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Case study

Finding synthetic-lethal partners for KRAS G12C: a graph traversal

Which functionally-coupled partners of KRAS are still development whitespace?

Tools exercised:synthetic_lethal_whitespace
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The question

Operator-authored prose pending

the strategic R&D question: how to find development whitespace partners for KRAS that are functionally coupled enough to be worth a screen — operator writes this section as long-form prose, ~150–250 words, footnoted, slow. Scaffold only.

Strategic context

Operator-authored prose pending

KRAS G12C landscape: sotorasib + adagrasib approvals, the rapid acquisition of resistance, why combinations matter, why synthetic-lethal partners are the most promising combination space — operator writes this section as long-form prose, ~150–250 words, footnoted, slow. Scaffold only.

The Mosaic-derived answer

Operator-authored prose pending

interpret the figure: which partners cleared the whitespace bar, why each matters, what the score is telling you, and how to read the 'outside-KG' partners — operator writes this section as long-form prose, ~150–250 words, footnoted, slow. Scaffold only.

Figure 1 — illustrative. Same shape as a live tool response, fixture values until the operator captures a live run.
Fig 1. mosaic_synthetic_lethal_whitespace(KRAS, limit=20) — top whitespace partners ranked by score. Real coess (r) on rows where DepMap co-essentiality dominates; PPI/pathway proxy where DepMap is silent. The RBM10 row is an outside-KG partner surfaced from DepMap Mosaic-vs-all-genes, flagged for ingest review.

The graph reasoning, step by step

Operator-authored prose pending

the traversal in five lines: anchor target → coess+PPI+shared-pathway union → patent/compound activity filter (< 5 patents, no clinical compound) → whitespace_score ranking → suggested_approach generator — operator writes this section as long-form prose, ~150–250 words, footnoted, slow. Scaffold only.

Implications

Operator-authored prose pending

what a med-chem team takes from this: which partner to prioritise for an in-vitro CRISPR screen first, which to deprioritise because patent activity is already crowding, which to bring up at IC — operator writes this section as long-form prose, ~150–250 words, footnoted, slow. Scaffold only.

Limitations & honesty

Operator-authored prose pending

scoring is heuristic; co-essentiality is partial (Mosaic-vs-all-genes only); patent counts are noisy; not every high score reflects a tractable target — operator writes this section as long-form prose, ~150–250 words, footnoted, slow. Scaffold only.

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