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fix: correct SEED-020 novelty — VAR_004/VAR_002 carry patent risk (DRAMP05502/05504) - #110
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…th patent risk Full BLOSUM62 audit against 27,234-sequence DB (APD6+DRAMP general+patent+UniProt) reveals the preliminary broad novelty check (72-AMP curated DB, no patent sequences) was misleading: - SEED-020_VAR_004 (RLRIRVLKRLLK): 75% identity to DRAMP05502 (patent) - SEED-020_VAR_002 (KVRIRVLKRLLK): 67% identity to DRAMP05504 (patent) Both reclassified CLOSE_RELATIVE / POSSIBLE_PATENT_RISK. Docs updated: - WET_LAB_HANDOFF.md: table corrected, IP NOTE expanded to cover all three SEED-019/020 candidates, Novelty paragraph rewritten; SEED-020_VAR_008 (RVRIKVLKRLLK; CLEAR, no patent DB hit) added as the safe fallback - EXPERT_REVIEW_PACK.md: family table corrected; wave 0.5b addendum rewritten with explicit ⚠ correction block naming DRAMP05502/05504 alignments Local outputs/wave1_final_panel.csv updated (gitignored): novelty_class corrected from NOVEL → CLOSE_RELATIVE for VAR_004 and VAR_002. All 1372 tests pass.
- EXPERT_REVIEW_PACK.md table: expand DRAMP shorthand to "VAR_004/VAR_019→DRAMP05502; VAR_002→DRAMP05504" to eliminate ambiguity about which accession covers which candidate - WET_LAB_HANDOFF.md table: mark VAR_008 row as "(fallback — see IP NOTE)" to prevent technicians from treating it as a current panel member - WET_LAB_HANDOFF.md Novelty prose: tighten "no patent DB match" to "public DRAMP entry, no patent sub-database hit" matching EXPERT_REVIEW_PACK phrasing for precision All 1372 tests pass.
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Summary
The preliminary broad novelty check (72-AMP curated DB, no patent sequences) returned
NOVEL for SEED-020_VAR_004 and SEED-020_VAR_002, and this was incorrectly propagated into
the merged wave 0.5b docs. The full BLOSUM62 audit against 27,234 sequences (APD6 + DRAMP
general + DRAMP patent + UniProt) shows both candidates have patent proximity:
The alignment for VAR_004 vs DRAMP05502 C-terminal repeat:
Changes
docs/WET_LAB_HANDOFF.md: Table corrected (NOVEL → CLOSE_RELATIVE + patent %);IP NOTE expanded to cover all three SEED-019/020 candidates; SEED-020_VAR_008 added
as the publication-safe fallback row; Novelty paragraph rewritten
docs/EXPERT_REVIEW_PACK.md: Family table novelty column corrected; wave 0.5baddendum rewritten with explicit ⚠ correction block naming the DRAMP05502/05504
alignments; "no patent DB matches" claim removed
Local
outputs/wave1_final_panel.csv(gitignored) updated separately: novelty_classcorrected from NOVEL → CLOSE_RELATIVE for VAR_004 and VAR_002.
Test plan
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