Chris Wallace

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.