Fine-tuning genomic models on rare splicing events identifies a novel biomarker of TDP-43 pathology

Genomic foundation models (GFMs) are pretrained on large genomic datasets, but their ability to predict rare disease-associated events after fine-tuning remains unclear. We tested this using TDP-43 cryptic exons, well characterized splicing events linked to neurodegenerative disease that are poorly represented in standard annotations. We compared the state-of-the-art GFM AlphaGenome with OpenSpliceAI, a specialized splice site prediction model. Fine-tuned Open-SpliceAI detected held-out cryptic exons in human and mouse and captured allele-specific splicing effects at the disease-associated UNC13A locus. In contrast, a splicing prediction head trained on AlphaGenome's frozen pretrained backbone failed to predict cryptic exons. Unfreezing and fine-tuning all model weights, however, enabled AlphaGenome to generalize to held-out data. To investigate cryptic splicing in cell types that are difficult to study experimentally, we applied fine-tuned OpenSpliceAI across the genome to study cell type-specific genes. This led to the identification of new cryptic splicing events in CLDN11 and ARHGAP23 , which were subsequently validated in FTLD-TDP brain tissue. Notably, the cryptic exon in CLDN11 is predicted to generate a neoepitope that could serve as an oligodendrocyte-specific biomarker of TDP-43 pathology. Our results show that even a state-of-the-art GFM can fail to generalize to rare splicing events, even with substantial pretraining. However, both foundation and specialized models that learn to generalize to rare biological events can have broad applications in biological discovery and medicine.