000007585 001__ 7585
000007585 005__ 20231214104151.0
000007585 0247_ $$2DOI$$a10.6083/fq977v472
000007585 037__ $$aETD
000007585 245__ $$aVarGraph: a decision support tool for variant classification using pathway databases
000007585 260__ $$bOregon Health and Science University
000007585 260__ $$bOregon Health and Science University
000007585 269__ $$a2019
000007585 336__ $$aCapstone
000007585 502__ $$bM.S.
000007585 520__ $$aGenomic screening is an increasingly important part of cancer care. Screening often detects somatic variants in the tumor sample of varied clinical significance: some are well understood, some are connected to only loose evidence, and some are unknown altogether. The purpose of this project was to construct a tool that could present state-of-the-art pathway information to genomics experts evaluating the clinical significance of variants. A web service was created that runs queries against the Reactome pathway database in search of common pathway activity between variants of a clinical case that are known to be pathogenic and those that are of unknown significance. It was integrated into the software infrastructure of a high-volume genomics lab at Providence St. Joseph?s Health. A very different approach to the same problem was attempted via the cloud database product Google BigQuery. The project so far has failed to be of clinical utility.  Two areas of improvement could remedy that situation in future iterations: a more stable network visualization technique, and higher resolution mapping of novel variants to pathway databases via accounting for the effect of alterations on particular protein subdomains.  In its current form the project was not able to reap the benefits of a graph database in particular.  A simpler focus on a small number of ?canonical pathways? looks like a quicker path to a value-added user interface.
000007585 542__ $$fIn copyright - single owner
000007585 650__ $$aGenomics$$033016
000007585 650__ $$aSoftware$$026159
000007585 650__ $$aNeoplasms$$022758
000007585 6531_ $$adatabases
000007585 6531_ $$agenetic
000007585 691__ $$aSchool of Medicine$$041369
000007585 692__ $$aDepartment of Medical Informatics and Clinical Epidemiology$$041422
000007585 7001_ $$aBall, David$$uOregon Health and Science University$$041354
000007585 8564_ $$95d74080b-22e6-4edf-b967-40ee658fa006$$s2873489$$uhttps://digitalcollections.ohsu.edu/record/7585/files/ball.david._2019.pdf
000007585 905__ $$a/rest/prod/fq/97/7v/47/fq977v472
000007585 909CO $$ooai:digitalcollections.ohsu.edu:7585$$pstudent-work
000007585 980__ $$aBiomedical Informatics