Automatic variant prioritization in suspected genetic kidney disease using the Nephro Candidate Score (N-CS)

Research QuestionDespite the identification of >700 genes linked to rare and inherited kidney diseases (IKD), many individuals with presumed IKD do not receive a diagnosis through genetic testing of known disease genes. Therefore, the identification of new disease genes is crucial to ending diagnostic odysseys, improving genetic counseling, and expanding treatment options. While the generation of large-scale sequencing data is no longer a substantial bottleneck, its interpretation remains challenging and offers room for improvement, notably in the discovery of novel disease genes. MethodsWe developed the Nephro Candidate Score (N-CS), a machine learning (ML) tool that prioritizes variants by combining a Nephro Gene Score (N-GS), a Nephro Variant Score (N-VS), and an Inheritance Score (IS). The ML-based N-GS and N-VS were trained on a wide range of genomic features to predict gene-disease relevance and variant pathogenicity, while the IS incorporates the mode of inheritance via a scoring heuristic. A Gene Set Enrichment Analysis (GSEA) was used to test whether genes top-ranked by the N-GS were enriched for kidney-related biological processes. Additionally, we tested the N-CS on an independent set of novel IKD candidate genes identified through a systematic literature search to validate its real-world performance. ResultsThe machine learning models for the N-CS subscores demonstrated high predictive accuracy, with an XGBoost algorithm for the N-GS achieving an AUC of 0.94 and a Logistic Regression model for the N-VS reaching an AUC of 0.99 in independent test sets. The biological relevance of the N-GS ranking was confirmed by the GSEA showing a significant enrichment of kidney-associated biological processes among top-scoring genes (p < 0.001). In the independent validation using recently published literature, the N-CS assigned compellingly high scores to the majority (10 of 11) of novel candidate genes for kidney disease, demonstrating its ability to generalize to new discoveries. ConclusionThe N-CS is a robust digital solution that can accelerate disease gene discovery and comes with the potential to reduce time to diagnosis. To support standardization and collaboration, the full N-CS framework is freely available, including a user-friendly web tool (NC-Scorer: https://nc-scorer.kidney-genetics.org/) and a command-line interface for high-throughput analysis, enabling standardized, sharable evaluation of candidate variants.