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

▶ 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)

▶ list_studies
{
 "search": "MSK-CHORD",
 "verbose": true
}

◀ result
{"result":[{"cancer_study_identifier":"msk_chord_2024","name":"MSK-CHORD (MSK, Nature 2024)","description":"Targeted sequencing of 25040 tumors from 24950 patients and their matched normals via MSK-IMPACT, along with clinical annotations, some of which are derived from natural language processing (denoted NLP). This data is available under the <a href=\"https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en\">Creative Commons BY-NC-ND 4.0 license</a>. For commercial use, please contact <a href=\"mailto: datarequests@mskcc.org\">datarequests@mskcc.org</a>","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 20;",
 "max_rows": 20
}

◀ 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)
## Most Common Treatments in MSK-CHORD Study

In the **MSK-CHORD Study** (25,040 tumors from 24,950 patients), the most common treatments received were:

**Top 5 Agents:**
1. **FLUOROURACIL** – 6,319 patients (29.4% of treated patients)
2. **LEUCOVORIN** – 5,573 patients (26.0% of treated patients)
3. **OXALIPLATIN** – 5,489 patients (25.6% of treated patients)
4. **CAPECITABINE** – 4,808 patients (22.4% of treated patients)
5. **CARBOPLATIN** – 4,604 patients (21.4% of treated patients)

**Treatment Category Summary:**
- **Chemotherapy** agents dominate, with fluorouracil-based regimens (fluorouracil + leucovorin ± oxaliplatin) being the most prevalent
- **Investigational** agents were given to 4,114 patients (19.2%)
- **Hormone therapies** (leuprolide, letrozole, anastrozole) were the next most common category
- **Immunotherapy** (e.g., pembrolizumab) was given to 2,061 patients (9.6%)

**Important note:** These represent raw patient counts with treatment records in the study. The percentages reflect the proportion among the 21,473 patients with documented treatment events, not the total cohort.

You can explore the full study data and treatment timelines in [MSK-CHORD Study on cBioPortal](https://www.cbioportal.org/study/summary?id=msk_chord_2024).