Q (haiku): What treatment did most patients receive in the MSK-CHORD Study?

▶ list_tables
{}

✗ error
<tool_use_error>Error: No such tool available: mcp__claude_ai_cBioPortal_MCP__list_tables</tool_use_error>

▶ read_guide
{
 "uri": "cbioportal://treatment-guide"
}

◀ result
# Treatment Data Query Guide

## Overview

Treatment data in cBioPortal is stored in **clinical event tables**, separate from clinical attributes. This allows for timeline-based treatment records with start/stop dates.

## Start Here: Treatment Views

For "most common treatments / agents / regimens in study X", use the parameterized views (documented in `cbioportal://clinical-data-guide`, Study-View Chart Counts):

```sql
-- Patients per agent (the portal's Treatment chart), with type/subtype arrays
SELECT * FROM treatment_counts_in_study(study='msk_chord_2024') ORDER BY patients DESC LIMIT 20;

-- Same-day agent combinations (investigational, prior-medication and radiation events excluded)
SELECT * FROM treatment_regimens_in_study(study='msk_chord_2024') ORDER BY patients DESC LIMIT 20;
```

Write raw event queries (below) only for subgroups, timelines or keys the views do not expose.

## Key Tables

| Table | Description |
|-------|-------------|
| `clinical_event` | Event records with patient_id, event_type, start_date, stop_date |
| `clinical_event_data` | Key-value pairs linked to each clinical_event_id |

## Schema

```
clinical_event
├── clinical_event_id (PK)
├── patient_id (FK → patient.internal_id)
├── event_type (Treatment, TREATMENT, Diagnosis, SURGERY, etc.)
├── start_date (days from diagnosis)
└── stop_date (days from diagnosis)

clinical_event_data
├── clinical_event_id (FK)
├── key (AGENT, SUBTYPE, etc.)
└── value
```

## Event Types

Not all studies have all event types. Common ones include:

| Event Type | Description |
|------------|-------------|
| `Treatment` / `TREATMENT` | Drug/therapy administration |
| `SURGERY` | Surgical procedures |
| `Diagnosis` | Diagnosis events |
| `LAB_TEST` | Laboratory results |
| `Sequencing` | Sequencing events |
| `Sample acquisition` | Sample collection |
| `PATHOLOGY` / `Pathology` | Pathology reports |

## Basic Treatment Queries

### List Available Event Types in a Study

```sql
SELECT DISTINCT ce.event_type, COUNT(*) as event_count
FROM clinical_event ce
JOIN patient p ON ce.patient_id = p.internal_id
JOIN cancer_study cs ON p.cancer_study_id = cs.cancer_study_id
WHERE cs.cancer_study_identifier = 'your_study_id'
GROUP BY ce.event_type
ORDER BY event_count DESC;
```

### List Treatment Data Keys in a Study

```sql
SELECT DISTINCT ced.key, COUNT(*) as cnt
FROM clinical_event ce
JOIN clinical_event_data ced ON ce.clinical_event_id = ced.clinical_event_id
JOIN patient p ON ce.patient_id = p.internal_id
JOIN cancer_study cs ON p.cancer_study_id = cs.cancer_study_id
WHERE cs.cancer_study_identifier = 'your_study_id'
  AND ce.event_type IN ('Treatment', 'TREATMENT')
GROUP BY ced.key
ORDER BY cnt DESC;
```

### Get Most Common Treatment Agents

```sql
SELECT 
    ced.value as agent,
    COUNT(DISTINCT ce.patient_id) as patient_count
FROM clinical_event ce
JOIN clinical_event_data ced ON ce.clinical_event_id = ced.clinical_event_id
JOIN patient p ON ce.patient_id = p.internal_id
JOIN cancer_stud … (6220 more chars)

▶ clickhouse_run_select_query
{
 "query": "SELECT * FROM treatment_counts_in_study(study='msk_chord_2024') ORDER BY patients DESC LIMIT 20;",
 "max_rows": 100
}

◀ result
{"rows":[{"agent":"FLUOROURACIL","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":6319,"treated_patients":21473,"pct_of_treated_patients":29.4},{"agent":"LEUCOVORIN","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":5573,"treated_patients":21473,"pct_of_treated_patients":26},{"agent":"OXALIPLATIN","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":5489,"treated_patients":21473,"pct_of_treated_patients":25.6},{"agent":"CAPECITABINE","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":4808,"treated_patients":21473,"pct_of_treated_patients":22.4},{"agent":"CARBOPLATIN","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":4604,"treated_patients":21473,"pct_of_treated_patients":21.4},{"agent":"IRINOTECAN","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":4329,"treated_patients":21473,"pct_of_treated_patients":20.2},{"agent":"INVESTIGATIONAL","treatment_types":[],"treatment_subtypes":["Investigational"],"patients":4114,"treated_patients":21473,"pct_of_treated_patients":19.2},{"agent":"GEMCITABINE","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":4038,"treated_patients":21473,"pct_of_treated_patients":18.8},{"agent":"LEUPROLIDE","treatment_types":[],"treatment_subtypes":["Hormone"],"patients":3708,"treated_patients":21473,"pct_of_treated_patients":17.3},{"agent":"PACLITAXEL","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":3679,"treated_patients":21473,"pct_of_treated_patients":17.1},{"agent":"PEMETREXED","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":3357,"treated_patients":21473,"pct_of_treated_patients":15.6},{"agent":"BEVACIZUMAB","treatment_types":[],"treatment_subtypes":["Biologic"],"patients":2629,"treated_patients":21473,"pct_of_treated_patients":12.2},{"agent":"CYCLOPHOSPHAMIDE","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":2494,"treated_patients":21473,"pct_of_treated_patients":11.6},{"agent":"PACLITAXEL PROTEIN-BOUND","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":2357,"treated_patients":21473,"pct_of_treated_patients":11},{"agent":"LETROZOLE","treatment_types":[],"treatment_subtypes":["Hormone"],"patients":2260,"treated_patients":21473,"pct_of_treated_patients":10.5},{"agent":"DOXORUBICIN","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":2107,"treated_patients":21473,"pct_of_treated_patients":9.8},{"agent":"ZOLEDRONIC ACID","treatment_types":[],"treatment_subtypes":["Bone Treatment"],"patients":2101,"treated_patients":21473,"pct_of_treated_patients":9.8},{"agent":"PEMBROLIZUMAB","treatment_types":[],"treatment_subtypes":["Immuno"],"patients":2061,"treated_patients":21473,"pct_of_treated_patients":9.6},{"agent":"DOCETAXEL","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":1917,"treated_patients":21473,"pct_of_treated_patients":8.9},{"agent":"ANASTROZOLE","treatment_types":[],"treatment_subtypes":["Hormone"],"patients":1676,"treated_patients":21473,"pct_of_treated_patie … (11 more chars)

═ answer (success)
## Results

In the **MSK-CHORD Study**, **fluorouracil** is the most commonly received treatment:

| Agent | Treatment Type | Patients | % of Treated Patients |
|-------|----------------|----------|----------------------|
| **FLUOROURACIL** | Chemo | **6,319** | **29.4%** |
| LEUCOVORIN | Chemo | 5,573 | 26.0% |
| OXALIPLATIN | Chemo | 5,489 | 25.6% |
| CAPECITABINE | Chemo | 4,808 | 22.4% |
| CARBOPLATIN | Chemo | 4,604 | 21.4% |

**Context:** The study includes 21,473 patients who received at least one documented treatment. Fluorouracil was administered to 6,319 patients—the highest of any single agent. The top treatments are predominantly chemotherapy agents (especially used in colorectal cancer regimens like FOLFOX and FOLFIRI), followed by hormone therapies, investigational drugs, and immunotherapies.