AlphaGenome deletion responses complement supervised enhancer-gene relation prediction in primary human astrocytes

Abstract

Sequence-to-function models predict molecular readouts directly from DNA, but recognizing a functional regulatory element is not equivalent to assigning the gene it regulates. We evaluated whether AlphaGenome deletion responses identify experimentally supported enhancer-gene relations, using a frozen K562 analysis and a primary-human-astrocyte CRISPR interference (CRISPRi) resource external to our analysis. The K562 mean contrast was positive but heavy-tailed, and exact joins showed direct collision with released Gasperini and ENCODE-rE2G resources; we therefore treated K562 as supporting evidence. In a frozen evaluation of 2,307 AstroREG relations, AlphaGenome deletion strength discriminated 133 functional relations from 2,174 well-powered nonfunctional relations (average precision 0.479, enhancer-cluster 95% confidence interval 0.394-0.561, prevalence 0.058; area under the receiver-operating-characteristic curve 0.726, 0.659-0.786). Adding AlphaGenome to distance, ABC score, enhancer length, measured expression and assay-depth context increased enhancer-grouped out-of-fold average precision from 0.396 to 0.534 and improved log loss from 0.169 to 0.150. The authors cross-fitted EGrf score was stronger alone (average precision 0.559); in a post-hoc calibration that held out both gene and enhancer folds, adding AlphaGenome increased average precision from 0.550 to 0.619 (paired enhancer-cluster increment 0.068, interval 0.023-0.115) and improved log loss from 0.143 to 0.132. This comparison had asymmetric inputs: EGrf was supervised on AstroREG labels and used local epigenomic and context features, whereas the AlphaGenome score was not fitted in this study to those labels or that feature panel but was read from a pre-existing primary-astrocyte RNA-seq output track. A post-hoc same-enhancer analysis gave conditional AUC 0.741 (0.663-0.814); a smaller same-gene analysis (34 genes, 155 relations) gave 0.701 (0.571-0.823). AstroREG labels and EGrf outputs were public before AlphaGenomes public release, so this evaluation is external to our study but not a post-release or proven-unseen benchmark. The results support complementary relation-level utility, not EGrf superiority, sequence-only deployment, causal assignment at arbitrary loci or equivalence between sequence deletion and CRISPRi.