Graphylo Var: Predicting the impact of non-coding variants using a multi-species sequence model

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ID: 318195
2026
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Abstract
Abstract Motivation Understanding the functional impact of genetic variants is a key problem for precision medicine. Tools like CADD, PhyloP, and PhastCons are useful, but they often look at each position in the genome in isolation. This means they can miss important information from the evolutionary history that connects different species. In this paper, we extend our previous model, Graphylo, to predict the effects of variants. Our new model, GraphyloVar, is built to directly utilize the phylogenetic tree that relates the species. Results GraphyloVar is a deep learning model that considers both DNA sequence and evolutionary patterns from many species. It uses two main components: Graph Convolutional Networks (GCNs) to process the phylogenetic tree, and Transformer encoders to extract features from the DNA sequences. Pre-trained to predict population-level allele frequencies on the TOPMed whole-genome sequencing cohort, GraphyloVar achieves an AUROC of 0.6246 zero-shot on ∼149M held-out variants, and an ensemble with CADD reaches 0.6442 (+0.020, p < 10−15). Fine-tuned GraphyloVar achieves the highest AUROC across all 13 MPRA benchmark datasets. By integrating deep learning with explicit phylogenetic input, GraphyloVar offers a powerful and complementary approach to variant effect prediction that utilizes the full evolutionary history from many species to better identify and prioritize important non-coding variants. Availability and implementation Code and datasets are available at https://github.com/DongjoonLim/GraphyloVar under DOI : 10.5281/zenodo.20616818
Reference Key
openalex_W7165529342 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Dongjoon Lim, Mathieu Blanchette
Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag426
URL
https://doi.org/10.1093/bioinformatics/btag426
Keywords Keywords not found

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