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

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

▶ list_studies
{
 "search": "CHORD"
}

◀ 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)

◀ result
{"result":[{"cancer_study_identifier":"msk_chord_2024","name":"MSK-CHORD (MSK, Nature 2024)","type_of_cancer_id":"mixed","sample_count":25040,"has_guide":true,"url":"https://www.cbioportal.org/study/summary?id=msk_chord_2024"}]}

▶ clickhouse_run_select_query
{
 "query": "SELECT * FROM treatment_counts_in_study(study='msk_chord_2024') ORDER BY patients DESC LIMIT 10"
}

◀ 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}]}

═ answer (success)
In the [MSK-CHORD study](https://www.cbioportal.org/study/summary?id=msk_chord_2024) (MSK, *Nature* 2024; 25,040 samples), the most commonly received single agent among treated patients was **fluorouracil (5-FU)** — a chemotherapy drug — given to **6,319 of 21,473 treated patients (29.4%)**.

The next most common agents were also predominantly chemotherapy: leucovorin (5,573 patients, 26.0%), oxaliplatin (5,489, 25.6%), capecitabine (4,808, 22.4%), and carboplatin (4,604, 21.4%) — several of these (5-FU/leucovorin/oxaliplatin) are typically co-administered as part of FOLFOX-type regimens.

You can explore the full treatment breakdown (by agent and by category — chemo, immuno, targeted, hormone) directly in the Study View:

[View MSK-CHORD treatment data](https://www.cbioportal.org/study/summary?id=msk_chord_2024)

*Note: because treatment collection isn't uniform across all patients, these counts/percentages are relative to the 21,473 patients with any recorded treatment, not the full cohort of 25,040.*