The Bioinformatics Core develops and supports computational and bioinformatics methods and tools to assess, monitor, track and disseminate all variant and model information to center staff and collaborators.
Variant Quality Assessment Pipeline
The Bioinformatics core supports center activities by providing a bioinformatics environment for the evaluation of:
- Pathogenicity of submitted variations
- Gene/variant-phenotype associations
- Orthologs and conservation of gene/variants across species
- Human-model multi-omics data
The core achieves this through the use of a broad array of center and public resources, non-standard repositories, and distributed annotation tools to rigorously assess variant quality and inform model development by Disease Modeling Core scientists and clinicians. Variant information obtained through the resources utilized in our submission process is used to evaluate the quality of variant submissions.
In addition, the core works closely with the Clinical Translational Core to utilize that information to inform clinical diagnostics, clinical care and clinical trials, and to provide new insight into genotype-phenotype relationships and understanding of human disease.
Center Laboratory Information Management System
The Core Laboratory Information Management System (LIMS) is used by the Resource and Services Core to track mouse and fly model production and phenotyping data, which is linked to variant quality and assessment results.
The LIMS also contains modules for monitoring the following:
- Allele creation
- Microinjection
- Genotyping
- Husbandry, breeding and welfare issues
- Colony management
- Cryopreservation
- Phenotyping cohort allocation
- Scheduling experiments
- Specific CRISPR/SpCas9 guide RNA sequences, genotyping strategies and assay test results
Core Members
- Matthew Roth, Ph.D. (Lead)
- Aleks Milosavljevic, Ph.D. (Co-Lead)
- Shamika Ketkar, Ph.D.
- Zhandong Liu, Ph.D.
- Uma Ramamurthy, Ph.D.
- Ramin Zahedi Darshoori, M.S.