Q (haiku): What are the top 5 most common primary diagnosis sites in the MSK-CHORD Study?

▶ read_guide
{
 "uri": "cbioportal://clinical-data-guide"
}

▶ list_studies
{
 "search": "MSK-CHORD"
}

◀ result
# Clinical Data Query Guide

## Overview
Clinical data in cBioPortal is stored at both patient and sample levels. Understanding the distinction is crucial for accurate analysis.

## Data Organization

### Patient-Level vs Sample-Level Data
- **Patient-level**: Demographics, overall survival, disease stage (stored once per patient)
- **Sample-level**: Sample type, sequencing platform, purity (can have multiple per patient)

### Key Tables
- `clinical_patient`: Patient-level clinical attributes
- `clinical_sample`: Sample-level clinical attributes
- `clinical_data_derived`: Pre-joined view combining both levels
- `clinical_attribute_meta`: Metadata about available clinical attributes

## Recommended Approach: Use clinical_data_derived

The `clinical_data_derived` table is pre-joined and optimized for most queries:

```sql
-- Get clinical data for specific attributes
SELECT
    sample_unique_id,
    patient_unique_id,
    attribute_name,
    attribute_value
FROM clinical_data_derived
WHERE
    cancer_study_identifier = 'your_study_id'
    AND attribute_name IN ('CANCER_TYPE', 'SAMPLE_TYPE', 'TMB_NONSYNONYMOUS');
```

## Clinical Attribute Discovery

### Use clinical_attribute_meta for Discovering Available Attributes
**Always start here** to see what clinical attributes are available for a specific study:

```sql
-- Discover available clinical attributes for a study
SELECT
    attr_id,
    description,
    patient_attribute,
    cancer_study_id
FROM clinical_attribute_meta
WHERE
    cancer_study_id = (
        SELECT cancer_study_id
        FROM cancer_study
        WHERE cancer_study_identifier = 'your_study_id'
    )
ORDER BY patient_attribute, attr_id;
```

**Key Fields:**
- **attr_id**: matches attr_id in clinical_sample/clinical_patient tables
- **description**: human-readable description of the attribute
- **patient_attribute**: true = patient attribute, false = sample attribute
- **cancer_study_id**: links to cancer_study table (filter by study)

## Attribute Semantics and Matching

### Case-Insensitive Matching for Attribute Values

Clinical values are free text across studies and may differ only by case. For example, a controlled-looking value such as germline mutation status may appear as `GERMLINE`, `Germline`, or another case variant.

When filtering `clinical_data_derived.attribute_value`, use case-insensitive matching unless you have already profiled the exact values in the target study:

```sql
-- Correct: case-insensitive clinical value filter
SELECT DISTINCT sample_unique_id, patient_unique_id
FROM clinical_data_derived
WHERE cancer_study_identifier = 'your_study_id'
  AND attribute_name = 'MUTATION_STATUS'
  AND upper(attribute_value) = 'GERMLINE';
```

Do not write `attribute_value = 'GERMLINE'` without first checking all distinct values for that attribute in the study.

### Query the Requested Attribute, Not a Proxy

Do not infer one clinical attribute from a related subtype or marker. Query the actual requested attribute when it … (17073 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_list_table_columns
{
 "table": "clinical_attribute_meta"
}

◀ result
{"columns":[{"name":"attr_id","type":"String"},{"name":"display_name","type":"String"},{"name":"description","type":"String"},{"name":"datatype","type":"String"},{"name":"patient_attribute","type":"Int32"},{"name":"priority","type":"String"},{"name":"cancer_study_id","type":"Int64"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT attr_id, description
FROM clinical_attribute_meta
WHERE cancer_study_id = (
    SELECT cancer_study_id
    FROM cancer_study
    WHERE cancer_study_identifier = 'msk_chord_2024'
)
AND (
    LOWER(attr_id) LIKE '%diagnosis%'
    OR LOWER(attr_id) LIKE '%site%'
    OR LOWER(attr_id) LIKE '%primary%'
    OR LOWER(description) LIKE '%diagnosis%'
    OR LOWER(description) LIKE '%site%'
)
ORDER BY attr_id
",
 "max_rows": 50
}

◀ result
{"rows":[{"attr_id":"ADRENAL_GLANDS","description":"DESCRIPTION: History of Adrenal Gland as a tumor site as indicated in radiology report impression ---MISSING DATA: No CT/PET/MRI radiology report available for patient. impression section MISSING from report. ---SOURCE:(CDM) Generated (NLP)"},{"attr_id":"BONE","description":"DESCRIPTION: History of Bone as a tumor site as indicated in radiology report impression ---MISSING DATA: No CT/PET/MRI radiology report available for patient. impression section MISSING from report. ---SOURCE:(CDM) Generated (NLP)"},{"attr_id":"CNS_BRAIN","description":"DESCRIPTION: History of CNS/Brain as a tumor site as indicated in radiology report impression ---MISSING DATA: No CT/PET/MRI radiology report available for patient. impression section MISSING from report. ---SOURCE:(CDM) Generated (NLP)"},{"attr_id":"DIAGNOSIS_DESCRIPTION","description":"Diagnosis Description"},{"attr_id":"LIVER","description":"DESCRIPTION: History of Liver as a tumor site as indicated in radiology report impression ---MISSING DATA: No CT/PET/MRI radiology report available for patient. impression section MISSING from report. ---SOURCE:(CDM) Generated (NLP)"},{"attr_id":"LUNG","description":"DESCRIPTION: History of Lung as a tumor site as indicated in radiology report impression ---MISSING DATA: No CT/PET/MRI radiology report available for patient. impression section MISSING from report. ---SOURCE:(CDM) Generated (NLP)"},{"attr_id":"LYMPH_NODES","description":"DESCRIPTION: History of LN as a tumor site as indicated in radiology report impression ---MISSING DATA: No CT/PET/MRI radiology report available for patient. impression section MISSING from report. ---SOURCE:(CDM) Generated (NLP)"},{"attr_id":"METASTATIC_SITE","description":"Location of profiled metastatic site"},{"attr_id":"OTHER","description":"DESCRIPTION: History of another site as a tumor site as indicated in radiology report impression ---MISSING DATA: No CT/PET/MRI radiology report available for patient. impression section MISSING from report. ---SOURCE:(CDM) Generated (NLP)"},{"attr_id":"PLEURA","description":"DESCRIPTION: History of Pleura as a tumor site as indicated in radiology report impression ---MISSING DATA: No CT/PET/MRI radiology report available for patient. impression section MISSING from report. ---SOURCE:(CDM) Generated (NLP)"},{"attr_id":"PRIMARY_SITE","description":"The organ sub-division term assigned to the primary tumor location of the sample. Source: MPath"},{"attr_id":"REPRODUCTIVE_ORGANS","description":"DESCRIPTION: History of Reproductive Organs as a tumor site as indicated in radiology report impression ---MISSING DATA: No CT/PET/MRI radiology report available for patient. impression section MISSING from report. ---SOURCE:(CDM) Generated (NLP)"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT 
    attribute_value AS primary_site,
    COUNT(DISTINCT patient_unique_id) AS patient_count,
    COUNT(DISTINCT sample_unique_id) AS sample_count,
    ROUND(100.0 * COUNT(DISTINCT patient_unique_id) / (SELECT COUNT(DISTINCT patient_unique_id) FROM clinical_data_derived WHERE cancer_study_identifier = 'msk_chord_2024' AND attribute_name = 'PRIMARY_SITE' AND attribute_value != ''), 2) AS pct_of_patients
FROM clinical_data_derived
WHERE cancer_study_identifier = 'msk_chord_2024'
    AND attribute_name = 'PRIMARY_SITE'
    AND attribute_value != ''
GROUP BY attribute_value
ORDER BY patient_count DESC
LIMIT 5
",
 "max_rows": 10
}

◀ result
{"rows":[{"primary_site":"Lung","patient_count":7773,"sample_count":7773,"pct_of_patients":31.15},{"primary_site":"Breast","patient_count":5358,"sample_count":5358,"pct_of_patients":21.47},{"primary_site":"Prostate","patient_count":3208,"sample_count":3208,"pct_of_patients":12.86},{"primary_site":"Pancreas","patient_count":3104,"sample_count":3104,"pct_of_patients":12.44},{"primary_site":"Colon","patient_count":2516,"sample_count":2516,"pct_of_patients":10.08}]}

═ answer (success)
## Top 5 Most Common Primary Diagnosis Sites in MSK-CHORD

Based on the MSK-CHORD study (25,040 samples), here are the top 5 most common primary diagnosis sites:

| Rank | Primary Site | Patients | % of Cohort |
|------|--------------|----------|------------|
| 1 | **Lung** | 7,773 | 31.15% |
| 2 | **Breast** | 5,358 | 21.47% |
| 3 | **Prostate** | 3,208 | 12.86% |
| 4 | **Pancreas** | 3,104 | 12.44% |
| 5 | **Colon** | 2,516 | 10.08% |

**Key observations:**
- Lung cancer dominates the cohort, accounting for nearly one-third of all patients.
- The top 5 sites together represent ~88% of the MSK-CHORD patient population.
- These sites reflect common malignancies in MSK's clinical practice (a tertiary cancer center).

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