SVI: A simple single-nucleotide human variant interpretation tool for clinical use

Abstract

The rapid evolution of Next Generation Sequencing technology will soon make it possible to test patients for genetic disorders at population scale. However, clinical interpretation of human variants extracted from raw NGS data in the clinical setting is likely to become a bottleneck, as long as it requires expert human judgement. While several attempts are under way to try and automate the diagnostic process, most still assume a specialist’s understanding of the variants’ significance. In this paper we present our early experiments with a simple process and prototype clinical tool for single-nucleotide variant filtering, called SVI, which automates much of the interpretation process by integrating disease-gene and disease-variant mapping resources. As the content and quality of these resources improve over time, it is important to identify past patients’ cases which may benefit from re-analysis. By persistently recording the entire diagnostic process, SVI can selectively trigger case re-analysis on the basis of updates in the external knowledge sources.