Advancing Precision Oncology with Scalable Software Solutions for Clinical Variant Interpretation and Expert Curation

Project Summary/Abstract Adam Coffman is a lead software engineer on CIViC, an open access, community-driven web resource for Clinical Interpretation of Variants in Cancer. CIViC is a critical and integral part of the cancer variant interpretation ecosystem, and has been integrated into dozens of academic, clinical, and commercial resources. This application aims to support Mr. Coffman as a Research Software Engineer in the Griffith Lab at Washington University St. Louis School of Medicine so that he can continue to make significant contributions to the CIViC platform under the supervision of Dr. Obi Griffith, PhD. Mr. Coffman studied Computer Science as an undergraduate, has worked as a software developer in industry, and has over a dozen years of experience in research lab settings developing open source web applications in support of precision oncology and bioinformatics projects. The three years of funding provided by the Research Software Engineer award would grant stability and protected time for Mr. Coffman to focus on the CIViC project’s most high priority development needs. He will build features to help reduce the bottleneck caused by editorial review including tools commonly requested by the ClinGen Somatic Cancer Variant Curation Expert Panels (SC-VCEPs) such as dependent task assignment, automated variant coordinate curation, and variant pathogenicity scoring based on assigned criteria. Additionally, he will build out novel visualization and search tools that fully leverage the underlying knowledge graph to allow users to explore the data available in CIViC in a more accessible and intuitive manner. Mr. Coffman will ensure CIViC remains current in implementing emerging data standards for variant representation developed by the Global Alliance for Genomics and Health (GA4GH) and other relevant standards bodies. This support will be critical to maintain and improve upon CIViC’s wide adoption and ease of integration into other resources. Finally, Mr. Coffman will develop new training materials to enable further community adoption and continue to provide direct support to labs, clinics, and companies integrating CIViC’s free and open data into their platforms. Over the course of this award, Mr. Coffman expects to build upon his already extensive experience in web application development by obtaining additional skills in areas such as data visualization and graph algorithms.