data/sample_input/act.json

{
  "extraction_version": "1.0",
  "extraction_date": "2026-02-23",
  "patient": {
    "id": "UMC-556219",
    "age": 60,
    "gender": "Male"
  },
  "cancer": {
    "type": "Diffuse Large B-Cell Lymphoma",
    "subtype": "non-GCB (ABC type)",
    "stage": "IV",
    "primary_site": "Lymphoma",
    "metastases": [
      "Bone marrow (15% involvement)",
      "Retroperitoneal nodes (3.2cm)",
      "Mesenteric mass (4.8cm)"
    ],
    "biomarkers": {
      "pdl1_expression": "N/A",
      "tmb": "N/A",
      "msi_status": "MSS"
    },
    "diagnosis_date": "2024-03-18"
  },
  "immunotherapy": {
    "therapy_type": "ACT",
    "drug_name": "Axicabtagene ciloleucel",
    "drug_class": "CAR-T",
    "treatment_setting": "metastatic",
    "line_of_therapy": "Second-line",
    "planned_start_date": "2026-03-10",
    "ici_details": null,
    "act_details": {
      "act_type": "CAR-T",
      "target_antigen": "CD19",
      "cell_source": "autologous",
      "preconditioning_regimen": "Fludarabine + Cyclophosphamide",
      "t_cell_harvest_date": "2026-02-14",
      "expected_crs_risk": "moderate-high",
      "expected_neurotoxicity_risk": "moderate"
    }
  },
  "prior_treatments": {
    "chemotherapy": {
      "received": true,
      "regimens": [
        "R-CHOP",
        "R-ICE",
        "Gemcitabine (bridging)"
      ],
      "response": "CR (R-CHOP), PR (R-ICE), Stable disease (Gemcitabine)"
    },
    "prior_immunotherapy": {
      "received": true,
      "drugs": [],
      "response": ""
    }
  },
  "medications": {
    "ppi_use": {
      "currently_on_ppi": false,
      "ppi_name": "",
      "duration_months": 0
    },
    "antibiotic_history": {
      "recent_antibiotics": true,
      "exposures": [
        {
          "antibiotic_name": "Levofloxacin 500mg",
          "antibiotic_class": "fluoroquinolone",
          "start_date": "2026-01-25",
          "end_date": "2026-02-05",
          "days_before_ici": 14
        },
        {
          "antibiotic_name": "Piperacillin-tazobactam 4.5g",
          "antibiotic_class": "beta-lactam",
          "start_date": "2025-12-18",
          "end_date": "2025-12-27",
          "days_before_ici": 73
        }
      ]
    }
  },
  "comorbidities": [
    "Hypertension",
    "hyperlipidemia",
    "Type 2 diabetes",
    "chronic back pain"
  ],
  "microbiome": {
    "sample_date": "2026-02-05",
    "sequencing_method": "Shotgun metagenomic sequencing (Illumina NovaSeq, 12M reads)",
    "diversity": {
      "shannon_index": 2.7,
      "simpson_index": 0.82,
      "observed_species": 164
    },
    "key_bacteria": {
      "Akkermansia muciniphila": 1.8,
      "Faecalibacterium prausnitzii": 3.6,
      "Ruminococcaceae": 9.2,
      "Ruminococcus lactaris": 1.8,
      "Lachnospiraceae": 8.8,
      "Lachnospira pectinoschiza": 1.2,
      "Roseburia": 1.8,
      "Bifidobacterium spp.": 2.2,
      "Bacteroides eggerthii": 2.4,
      "Proteobacteria": 8.4,
      "E. coli": 4.2,
      "Klebsiella pneumoniae": 1.8,
      "Enterococcus faecalis": 2.1,
      "Bacteroides uniformis": 3.6,
      "Blautia spp.": 4.2
    },
    "metabolites": {
      "scfa": {
        "butyrate_uM": 15.8,
        "propionate_uM": 11.2,
        "acetate_uM": 38.4
      },
      "bile_acids_available": true,
      "tryptophan_metabolites_available": false
    },
    "data_quality": {
      "completeness": "moderate",
      "source": "Precision Microbiome Diagnostics",
      "limitations": [
        "Single time-point during active antibiotics",
        "Reduced diversity from antibiotics + chemotherapy"
      ]
    }
  },
  "clinical_context": {
    "urgency": "",
    "patient_goals": [
      "CAR-T therapy consultation",
      "Relapsed/Refractory DLBCL treatment"
    ],
    "specific_concerns": [
      "CAR-T efficacy",
      "CAR-T toxicity (CRS, neurotoxicity)",
      "Microbiome dysbiosis",
      "Low butyrate",
      "Antibiotic disruption"
    ]
  }
}