development. By grouping such variables as gene expression, methylation patterns and structural alteration, mapping tumors to a genome coordinate becomes possible.
The Soares laboratory collects information for samples in a home-grown system, which currently contains no clinical data. However, the Division of Neurosurgery maintains every piece of information about each child who has been treated in the Falk Center. All of this data will be loaded into the pilot system. XB-BIS will significantly strengthen the ability to perform queries and coordinate data. VARI will follow the project to observe and facilitate the integration.
Food Allergy Project— Xiaobin Wang, MD, MPH, ScD, and Jacqueline Pongracic, MD
Food allergy is a complex trait, one that entails gene and environment interactions. Individuals may have different types of food allergies or with various degree of severity. Some may be minor while others may be life threatening. Food allergies often co-exist with other morbidities such as eczema, seasonal allergy and asthma, manifesting clinically as “allergic march”.
The Children’s Memorial Food Allergy Project, Inc., led by Dr. Xiaobin Wang (PI) and Dr. Jacqueline Pongracic (co-PI), is a multi-center study. Its goal is to unravel some of these mysteries, using data collected from three large cohorts of children and families longitudinally. This project is the perfect case in need of great capacity for data integration and manipulation. Launched with a generous gift from the Bunning family (the Food Allergy Project), the project is also supported by the Sacks Family Fund and a grant from the Chicago Community Trust.
Dr. Wang sees XB-BIS as an efficient management tool for complex data and different types of data. It will greatly facilitate extraction from the electronic medical record, data mining and display.
Pediatric Critical Care—Mark Wainwright, MD, PhD
Critical care medicine is a specialty that involves high costs and complexity, with medical complications on the rise. Knowledge is lacking about causes of disease, how treatments work, or even whether they work. Simply having more information is not enough—clinicians need to be able to filter, analyze and use the data. In addition, patient data trends aren’t obvious unless the interested party knows what to look for. No existing tools are effective for solving this conundrum, but XB-BIS promises to fill the void.
The NIH recognizes that pediatric critical care medicine requires interdisciplinary collaborations. These interactions are not only clinically necessary, but they open doors for research opportunities and collaborations.
One goal of the Wainwright project is to link patient data to external sources such as databases that track costs. Some interesting questions that could be answered by this linking include: How much does it cost to treat children with stroke? What is the benefit of thrombolysis?
In compliance with patient confidentiality regulations, all data used in the projects will be de-identified.
Stay tuned for updates on these projects and related developments.
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