{
  "schema": "oncoref.cta-policy.v1",
  "policy": "oncoref.target-sets.2026-10-25.2",
  "baseline_policy": "oncoref.target-sets.2026-10-24.1",
  "reference": "openvax:reference:v1:sha256:0fefb51755788901693be9987fadc31e61f945cd53c08a170e0e1d4ad4a09b61",
  "taxonomy_id": 9606,
  "scope": {
    "canonical_genes": 20097,
    "source_nominations": 2540,
    "additional_sequence_loci": 1721,
    "legacy_cta_api": "Unchanged historical 624-gene selection; not this current policy",
    "other_species": "Anatomy mappings available; numerical policy is human-only",
    "clinical_products": "Product-specific evidence does not confer gene-wide clearance",
    "protein_precedence": [
      "Unsafe",
      "Neither",
      "CTA"
    ],
    "missing_evidence": "Unknown; never zero or proof of absence"
  },
  "measurement_policy": "oncoref.cta-screen.2026-10-23.1",
  "evidence_order": [
    "accepted normal exclusion",
    "unresolved or insufficient",
    "qualified CTA"
  ],
  "rna_admission_ntpm": 5,
  "hard_normal_rna_ceiling": {
    "value": 30,
    "comparison": ">",
    "units_separately": [
      "TPM",
      "nTPM"
    ]
  },
  "ihc_columns": [
    "missing_or_uncertain",
    "Approved_negative",
    "Supported_negative",
    "Enhanced_negative"
  ],
  "rna_ceiling_ntpm": {
    "vital": [
      2,
      4,
      6,
      12
    ],
    "protected": [
      6,
      8,
      12,
      24
    ],
    "manageable": [
      10,
      20,
      30,
      60
    ]
  },
  "selectivity_setting": {
    "vital": [
      0.8,
      0.75,
      0.7,
      0.65
    ],
    "protected": [
      0.75,
      0.7,
      0.65,
      0.6
    ],
    "manageable": [
      0.7,
      0.65,
      0.6,
      0.55
    ]
  },
  "bulk_rule": "N <= C AND N <= R*(1-s)/s + 0.1 AND N < R; independent >30 rule also applies",
  "ihc_relaxation": "Complete local routine negative IHC at the weakest confidence, plus reliable reproductive-positive curated profile; not paired specimens or sensitivity calibration",
  "normal_cell_rules": "Pinned native-unit triggers in normal_cell_screen.py; no unit pooling or antibody relaxation of unpaired cell RNA",
  "normal_cell_triggers": {
    "hpa_single_cell": {
      "minimum_ntpm": 5,
      "minimum_reads": 20,
      "comparison": ">=",
      "relative_rule": "At least the reproductive-cell maximum, or missing reproductive coverage/unresolved anatomy"
    },
    "dice_distributions": {
      "minimum_tpm": 5,
      "minimum_reported_values": 3,
      "comparison": ">=",
      "identity_limit": "Distribution values are not stable cross-gene donor identities"
    },
    "hpa_monaco_immune": {
      "minimum": 5,
      "units_separately": [
        "TPM",
        "nTPM"
      ],
      "comparison": ">="
    },
    "cornea": {
      "minimum_mean_cp10k": 1,
      "minimum_positive_cells": 5,
      "minimum_counts": 20,
      "minimum_sample_groups": 2,
      "comparison": ">="
    },
    "outcome": "Neither unless a stronger exclusion applies; no unpaired IHC relaxation"
  },
  "counts": {
    "policy": "oncoref.target-sets.2026-10-25.2",
    "genome": {
      "Unsafe": 17705,
      "Neither": 2179,
      "CTA": 213
    },
    "nominated": {
      "Unsafe": 1586,
      "Neither": 741,
      "CTA": 213
    },
    "proteins": {
      "Unsafe": 126396,
      "Neither": 3230,
      "CTA": 359
    },
    "changes": [
      {
        "from": "CTA",
        "to": "Neither",
        "genes": 180
      },
      {
        "from": "CTA",
        "to": "Unsafe",
        "genes": 6
      }
    ],
    "baseline_replayed_exactly": true,
    "antibody_reviews_completed": 178,
    "antibody_review_outcomes": {
      "Neither": 177,
      "Unsafe": 1
    },
    "changes_from_local_draft": 178,
    "followup_genes": 201,
    "neither_or_cta_above_30": 0,
    "extra_sequence_loci": 1721,
    "incomplete_translations": 34361,
    "genes_without_complete_proteins": 942,
    "literature_review_limit": "32 genes newly read in the initial primary-paper review; 46 have specific notes including earlier work. Search hits are not adjudications.",
    "remaining_primary_ihc_queue": 0
  },
  "forbidden_categories": [
    "Unsafe"
  ],
  "report": "docs/audits/cta-policy-20261025/index.md",
  "report_url": "https://pirl-unc.github.io/oncoref/audits/cta-policy-20261025/",
  "reports_at_release": "https://github.com/pirl-unc/oncoref/tree/v1.20.0/docs/audits/cta-policy-20261025",
  "decision_artifact_sha256": {
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  "sequence_artifacts": {
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    "download_base": "https://github.com/pirl-unc/oncoref/releases/download/v1.20.0/",
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      "genes-without-complete-proteins.csv.gz": "3a69eaed2467e9535c75b5eae584ea54bb6ded000ae96bc9bc73d8c034359951",
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      "translations-for-review.csv.gz": "1bf3f07dbc50078568fa8cdff0a68da03e3f832795e5f1b369fa91f498b6dcc8",
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      "unclassified-sequence-genes.csv.gz": "e1d4263cc49b70e8e5020166232b8a1e19111407abbb196112e50d87e1c7a975",
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      "unsafe.fasta.gz": "d93c7c202c0b70d61d53fdc785f2daf4584b062528d2a7a07858fa660a13106f"
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  },
  "data_sha256": {
    "target-gene-sets.csv.gz": "4710adbd27657d00e643b8d82882724e023e9dee15dd5a2c02c67e75045ffdc3",
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}