ARCHCODE reveals enhancer-proximal structural pathogenicity in nine genomic loci, indicating improved detection of variants.
30,318 ClinVar variants across 9 loci. 27 pearl variants invisible to VEP (0), SpliceAI (0.00), CADD (15.7), MPRA (null), gnomAD (85% AF=0) — only ARCHCODE detects via 3D enhancer-promoter contact. Hi-C validation r=0.28-0.59. AlphaGenome multimodal: 2.8x RNA-seq (p<0.0001). Version 2.9 (gnomAD population analysis added). Code: https://github.com/sergeeey/ARCHCODE
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Sergey V. Boyko (2026) studied this question.
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