Q (sonnet): 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)

▶ 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}]}

▶ resolve_and_route
{
 "studyIds": [
  "msk_chord_2024"
 ]
}

◀ result
{"success":true,"message":"Found 1 study. Use the metadata to call the appropriate navigation tool(s).","data":{"totalCount":1,"studiesWithMetadata":[{"studyId":"msk_chord_2024","name":"MSK-CHORD (MSK, Nature 2024)","sampleCount":25040,"studyViewUrl":"https://www.cbioportal.org/study?id=msk_chord_2024","metadata":{"clinicalAttributeIds":["ADRENAL_GLANDS","BONE","CANCER_TYPE","CANCER_TYPE_DETAILED","CLINICAL_GROUP","CLINICAL_SUMMARY","CNS_BRAIN","CURRENT_AGE_DEID","DIAGNOSIS_DESCRIPTION","ETHNICITY","FRACTION_GENOME_ALTERED","GENDER","GENE_PANEL","GLEASON_FIRST_REPORTED","GLEASON_HIGHEST_REPORTED","GLEASON_SAMPLE_LEVEL","HER2","HISTORY_OF_PDL1","HR","ICD_O_HISTOLOGY_DESCRIPTION","INTRA_ABDOMINAL","LIVER","LUNG","LYMPH_NODES","METASTATIC_SITE","MSI_COMMENT","MSI_SCORE","MSI_TYPE","MUTATION_COUNT","NUM_ICDO_DX","ONCOTREE_CODE","OS_MONTHS","OS_STATUS","OTHER","PATHOLOGICAL_GROUP","PDL1_POSITIVE","PLEURA","PRIMARY_SITE","PRIOR_MED_TO_MSK","RACE","REPRODUCTIVE_ORGANS","SAMPLE_CLASS","SAMPLE_COUNT","SAMPLE_COVERAGE","SAMPLE_TYPE","SMOKING_PREDICTIONS_3_CLASSES","SOMATIC_STATUS","STAGE_HIGHEST_RECORDED","TMB_NONSYNONYMOUS","TUMOR_PURITY"],"molecularProfileIds":["msk_chord_2024_cna","msk_chord_2024_mutations","msk_chord_2024_structural_variants"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations"]}}]}}

═ answer (success)
In the **MSK-CHORD Study** (Nature 2024), among the 21,473 patients with recorded treatment data, **fluorouracil (5-FU)** was the most commonly administered agent:

| Agent | Category | 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% |

Note: fluorouracil, leucovorin, and oxaliplatin frequently co-occur as components of combination chemotherapy regimens (e.g., FOLFOX), consistent with the colorectal-cancer-heavy composition of this cohort.

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