{
  "report_schema": "oncoref.cta-permitted-report.v1",
  "taxonomy_id": "oncoref:normal-tissues:v1:sha256:4c2dbfc0a9b9cda5d59a354dacd31d03312a5339a569ace67f0a85dd3bbf6787",
  "policy": {
    "policy_id": "oncoref.cta-permitted-screen.2026-10-19.1",
    "permitted_scope": "reproductive_or_permitted_normal",
    "rna_source": "hpa_rna_consensus",
    "rna_source_version": "v23",
    "rna_species": "human",
    "rna_unit": "nTPM",
    "minimum_permitted_rna": 1.0,
    "positive_ihc_levels": [
      "Low",
      "Medium",
      "High",
      "Ascending",
      "Descending"
    ],
    "vital": {
      "maximum_rna": 1.0,
      "roots": [
        "heart",
        "lung",
        "bronchus",
        "brain",
        "spinal_cord",
        "liver",
        "kidney",
        "bone_marrow",
        "blood",
        "adrenal_gland",
        "pituitary_gland",
        "pancreas",
        "small_intestine",
        "skeletal_muscle",
        "smooth_muscle",
        "peripheral_nerve",
        "endothelium"
      ],
      "description": "Conservative project tier for critical organs and broadly sampled systems whose extensive injury can threaten life. Includes all mapped descendants."
    },
    "protected": {
      "maximum_rna": 5.0,
      "roots": [
        "adipose_tissue",
        "retina",
        "eye",
        "inner_ear",
        "thyroid_gland",
        "parathyroid_gland",
        "lymph_node",
        "spleen",
        "tonsil",
        "appendix",
        "esophagus",
        "stomach",
        "colon",
        "rectum",
        "gallbladder",
        "urinary_bladder",
        "ureter",
        "cartilage",
        "oral_mucosa",
        "nasopharynx",
        "tongue"
      ],
      "description": "Protected normal tissues outside the permitted scope, with a higher RNA ceiling but the same exclusion for any positive IHC. This tier does not assert that loss is harmless or that severe injury cannot be fatal."
    },
    "unresolved_roots": [
      "head",
      "foot",
      "soft_tissue"
    ],
    "references": [
      "project_policy",
      "hpa_tissues",
      "nci_organ_inflammation",
      "niddk_adrenal"
    ],
    "coverage": "Complete routine bulk RNA is required. Missing or partial IHC is reported explicitly and cannot establish protein absence. Unresolved positive anatomy, unusable measurements and reviewed unreliable IHC block retention.",
    "species_note": "Anatomical tiers apply to human, dog and mouse. The numerical policy is calibrated only as a project screen for human HPA v23 nTPM; numerical thresholds and clinical tolerability do not transfer to other species."
  },
  "input_report": "docs/audits/cta-tissue-scopes-20261019",
  "input_manifest_sha256": "8df815a0eac6870a701a3db00521b32c72c520f07c7e03a893624de07ef9a260",
  "inputs": {
    "candidate-decisions.csv": "33a20f18d17559c7034c8c4eccddb35169c0f4fc1e7e8971b2de64fc28efa9ce",
    "normal-observations.csv.gz": "f1fbcb17b583d6f5fa27630271a29bfde13792ee6158dcf71f65961ed07a67e9",
    "source-membership.csv.gz": "a506dee098bf48cb73375c6c5f85cae63dbf8cf3900c82b08f3dcb7461b82c28",
    "source-counts.csv": "1c58d94159bd04339716fec1810c87782d847d920229e133e8ee132879a8c861"
  },
  "scenarios": {
    "previous_1": [
      "reproductive_or_disposable",
      1.0,
      1.0
    ],
    "expanded_1": [
      "reproductive_or_permitted_normal",
      1.0,
      1.0
    ],
    "tiered": [
      "reproductive_or_permitted_normal",
      1.0,
      5.0
    ]
  },
  "routine_contexts": {
    "bulk_rna": [
      [
        "adipose tissue",
        ""
      ],
      [
        "adrenal gland",
        ""
      ],
      [
        "amygdala",
        ""
      ],
      [
        "appendix",
        ""
      ],
      [
        "basal ganglia",
        ""
      ],
      [
        "bone marrow",
        ""
      ],
      [
        "breast",
        ""
      ],
      [
        "cerebellum",
        ""
      ],
      [
        "cerebral cortex",
        ""
      ],
      [
        "cervix",
        ""
      ],
      [
        "choroid plexus",
        ""
      ],
      [
        "colon",
        ""
      ],
      [
        "duodenum",
        ""
      ],
      [
        "endometrium",
        ""
      ],
      [
        "epididymis",
        ""
      ],
      [
        "esophagus",
        ""
      ],
      [
        "fallopian tube",
        ""
      ],
      [
        "gallbladder",
        ""
      ],
      [
        "heart muscle",
        ""
      ],
      [
        "hippocampal formation",
        ""
      ],
      [
        "hypothalamus",
        ""
      ],
      [
        "kidney",
        ""
      ],
      [
        "liver",
        ""
      ],
      [
        "lung",
        ""
      ],
      [
        "lymph node",
        ""
      ],
      [
        "midbrain",
        ""
      ],
      [
        "ovary",
        ""
      ],
      [
        "pancreas",
        ""
      ],
      [
        "parathyroid gland",
        ""
      ],
      [
        "pituitary gland",
        ""
      ],
      [
        "placenta",
        ""
      ],
      [
        "prostate",
        ""
      ],
      [
        "rectum",
        ""
      ],
      [
        "retina",
        ""
      ],
      [
        "salivary gland",
        ""
      ],
      [
        "seminal vesicle",
        ""
      ],
      [
        "skeletal muscle",
        ""
      ],
      [
        "skin",
        ""
      ],
      [
        "small intestine",
        ""
      ],
      [
        "smooth muscle",
        ""
      ],
      [
        "spinal cord",
        ""
      ],
      [
        "spleen",
        ""
      ],
      [
        "stomach",
        ""
      ],
      [
        "testis",
        ""
      ],
      [
        "thymus",
        ""
      ],
      [
        "thyroid gland",
        ""
      ],
      [
        "tongue",
        ""
      ],
      [
        "tonsil",
        ""
      ],
      [
        "urinary bladder",
        ""
      ],
      [
        "vagina",
        ""
      ]
    ],
    "ihc": [
      [
        "adipose tissue",
        "adipocytes"
      ],
      [
        "adrenal gland",
        "glandular cells"
      ],
      [
        "appendix",
        "glandular cells"
      ],
      [
        "appendix",
        "lymphoid tissue"
      ],
      [
        "bone marrow",
        "hematopoietic cells"
      ],
      [
        "breast",
        "adipocytes"
      ],
      [
        "breast",
        "glandular cells"
      ],
      [
        "breast",
        "myoepithelial cells"
      ],
      [
        "bronchus",
        "respiratory epithelial cells"
      ],
      [
        "caudate",
        "glial cells"
      ],
      [
        "caudate",
        "neuronal cells"
      ],
      [
        "cerebellum",
        "Purkinje cells"
      ],
      [
        "cerebellum",
        "cells in granular layer"
      ],
      [
        "cerebellum",
        "cells in molecular layer"
      ],
      [
        "cerebral cortex",
        "endothelial cells"
      ],
      [
        "cerebral cortex",
        "glial cells"
      ],
      [
        "cerebral cortex",
        "neuronal cells"
      ],
      [
        "cerebral cortex",
        "neuropil"
      ],
      [
        "cervix",
        "glandular cells"
      ],
      [
        "cervix",
        "squamous epithelial cells"
      ],
      [
        "colon",
        "endothelial cells"
      ],
      [
        "colon",
        "glandular cells"
      ],
      [
        "colon",
        "peripheral nerve/ganglion"
      ],
      [
        "duodenum",
        "glandular cells"
      ],
      [
        "endometrium 1",
        "cells in endometrial stroma"
      ],
      [
        "endometrium 1",
        "glandular cells"
      ],
      [
        "endometrium 2",
        "cells in endometrial stroma"
      ],
      [
        "endometrium 2",
        "glandular cells"
      ],
      [
        "epididymis",
        "glandular cells"
      ],
      [
        "esophagus",
        "squamous epithelial cells"
      ],
      [
        "fallopian tube",
        "glandular cells"
      ],
      [
        "gallbladder",
        "glandular cells"
      ],
      [
        "heart muscle",
        "cardiomyocytes"
      ],
      [
        "hippocampus",
        "glial cells"
      ],
      [
        "hippocampus",
        "neuronal cells"
      ],
      [
        "kidney",
        "cells in glomeruli"
      ],
      [
        "kidney",
        "cells in tubules"
      ],
      [
        "liver",
        "cholangiocytes"
      ],
      [
        "liver",
        "hepatocytes"
      ],
      [
        "lung",
        "alveolar cells"
      ],
      [
        "lung",
        "macrophages"
      ],
      [
        "lymph node",
        "germinal center cells"
      ],
      [
        "lymph node",
        "non-germinal center cells"
      ],
      [
        "nasopharynx",
        "respiratory epithelial cells"
      ],
      [
        "oral mucosa",
        "squamous epithelial cells"
      ],
      [
        "ovary",
        "follicle cells"
      ],
      [
        "ovary",
        "ovarian stroma cells"
      ],
      [
        "pancreas",
        "exocrine glandular cells"
      ],
      [
        "pancreas",
        "pancreatic endocrine cells"
      ],
      [
        "parathyroid gland",
        "glandular cells"
      ],
      [
        "placenta",
        "decidual cells"
      ],
      [
        "placenta",
        "trophoblastic cells"
      ],
      [
        "prostate",
        "glandular cells"
      ],
      [
        "rectum",
        "glandular cells"
      ],
      [
        "salivary gland",
        "glandular cells"
      ],
      [
        "seminal vesicle",
        "glandular cells"
      ],
      [
        "skeletal muscle",
        "myocytes"
      ],
      [
        "skin 1",
        "Langerhans"
      ],
      [
        "skin 1",
        "fibroblasts"
      ],
      [
        "skin 1",
        "keratinocytes"
      ],
      [
        "skin 1",
        "melanocytes"
      ],
      [
        "skin 2",
        "epidermal cells"
      ],
      [
        "small intestine",
        "glandular cells"
      ],
      [
        "smooth muscle",
        "smooth muscle cells"
      ],
      [
        "soft tissue 1",
        "fibroblasts"
      ],
      [
        "soft tissue 1",
        "peripheral nerve"
      ],
      [
        "soft tissue 2",
        "fibroblasts"
      ],
      [
        "soft tissue 2",
        "peripheral nerve"
      ],
      [
        "spleen",
        "cells in red pulp"
      ],
      [
        "spleen",
        "cells in white pulp"
      ],
      [
        "stomach 1",
        "glandular cells"
      ],
      [
        "stomach 2",
        "glandular cells"
      ],
      [
        "testis",
        "Leydig cells"
      ],
      [
        "testis",
        "cells in seminiferous ducts"
      ],
      [
        "thyroid gland",
        "glandular cells"
      ],
      [
        "tonsil",
        "germinal center cells"
      ],
      [
        "tonsil",
        "non-germinal center cells"
      ],
      [
        "tonsil",
        "squamous epithelial cells"
      ],
      [
        "urinary bladder",
        "urothelial cells"
      ],
      [
        "vagina",
        "squamous epithelial cells"
      ]
    ]
  },
  "manual_reviews": "Existing family and nomination/manual-review decisions preserved and exposed separately from the new expression gates.",
  "checks": [
    "547-candidate previous-sensitivity parity",
    "nested scope expansion and ceiling relaxation"
  ],
  "implementation_sha256": {
    "scripts/cta_permitted_report.py": "d6ae40b145b8a10be52f10aed9a86c210b929120a796fdc4a3ed55fa6cf2ff08",
    "scripts/cta_permitted_report_render.py": "5241ebc3957f78dd1b44f40e86de56ae5063c0a689492616db0f7e5564430772",
    "scripts/cta_scope_report.py": "f68f0cda6bee98a31429ef56f758116034dc962b361c4c7b61426511f4a72cd7",
    "oncoref/normal_tissues.py": "cffb88e0555fa7eb4a86796f174312bf6b56d9d296a12aca120762ed7c5cef99",
    "oncoref/data/normal-tissue-taxonomy.yaml": "f8ffd164ff4e42c26349419ea0306a731057c397080ab1fbee02236ab020b8ca",
    "oncoref/data/normal-tissue-mappings.csv": "9e852c13dfea2638e804f855fef8d7a19c7fe5902ae55c9aee1b094e43eca4f5"
  },
  "outputs": {
    "candidate-decisions.csv": "d9a20ba45f2dd72b234ae467c270de7596ae113f1571da73d9406007611473de",
    "cta-permitted-tissue-report.pdf": "c138128213738772f129b5bc1e463b254e7d4cd461cdd337c0d169c1cb875c98",
    "index.md": "1158c63656d712b2a0e74daa40d4234567fa10fc77c8ae0f3fdf04a5170ae0b1",
    "normal-observations.csv.gz": "3a11937bd41d01f1dc2d80e6a5804b2dd15d01b568b49b1c411276cd3afd75ea",
    "notable-targets.csv": "7d5f714fe9ef29accd44510e0d46df435f0cd1d18d1982df44bdd03696be3fcf",
    "policy-comparison.png": "e14b4d96916a3fbf39a07f8d4528e6d2da540382d459e15d1be09d45cfe76fa6",
    "policy-comparison.svg": "e216ba53ca05d25a7cbd8080df0d641a26ae20a27833b08fa7a14b943f7d0cab",
    "published-targets.png": "da0f1ba16bcc8df5231348d5a5f923c790a4a81999b1f084296c49e801a59257",
    "published-targets.svg": "013f405ed1a35c7049e1f79e9bc3c8545aa78f2136a16c72660cb46ebd020751",
    "scope-summary.csv": "17d4942403c2c4efcb7e13ac4039d317415f1cd2aaf52df31a401cf920f2e137",
    "source-counts.csv": "eeec46e3315ced5d95e902153939f8bd13b66de47a97f3b8958af16bd773890b",
    "source-retention.png": "66e6fe3e2686fa536d100166b46e9064550dd5e06d274fb81b67b5ffd2178dcf",
    "source-retention.svg": "6d1cc09b6ded24a36a660f7f4ecd2ea9b23ac589734c49b652394f5cf3af7cdb",
    "tissue-contexts.csv": "903a45f2ebfff495f5782c750c785eed3268b18b63abc95e8e99c4a68384cc38",
    "tissue-policy.json": "a27cdce11d4d37a5fdda590e76d3eb977a03c482c4ab567d574e2374d8dee3b0"
  }
}