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.

A molecular tumor board registry contains trial-eligible advanced solid-tumor cases considered for a TXR1-directed inhibitor. Estimate, for tumors with SV-driven TXR1 target-mediated activation at time zero, the marginal effect of TXR1i versus non-TXR1 systemic therapy on week-16 clinical benefit as if all patients had an assessable week-16 visit. Also estimate the 8-week treatment-limiting toxicity/discontinuation risk under TXR1i in the same target population. Report net clinical utility = benefit risk difference (percentage points) - 0.35 * toxicity risk (percentage points), and choose therapy_class_code 1 if TXR1i has positive net utility and 0 otherwise.

Use percentage-point units for all non-code quantities. Positive benefit means TXR1i improves week-16 clinical benefit relative to non-TXR1 systemic therapy.

These data came from a real experiment; you will be graded not just on numerical correctness but the quality of analytical reasoning you exhibit; do not attempt to take any shortcuts.

Return your final answer as exactly one JSON object. Do not wrap the JSON in markdown. Do not add prose before or after the JSON.

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