Division of Pathology Informatics

PATHOLOGY INFORMATICS

Data is everywhere, bombarding us in enormous volumes and at tremendous velocity.  The field of Pathology is no exception with datasets from various -omics technologies, electronic health records (EHR), laboratory information systems (LIS), digital pathology, and cohort metadata. Practical knowledge of informatics is becoming more and more essential among members of pathology for effectively organizing and converting this bigdata into meaningful information for improving patient care and discovery.

Our Pathology Informatics team at the University of Florida Department of Pathology, Immunology, and Laboratory Medicine is a growing group of dedicated faculty, staff, fellows, residents, and students working to provide efficient and novel informatics solutions, guidance, and training to address our big-data needs in anatomic, clinical, and experimental pathology.

Informatics Within Pathology

MISSION

The mission of the Division of Pathology Informatics is to apply, develop, and promote novel and efficient solutions to achieve our goals in Bioinformatics, Data Analytics, EHR/LIS Implementation, and Informatics Education within the UF Department of Pathology, Immunology and Laboratory Medicine to positively impact patient care, education & discovery.

VISION

The vision of the Division of Pathology Informatics is to lead and train current and next generation of anatomic, clinical, and experimental pathologists in practice of informatics within the purview of pathology practice and research.

 

GOALS

Bioinformatics

Clinical Bioinformatics: To provide bioinformatics guidance and solutions to UF Health Pathology Laboratories by developing custom genotyping and next-generation sequencing (NGS) clinical assays, bioinformatics data analysis and management workflows, and solutions for integrating genomic data into the clinical lab information systems (LIS) and electronic health records (EHR). Computational pipelines that were developed for our precision medicine assays include detection of SNVs, Translocations, CNVs, and MSIs in clinical oncology, germline, and pharmacogenomics tests.

Research Bioinformatics: To provide bioinformatics guidance and solutions for research spanning across multiple omics technology and analysis workflows (e.g., genomics, transcriptomics, methylation, proteomics, etc). This includes studies involving genome wide association (GWAS), Quantitative Trait Loci (QTL), epigenetics, genome variant analysis, differential gene expression, etc.

Data Analytics

To apply and develop data science techniques for creating centralized interactive dashboards and reports by consolidating data from various UF Health data sources such as EpicCare EHR, EPIC Beaker LIS, and others. These dashboards and reports will be available to administrative and operational faculty and staff for tracking and improving laboratory test utilization, send out test management, specimen logistics, clinical testing reimbursements, resource management, test volumes, business opportunities, and quality improvement research.

Laboratory Information Systems

To be primarily responsible for building, modifying, and validating Anatomical and Clinical Pathology workflows into EpicCare and Epic Beaker at UF Health Pathology Laboratories. Additionally, exploring and implementing new technologies for improving clinical test result communication with internal and external healthcare systems.

Education

To build informatics skills among students, residents, fellows, staff, and faculty in anatomic, clinical, and experimental pathology divisions. This is to be accomplished through traditional classroom didactics, ad hoc presentations, elective rotations, and research mentoring.  Formally taught courses will cover Python programming language, advanced data analysis and visualization, Unix operating system, database programming, and bioinformatics. Informal topics will include EHR and LIS workflows, digital pathology, and clinical data retrieval and analytics.


Srikar Chamala, PhDSrikar Chamala, PhD

Title: Division Director

Email: schamala@ufl.edu