GeneTerpret: a customizable multilayer approach to genomic variant prioritization and interpretation

ABSTRACT Variant interpretation is the main bottleneck in medical genomic sequencing efforts. This usually involves genome analysts manually scouring through a multitude of independent databases, often with the aid of several and mostly independent computational tools. To streamline the variant interpretation process, we developed GeneTerpret platform that collates data from current interpretation tools and databases, and applies a phenotype-driven query to categorize the variants identified in a given genome. The platform assigns quantitative validity scores to genes by query and assembly of the current genotype-phenotype data, sequence homology, molecular interactions, expression data, and animal models. The platform uses the American College of Medical Genetics (ACMG) criteria to categorize variants into five tiers (from benign to pathogenic). The platform then outputs a prioritized list of potentially causal variants/genes in a given genome for a specific case. GeneTerpret is a flexible and free platform designed to streamline the variant interpretation process through a unique interface, with improved ease, speed and accuracy. This unique integrated system provides effective validity and pathogenicity modules to assess genetic variant data and allows the user to decide which output and impact level should be considered in this process. The platform can be accessed and used online at https://geneterpret.com .