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# Genomic Foundation Models

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bioRxiv Oct 19, 2026
Genomic foundation models fail to add common-variant discoveries: standard annotations still lead across 27 UK Biobank traits
Across 27 UK Biobank traits, variant scores from genomic foundation models (GFMs) did not yield more common-variant loci, either alone or added to standard functional annotations. AlphaGenome and Borzoi alone raised locus discovery by median 1.8% and 3.8%, below baselineLD's 5.1%, while GPN-Star reduced it. Combined with baselineLD, locus counts changed by a median of −0.1% to 0.2%, suggesting the models largely recapture regulatory information already in the standard annotations.
Across 27 UK Biobank traits, variant scores from genomic foundation models (GFMs) did not yield more common-variant loci, either alone or added to standard functional annotations. AlphaGenome and Borzoi alone raised locus discovery by median 1.8% and 3.8%, below baselineLD's 5.1%, while GPN-Star reduced it. Combined with baselineLD, locus counts changed by a median of −0.1% to 0.2%, suggesting the models largely recapture regulatory information already in the standard annotations.
University of Cambridge University of Bonn
Andrew J. Bass（First author, Corresponding author）Chris Wallace（Corresponding author）
Surrogate Functional False Discovery Rate (sfFDR)Genomic Foundation Models Common Variant GWAS Discovery AlphaGenome Borzoi
bioRxiv Oct 26, 2026
Olive repeats get a genome-wide read: three plant DNA models agree on which STR loci shift their embeddings
Olive short tandem repeats (STRs, stretches whose repeat-unit copy number varies) had been read mainly through small microsatellite panels, leaving genome-wide variation and interpretation open. Across 212 Iranian and Mediterranean olive accessions, the study catalogued 117,119 polymorphic STR loci and passed natural allele series through three plant genomic language models, AgroNT, PlantCAD2 and GPN, measuring how far embeddings move as repeat length departs from the reference allele. On 62,847 loci, the three models shared 7,417 embedding-sensitive loci, and at most tested loci STR responses exceeded length-matched nonrepetitive indels.
Olive short tandem repeats (STRs, stretches whose repeat-unit copy number varies) had been read mainly through small microsatellite panels, leaving genome-wide variation and interpretation open. Across 212 Iranian and Mediterranean olive accessions, the study catalogued 117,119 polymorphic STR loci and passed natural allele series through three plant genomic language models, AgroNT, PlantCAD2 and GPN, measuring how far embeddings move as repeat length departs from the reference allele. On 62,847 loci, the three models shared 7,417 embedding-sensitive loci, and at most tested loci STR responses exceeded length-matched nonrepetitive indels.
SIB Swiss Institute of Bioinformatics University of Zurich
Mohammad Hossein Pakdel（First author）Feifei Xia（First author）
Short Tandem Repeat Variation Embedding Perturbation Analysis Genomic Foundation Models Olive Population Structure Quantitative Trait Locus Mapping

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