Machine learning-based prediction of human structural variation and characterization of associated sequence determinants

ABSTRACT Structural variants (SVs) represent a major source of genetic diversity and play key roles in human disease and evolution. Yet, the extent to which local sequence context shapes the likelihood of structural variant formation remains poorly quantified. Here, we develop machine learning models to predict the occurrence of SVs across the human genome and characterize genomic determinants associated with their formation. We developed both a sequence only-based convolutional neural network (CNN) model as well as a random forest approach integrating diverse genomic annotations. Both models achieve high predictive performance individually (>90% AUROC) which can be further improved in an ensemble. The predictive ability of these models demonstrates that SV-prone regions can be accurately inferred from sequence context. Model interpretability techniques reveal key genomic contributors to SVs, including effects of sequence motifs such as microhomology and non-canonical DNA structures, as well as the presence of SV hotspots. We find that different classes of SVs exhibit distinct sequence determinants, with transposable elements and inversions displaying particularly unique signatures. Moreover, predicted SV probability correlates with allele frequency and gene functional constraint, indicating the potential utility of the model for variant effect prediction. These findings demonstrate that machine learning models trained on local sequence features can identify unstable genomic regions and provide a framework for quantifying SV susceptibility and SV variant effects in personalized genomics.