Biomedical Informatics

As one of the five pillars of the CBCP, Biomedical Informatics (BMIX) has developed a comprehensive informatics system supporting the activities in all of the other 4 pillars. Biomedical Informatics also provides support to other research projects and leads its own research, by working with scientists both within and outside of the WRI. The team members and the system have made significant contributions to The Cancer Genome Atlas—Breast Cancer (TCGA-BC) project[1], and the Director has won several MCC Collaborative grants and the MCC-NCI Activation Funds grants, serving as a Co-PI or Co-Investigator. The team has also been tasked to lead the development of the MCC Informatics Infrastructure.

In the recent years, CBCP has been conducting or participating in several large-scale molecular studies, including the TCGA-BC, Massive Parallel Molecular Processing in collaboration with the Pacific North Western National Lab, a Komen Promise Grant for therapy relevant molecular stratification of breast cancers in collaboration with Thomas Jefferson, etc. New initiatives are in development. CBCP is now also addressing the collection of treatment and outcome data for invasive cancer patients enrolled in the study. These projects, combined with the research conducted by scientists at the WRI, has generated a large amount of molecular data as well as new types of clinical data. It is thus critical to expand our current informatics infrastructure to manage all these data, and more importantly, it is critical we expand our bioinformatics research capability to conduct integrative analysis to analyze these data, mine for new hypothesis for validation both computationally and experimentally, so as to make the best use of the data towards making important findings in understanding cancer development mechanisms, identifying cancer treatment drug targets, and develop physician decision support system to aid in cancer treatment.

Biomedical Informatics is now broadly defined as a multi-disciplinary subject for the management and utilization of biomedical information encompassing clinical informatics, public health informatics, and bioinformatics [2]. This definition is increasingly important as new concepts and technologies enter into medical practice and related basic research, and require new types of information management and data analysis that relies on sophisticated statistical and computational technologies. Figure DD.0 shows the major components in this definition of BMIX [3].

Figure DD.0. Major components of biomedical informatics

Clinically, patients receive treatment, subjects are enrolled in the study, and clinical data as well as specimens are collected.  To protect the privacy of human subjects, de-identified subject IDs and specimen IDs are created and properly mapped before being transferred to the research side with the corresponding clinical data and the specimens.  On the research side, clinical data are properly stored, tissues properly banked and genomic and proteomic studies conducted.  All data are then warehoused, analyzed, and mined for biomarkers, risk factors, and disease models.  Newly obtained knowledge is fed back to the clinic to aid in clinical decision-making.

From the data flow point of view, these BMIX components include 1) supporting data collection and generation across clinical, genomic, and proteomic platforms, 2) data tracking, 3) data centralization, 4) data analysis and mining, and 5) knowledge generation and presentation to research and clinical applications. We have been working towards developing a complete BMIX infrastructure for the BC-COE. The system we are developing was designed to be flexible to enable expansion to support translational research in other disease areas. In the following we will present the background, the current status, and the plan for each of these 5 components of BMIX.