Inside Genebench-Pro

These 10 case studies showcase representative questions from GeneBench-Pro. Each case study includes the original prompt, datasets, and supporting materials. For an overview of the benchmark and key findings, see the announcement blog .

Estimate whether a synthetic TXR1-directed inhibitor has positive clinical utility in tumors whose target activation is driven by a structural variant. TXR1, TXR1i, DLR1, and star-allele labels are synthetic benchmark labels.

The target subgroup has to be recovered from long-read, expression, tumor-quality, and pharmacogenomic evidence before benefit and toxicity can be interpreted as a treatment decision.

Estimate whether a nested structural subhaplotype inside an anonymous inversion-like locus has a calibrated clinical association and credible expression support.

A nested copy-dosage signal can be confounded by the broader inversion orientation, so dosage calibration, expression support, and clinical modeling have to remain distinct.

Decide whether an apparent lncRNA dependency is transcript-specific or driven by nearby-locus and neighbor-gene effects.

Transcript-directed evidence has to survive controls for local DNA-locus perturbation, neighbor-gene repression, guide swaps, GC toxicity, and plate effects.

Estimate direct disease effects for two nearby proteins using cis multivariable Mendelian randomization (cis-MVMR) while handling assay scale, allele orientation, winner's curse, LD, and residual local pleiotropy.