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Project Presentation - Sanghoon Lee

Project Title

Sanghoon Lee

Structuring Genomic Variant Data for the Electronic Health Record

Location: HSEB 5750C (BMI Conference Room)
Date: Apr. 30, 2012
Time: 10:00 am

Supervisory Committee: Bruce Bray, M.D.; Karen Eilbeck, Ph.D.; Joyce Mitchell, Ph.D.


Genetic testing of human genomic sequence plays a vital clinical role. Elucidation of gene variation can provide a precise diagnosis, as well as recommendations and prognosis for patients with heritable diseases. Unfortunately, the electronic dataflow from the hospital or clinic to the laboratory, then back to the ordering physician has not yet been fully implemented in a way that structures gene test results in a computationally amenable format. Furthermore, genomic variation data has historically not been well associated with patient data to support clinical decision making. This is due in part to the lack of a standardized and structured method to enter this information into the Electronic Health Record (EHR). The Health Level 7 (HL7) Clinical Genomics Work Group (CGWG) has developed a draft standard Genetic Test Report template, but has not resolved many of the issues pertaining to the standardized capture of genomic variants in the EHR and approaches to implementation remain a major issue. Creating a standard model for representing genomic variation data and genetic test reporting is a key challenge remaining in clinical genomics and personalized medicine. Here, we present an XML based strategy using the Genome Variation Format (GVF) - an ontology-typed, standard genomic variation file format - to annotate human genomic variation, and integrated into HL7 Clinical Document Architecture (CDA) standard format to represent structured gene test results.


Sanghoon lee is a Masters degree candidate in the Department of Biomedical Informatics at the University of Utah. He received a Masters degree in Biochemistry and Molecular Biology from Seoul National University, Korea. He worked in a pharmaceutical cosmetic company as a chief researcher in Korea and worked in Salt Lake City Veterans Affair as a research coordinator of Information Extraction Methods project. His research interests are Personalized Healthcare and representation of patient genomic variant data.