Digenic variant interpretation with hypothesis-driven explainable AI

Abstract

MotivationThe digenic inheritance hypothesis holds the potential to enhance diagnostic yield in rare diseases. Computational approaches capable of accurately interpreting and prioritizing digenic combinations based on the probands phenotypic profiles and familial information can provide valuable assistance to clinicians during the diagnostic process. ResultsWe have developed diVas, a hypothesis-driven machine learning approach that can effectively interpret genomic variants across different gene pairs. DiVas demonstrates strong performance both in classifying and prioritizing causative pairs, consistently placing them within the top positions across 11 real cases (achieving 73% sensitivity and a median ranking of 3). Additionally, diVas exploits Explainable Artificial Intelligence (XAI) to dissect the digenic disease mechanism for predicted positive pairs. Availability and ImplementationPrediction results of the diVas method on a high-confidence, comprehensive, manually curated dataset of known digenic combinations are available at oliver.engenome.com.