Q (haiku): What fraction of patients were older than five when diagnosed according to the Pediatric Neuroblastoma study from TARGET?

▶ list_studies
{
 "search": "TARGET neuroblastoma",
 "limit": "10"
}

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

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

◀ 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)

▶ list_studies
{
 "search": "TARGET neuroblastoma",
 "limit": 10
}

◀ result
{"result":[{"cancer_study_identifier":"nbl_target_gdc","name":"Neuroblastoma (TARGET GDC, 2025)","type_of_cancer_id":"nbl","sample_count":533,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=nbl_target_gdc"},{"cancer_study_identifier":"nbl_target_2018_pub","name":"Pediatric Neuroblastoma (TARGET, 2018)","type_of_cancer_id":"nbl","sample_count":1089,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=nbl_target_2018_pub"},{"cancer_study_identifier":"nbl_msk_2023","name":"Pediatric Neuroblastoma (MSK, Nat Genet 2023)","type_of_cancer_id":"nbl","sample_count":223,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=nbl_msk_2023"}]}

▶ 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 = 'nbl_target_2018_pub'
)
AND attr_id ILIKE '%AGE%'
ORDER BY attr_id;
",
 "max_rows": 50
}

◀ result
{"rows":[{"attr_id":"AGE","description":"Age at which a condition or disease was first diagnosed."},{"attr_id":"AGE_IN_DAYS","description":"Age at which a condition or disease was first diagnosed."},{"attr_id":"INSS_STAGE","description":"Staging according to the International Neuroblastoma Staging System"},{"attr_id":"PERCENTAGE_NECROSIS","description":"Percent necrosis."},{"attr_id":"PERCENTAGE_TUMOR_PURITY","description":"Percent tumor purity."}]}

▶ clickhouse_run_select_query
{
 "query": "
-- Check age distribution in the study to see if AGE is floored
SELECT
    MIN(toFloat64OrNull(attribute_value)) AS min_age,
    MAX(toFloat64OrNull(attribute_value)) AS max_age,
    COUNT(*) as total_rows,
    COUNTIF(toFloat64OrNull(attribute_value) = 18) as at_min_18,
    COUNTIF(toFloat64OrNull(attribute_value) IS NOT NULL) as non_null_age
FROM clinical_data_derived
WHERE cancer_study_identifier = 'nbl_target_2018_pub'
  AND attribute_name = 'AGE';
",
 "max_rows": 50
}

◀ result
{"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 46\n Code: 46. DB::Exception: Function with name `COUNTIF` does not exist. In scope SELECT MIN(toFloat64OrNull(attribute_value)) AS min_age, MAX(toFloat64OrNull(attribute_value)) AS max_age, COUNT(*) AS total_rows, COUNTIF(toFloat64OrNull(attribute_value) = 18) AS at_min_18, COUNTIF(toFloat64OrNull(attribute_value) IS NOT NULL) AS non_null_age FROM clinical_data_derived WHERE (cancer_study_identifier = 'nbl_target_2018_pub') AND (attribute_name = 'AGE'). Maybe you meant: ['count']. (UNKNOWN_FUNCTION) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_run_select_query
{
 "query": "
-- Check age distribution in the study
SELECT
    MIN(toFloat64OrNull(attribute_value)) AS min_age,
    MAX(toFloat64OrNull(attribute_value)) AS max_age,
    COUNT(*) as total_rows,
    countIf(toFloat64OrNull(attribute_value) = 18) as at_min_18,
    countIf(toFloat64OrNull(attribute_value) IS NOT NULL) as non_null_age
FROM clinical_data_derived
WHERE cancer_study_identifier = 'nbl_target_2018_pub'
  AND attribute_name = 'AGE';
",
 "max_rows": 50
}

◀ result
{"rows":[{"min_age":0,"max_age":21,"total_rows":1076,"at_min_18":1,"non_null_age":1076}]}

▶ clickhouse_run_select_query
{
 "query": "
-- Count patients older than 5 at diagnosis
WITH patient_ages AS (
    SELECT DISTINCT
        patient_unique_id,
        anyIf(toFloat64OrNull(attribute_value), attribute_name = 'AGE') as age_at_diagnosis
    FROM clinical_data_derived
    WHERE cancer_study_identifier = 'nbl_target_2018_pub'
      AND attribute_name = 'AGE'
    GROUP BY patient_unique_id
)
SELECT
    COUNT(*) as total_patients,
    countIf(age_at_diagnosis > 5) as older_than_5,
    round(100.0 * countIf(age_at_diagnosis > 5) / COUNT(*), 2) as pct_older_than_5
FROM patient_ages
WHERE age_at_diagnosis IS NOT NULL;
",
 "max_rows": 50
}

◀ result
{"rows":[{"total_patients":1076,"older_than_5":125,"pct_older_than_5":11.62}]}

▶ resolve_and_route
{
 "studyIds": [
  "nbl_target_2018_pub"
 ]
}

◀ result
{"success":true,"message":"Found 1 study. Use the metadata to call the appropriate navigation tool(s).","data":{"totalCount":1,"studiesWithMetadata":[{"studyId":"nbl_target_2018_pub","name":"Pediatric Neuroblastoma (TARGET, 2018)","sampleCount":1089,"studyViewUrl":"https://www.cbioportal.org/study?id=nbl_target_2018_pub","metadata":{"clinicalAttributeIds":["AGE","AGE_IN_DAYS","ANALYSIS_COHORT","CANCER_TYPE","CANCER_TYPE_DETAILED","CNS_SITE_OF_RELAPSE","DIAGNOSIS","EFSCENS","EFS_TIME","ETHNICITY","FIRST_EVENT","FRACTION_GENOME_ALTERED","GRADE","ICDO","ICDO_SNOMED_DESCRIPTION","INSS_STAGE","LAST_FOLLOWUP_YEAR","MKI","MUTATION_COUNT","MYCN","ONCOTREE_CODE","OS_DAYS","OS_MONTHS","OS_STATUS","PERCENTAGE_NECROSIS","PERCENTAGE_TUMOR_PURITY","PERCENT_TUMOR_CELLS_RELAPSE","PERCENT_TUMOR_VS_STROMA","PLOIDY","PROTOCOL","RACE","RELAPSE_PERCENT_NECROSIS","RELAPSE_PERCENT_STROMA","RISK_GROUP","SAMPLE_COUNT","SCENS","SEX","SNOMED","SOMATIC_STATUS","STIME","TMB_NONSYNONYMOUS","TUMOR_PLOIDY","TUMOR_SAMPLE_HISTOLOGY","TUMOR_TISSUE_SITE","YEAR_OF_DIAGNOSIS"],"molecularProfileIds":["nbl_target_2018_pub_gistic","nbl_target_2018_pub_mrna","nbl_target_2018_pub_mrna_median_Zscores","nbl_target_2018_pub_mrna_median_all_sample_Zscores","nbl_target_2018_pub_mutations","nbl_target_2018_pub_rna_seq_mrna","nbl_target_2018_pub_rna_seq_mrna_median_Zscores","nbl_target_2018_pub_rna_seq_mrna_median_all_sample_Zscores"],"heatmapProfileIds":["nbl_target_2018_pub_mrna_median_Zscores","nbl_target_2018_pub_mrna_median_all_sample_Zscores","nbl_target_2018_pub_rna_seq_mrna_median_Zscores","nbl_target_2018_pub_rna_seq_mrna_median_all_sample_Zscores"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations","mrna"]}}]}}

═ answer (success)
## Answer

In the **Pediatric Neuroblastoma (TARGET, 2018)** study, **125 out of 1,076 patients (11.62%)** were older than 5 years old at diagnosis.

This means that the vast majority (~88%) of patients were diagnosed at age 5 or younger, which is consistent with neuroblastoma typically manifesting in very young children.

[View the study](https://www.cbioportal.org/study?id=nbl_target_2018_pub)