The Bioinformatics Section in the Center for Precision Disease Modeling (CPDM) at the University of Maryland School of Medicine (UMSOM) is dedicated to delivering bioinformatics support for all four levels of service offered by the Center. By tightly collaborating with the Disease Modeling Unit, Preclinical Section, Service Section and Coordination Section, the Bioinformatics Section will conduct computational analyses on genetic, genomic and other omics datasets. Specific responsibilities for the Bioinformatics Section include the feasibility assessment of variants for Precision Disease modeling, analysis of patient and/or animal-driven omics data for a better understanding of disease mechanisms, and the generation and analyses of pharmacogenomics data in response to targeted therapeutic treatments. In addition, the Bioinformatics Section (together with the Service Section) manages the Center’s website and implements electronic tracking of the activities and outcomes of the Center, which expedites resource and information sharing with the biomedical community. The Section’s specific aims include: Develop and Optimize the Variant Feasibility Evaluation System together with the Preclinical Section and the Disease Modeling Unit; Integrate genotype and phenotype cross-species connections from patients and model organisms with better disease and gene ontology, as well as data sharing with the research community; and, Perform cross-species omics data comparison for the characterization of disease mechanisms and to demonstrate the clinical relevance of Precision Disease models. Achieving these aims will pave the way for the success of CPDM’s activities to benefit our customers and patients.
Roles of the Bioinformatics Section and its interaction with the other center sections
Our activities in the Bioinformatics Section will be highly interactive with the other groups at the Center at different levels of its service. Dr. Lee is responsible for the management of the website, through which our customers will submit patients’ genetic variant information. The variants will be evaluated, together with the Preclinical Section (PCS) and Disease Modeling Unit (DMU). Drs. White and Lee will compare the patients’ variants to population-based studies (e.g., Genome Aggregation Database (gnomAD) and the 1000 Genomes Project), which contains whole-genomes or exomes from more than 140,000 individuals. In addition to the comparisons, Dr. Lee will perform comparative genomics analyses on the associated genes to address the feasibility of modeling the variant with animals at the DNA or protein sequence, gene network, and anatomical levels. The information will be summarized as a “Feasibility Report”, which will be reviewed by the PCS, DMU, and Center’s Steering Committee for the prioritization of the community-nominated human genomic variants
Once the Center selects high-priority variants, Dr. Schriml will conduct the ontology and annotation process for both the disease phenotype to its genotype, as well as the model phenotype and genotype (Green). Such connections will be discussed with the PCS and DMU before they are added to our or other public databases. Also, the Bioinformatics Section will assist the Resource and Service Section in cataloging the animal models on our website, so they can be accessed by other members in the biomedical community. Drs. White and Lee will perform multi-omics analyses of the model and patient for a better understanding of the disease mechanism (Yellow and Red). Ideally, successful modeling will lead to a drug screen for the targeted therapeutics, which will be assisted by Drs. White and Lee for a pharmacogenomic analysis.
The Bioinformatics Section will assist the Coordination Section’s active program to monitor and collect information on the impact of the Center’s ongoing activities on biomedical research. The CPDM website has a feature for questionnaire-based surveys that will be used to improve our performance. The Bioinformatics Section will conduct periodic surveys sending automated emails to the customers. The survey data and the customers’ feedback will be discussed during the meetings the Bioinformatics Section participates in, including the monthly joint-section meetings, which will be organized by the Coordination Section