Q (haiku): How many patients have a shallow deletion for SMARCA4 in the POG study?

▶ read_guide
{
 "uri": "cbioportal://sample-filtering-guide"
}

▶ list_studies
{
 "search": "POG"
}

◀ result
# Sample and Study Filtering Guide

## Overview
Proper filtering is essential for meaningful cBioPortal analysis. This guide covers filtering by studies, sample types, and other criteria.

## Study-Level Filtering

### 1. Always Filter by Study
Every query should specify a study to ensure consistent results:

```sql
-- Always include study filtering
SELECT *
FROM your_table
WHERE
    cancer_study_identifier = 'your_study_id'
    -- Additional filters...
```

### 2. Find Available Studies

```sql
-- Discover available studies
SELECT
    cancer_study_identifier,
    name,
    description,
    type_of_cancer_id
FROM cancer_study
ORDER BY cancer_study_identifier;
```

### 3. Study Information

```sql
-- Get detailed study information
SELECT
    cs.cancer_study_identifier,
    cs.name as study_name,
    cs.description,
    cs.sample_count,
    COUNT(DISTINCT p.internal_id) as patient_count
FROM cancer_study cs
LEFT JOIN patient p ON cs.cancer_study_id = p.cancer_study_id
WHERE
    cs.cancer_study_identifier = 'your_study_id'
GROUP BY cs.cancer_study_identifier, cs.name, cs.description, cs.sample_count;
```

### 4. Find Studies by Available Data Types

Use this when the user asks *"which studies have mutation and copy-number data for X"*, *"studies with expression for Y"*, *"is there any imaging data"*, or any *"studies with Z data"* question. `cancer_study` has one precomputed sample count per data type — filter on them. No join and no schema exploration needed. These are the same counts as the portal's study list and its "Data type" filter.

**Canonical query — studies with ALL requested data types for a cancer type:**

```sql
SELECT
    cancer_study_identifier,
    name,
    sample_count,
    mutation_sample_count,
    cna_sample_count
FROM cancer_study
WHERE type_of_cancer_id = 'luad'          -- ← OncoTree code from search_oncotree
  AND mutation_sample_count > 0           -- ← one condition per required data type
  AND cna_sample_count > 0
ORDER BY sample_count DESC;
```

**Data type → column** (a count of 0 means the study doesn't have that data):

| Data type in the user's question | Column (portal "Data type" filter label) |
|---|---|
| samples in the study | `sample_count` |
| mutation / mutations | `mutation_sample_count` ("Mutations") |
| copy-number / CNA / amplification / deletion | `cna_sample_count` ("CNA") |
| structural variant / fusion | `structural_variant_sample_count` |
| RNA / mRNA / gene expression (any platform) | `mrna_expression_sample_count` — use this for "which studies have expression data" |
| specifically the portal's "RNA-Seq" filter | `rna_seq_sample_count` ("RNA-Seq") — counts only the `<study>_rna_seq_v2_mrna` list; 0 for many GDC and iAtlas studies that do have RNA-Seq |
| specifically the portal's "RNA (microarray)" filter | `mrna_microarray_sample_count` ("RNA (microarray)") — counts only the `<study>_mrna` list |
| microRNA | `mirna_sample_count` ("miRNA") |
| protein / RPPA | `rppa_sample_count` ("RPPA") |
| mas … (7866 more chars)

◀ result
{"result":[{"cancer_study_identifier":"pog570_bcgsc_2020","name":"Pan-cancer Analysis of Advanced and Metastatic Tumors (BCGSC, Nature Cancer 2020)","type_of_cancer_id":"mixed","sample_count":570,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=pog570_bcgsc_2020"}]}

▶ clickhouse_list_table_columns
{
 "table": "genomic_event_derived"
}

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

▶ clickhouse_list_table_columns
{
 "table": "genetic_alteration_derived"
}

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

▶ clickhouse_list_table_columns
{
 "table": "genomic_event_derived"
}

▶ clickhouse_list_table_columns
{
 "table": "genetic_alteration_derived"
}

◀ result
{"columns":[{"name":"sample_unique_id","type":"String"},{"name":"hugo_gene_symbol","type":"String","comment":"HUGO gene symbol (e.g., TP53, KRAS, BRAF). Use for gene-specific queries."},{"name":"entrez_gene_id","type":"Int32"},{"name":"gene_panel_stable_id","type":"LowCardinality(String)"},{"name":"cancer_study_identifier","type":"LowCardinality(String)"},{"name":"genetic_profile_stable_id","type":"LowCardinality(String)"},{"name":"variant_type","type":"LowCardinality(String)","comment":"Type of genomic event: \"mutation\" for SNVs/indels, \"cna\" for copy number alterations, \"structural_variant\" for SVs. Always filter by this."},{"name":"mutation_variant","type":"String","comment":"Protein change notation (e.g., p.V600E, p.R175H). Use for specific variant queries. \"NA\" for non-mutation events."},{"name":"mutation_type","type":"LowCardinality(String)"},{"name":"mutation_status","type":"LowCardinality(String)","comment":"For mutations: Somatic, Germline, UNKNOWN, or UNCALLED. Filter mutation_status != \"UNCALLED\" to exclude uncertain calls. Include all other statuses."},{"name":"driver_filter","type":"LowCardinality(String)"},{"name":"driver_filter_annotation","type":"String"},{"name":"driver_tiers_filter","type":"LowCardinality(String)"},{"name":"driver_tiers_filter_annotation","type":"String"},{"name":"cna_alteration","type":"Nullable(Int8)","comment":"Copy number alteration: only 2 = amplification (AMP) and -2 = deep deletion (HOMDEL) are stored. Shallow deletion (-1), diploid (0) and gain (1) are not in this table; query genetic_alteration_derived WHERE profile_type = 'gistic' (alteration_value is a String, e.g. '-1'). NULL for non-CNA events."},{"name":"cna_cytoband","type":"String"},{"name":"sv_event_info","type":"String"},{"name":"patient_unique_id","type":"String"},{"name":"off_panel","type":"Bool","comment":"Boolean: 1 = mutation outside gene panel coverage (off-panel), 0 = within panel (on-panel). Filter off_panel = 0 for reliable frequency calculations."}]}

◀ result
{"columns":[{"name":"sample_unique_id","type":"String"},{"name":"cancer_study_identifier","type":"LowCardinality(String)"},{"name":"hugo_gene_symbol","type":"String"},{"name":"profile_type","type":"LowCardinality(String)"},{"name":"alteration_value","type":"Nullable(String)"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT 
    COUNT(DISTINCT p.patient_unique_id) AS patient_count,
    COUNT(DISTINCT g.sample_unique_id) AS sample_count
FROM genetic_alteration_derived g
JOIN patient p ON g.sample_unique_id = SUBSTR(p.patient_id, 1, LENGTH(p.patient_id) - 3)
WHERE 
    g.cancer_study_identifier = 'pog570_bcgsc_2020'
    AND g.hugo_gene_symbol = 'SMARCA4'
    AND g.profile_type = 'gistic'
    AND g.alteration_value = '-1'
",
 "max_rows": 10
}

◀ result
{"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 47\n Code: 47. DB::Exception: Identifier 'p.patient_id' cannot be resolved from table with name p. In scope SELECT COUNTDistinct(p.patient_unique_id) AS patient_count, COUNTDistinct(g.sample_unique_id) AS sample_count FROM genetic_alteration_derived AS g INNER JOIN patient AS p ON g.sample_unique_id = SUBSTR(p.patient_id, 1, LENGTH(p.patient_id) - 3) WHERE (g.cancer_study_identifier = 'pog570_bcgsc_2020') AND (g.hugo_gene_symbol = 'SMARCA4') AND (g.profile_type = 'gistic') AND (g.alteration_value = '-1'). (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_list_table_columns
{
 "table": "patient"
}

◀ result
{"columns":[{"name":"internal_id","type":"Int64","comment":"Primary key. Unique internal identifier for the patient."},{"name":"stable_id","type":"String","comment":"Stable patient identifier within the study. Combined with cancer_study_identifier forms patient_unique_id."},{"name":"cancer_study_id","type":"Int64","comment":"Foreign key to cancer_study.cancer_study_id. Links patient to their study."}]}

▶ clickhouse_list_table_columns
{
 "table": "sample"
}

◀ result
{"columns":[{"name":"internal_id","type":"Int64","comment":"Primary key. Unique internal identifier for the sample."},{"name":"stable_id","type":"String","comment":"Stable identifier for the sample within the study. Combined with cancer_study_identifier forms sample_unique_id."},{"name":"patient_id","type":"Int64","comment":"Foreign key to patient.internal_id. Links sample to its patient."}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT 
    COUNT(DISTINCT p.internal_id) AS patient_count,
    COUNT(DISTINCT s.internal_id) AS sample_count
FROM genetic_alteration_derived g
JOIN sample s ON g.sample_unique_id = CONCAT(cs.cancer_study_identifier, '_', s.stable_id)
JOIN patient p ON s.patient_id = p.internal_id
JOIN cancer_study cs ON p.cancer_study_id = cs.cancer_study_id
WHERE 
    g.cancer_study_identifier = 'pog570_bcgsc_2020'
    AND g.hugo_gene_symbol = 'SMARCA4'
    AND g.profile_type = 'gistic'
    AND g.alteration_value = '-1'
",
 "max_rows": 10
}

◀ result
{"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 47\n Code: 47. DB::Exception: Unknown expression or function identifier `cs.cancer_study_identifier` in scope SELECT COUNTDistinct(p.internal_id) AS patient_count, COUNTDistinct(s.internal_id) AS sample_count FROM genetic_alteration_derived AS g INNER JOIN sample AS s ON g.sample_unique_id = CONCAT(cs.cancer_study_identifier, '_', s.stable_id) INNER JOIN patient AS p ON s.patient_id = p.internal_id INNER JOIN cancer_study AS cs ON p.cancer_study_id = cs.cancer_study_id WHERE (g.cancer_study_identifier = 'pog570_bcgsc_2020') AND (g.hugo_gene_symbol = 'SMARCA4') AND (g.profile_type = 'gistic') AND (g.alteration_value = '-1'). Maybe you meant: ['g.cancer_study_identifier']. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_run_select_query
{
 "query": "
WITH smarca4_shallow_del AS (
    SELECT DISTINCT
        sample_unique_id,
        hugo_gene_symbol
    FROM genetic_alteration_derived
    WHERE 
        cancer_study_identifier = 'pog570_bcgsc_2020'
        AND hugo_gene_symbol = 'SMARCA4'
        AND profile_type = 'gistic'
        AND alteration_value = '-1'
)
SELECT 
    COUNT(*) AS samples_with_shallow_deletion,
    hugo_gene_symbol
FROM smarca4_shallow_del
GROUP BY hugo_gene_symbol
",
 "max_rows": 10
}

◀ result
{"rows":[{"samples_with_shallow_deletion":111,"hugo_gene_symbol":"SMARCA4"}]}

▶ clickhouse_run_select_query
{
 "query": "
WITH smarca4_shallow_del AS (
    SELECT DISTINCT
        sample_unique_id
    FROM genetic_alteration_derived
    WHERE 
        cancer_study_identifier = 'pog570_bcgsc_2020'
        AND hugo_gene_symbol = 'SMARCA4'
        AND profile_type = 'gistic'
        AND alteration_value = '-1'
),
samples_to_patients AS (
    SELECT DISTINCT
        SUBSTR(sd.sample_unique_id, 1, POSITION('_' IN sd.sample_unique_id) - 1) as study_id,
        SUBSTR(sd.sample_unique_id, POSITION('_' IN sd.sample_unique_id) + 1) as sample_id
    FROM smarca4_shallow_del sd
)
SELECT 
    COUNT(DISTINCT sample_unique_id) as samples,
    uniqExact(SUBSTR(sample_unique_id, POSITION('_' IN sample_unique_id) + 1, 
                     POSITION('_' IN REVERSE(SUBSTR(sample_unique_id, POSITION('_' IN sample_unique_id) + 1))) - 1)) as patient_count
FROM genetic_alteration_derived
WHERE 
    cancer_study_identifier = 'pog570_bcgsc_2020'
    AND hugo_gene_symbol = 'SMARCA4'
    AND profile_type = 'gistic'
    AND alteration_value = '-1'
",
 "max_rows": 10
}

◀ result
{"rows":[{"samples":111,"patient_count":1}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT 
    sample_unique_id,
    COUNT(*) as count
FROM genetic_alteration_derived
WHERE 
    cancer_study_identifier = 'pog570_bcgsc_2020'
    AND hugo_gene_symbol = 'SMARCA4'
    AND profile_type = 'gistic'
    AND alteration_value = '-1'
GROUP BY sample_unique_id
LIMIT 20
",
 "max_rows": 100
}

◀ result
{"rows":[{"sample_unique_id":"pog570_bcgsc_2020_24295","count":1},{"sample_unique_id":"pog570_bcgsc_2020_25501","count":1},{"sample_unique_id":"pog570_bcgsc_2020_24177","count":1},{"sample_unique_id":"pog570_bcgsc_2020_30491","count":1},{"sample_unique_id":"pog570_bcgsc_2020_30311","count":1},{"sample_unique_id":"pog570_bcgsc_2020_28638","count":1},{"sample_unique_id":"pog570_bcgsc_2020_37719","count":1},{"sample_unique_id":"pog570_bcgsc_2020_28131","count":1},{"sample_unique_id":"pog570_bcgsc_2020_18843","count":1},{"sample_unique_id":"pog570_bcgsc_2020_31509","count":1},{"sample_unique_id":"pog570_bcgsc_2020_31043","count":1},{"sample_unique_id":"pog570_bcgsc_2020_31518","count":1},{"sample_unique_id":"pog570_bcgsc_2020_33532","count":1},{"sample_unique_id":"pog570_bcgsc_2020_36700","count":1},{"sample_unique_id":"pog570_bcgsc_2020_33740","count":1},{"sample_unique_id":"pog570_bcgsc_2020_28012","count":1},{"sample_unique_id":"pog570_bcgsc_2020_13268","count":1},{"sample_unique_id":"pog570_bcgsc_2020_30897","count":1},{"sample_unique_id":"pog570_bcgsc_2020_33033","count":1},{"sample_unique_id":"pog570_bcgsc_2020_23737","count":1}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT 
    COUNT(DISTINCT sample_unique_id) as samples_with_shallow_deletion
FROM genetic_alteration_derived
WHERE 
    cancer_study_identifier = 'pog570_bcgsc_2020'
    AND hugo_gene_symbol = 'SMARCA4'
    AND profile_type = 'gistic'
    AND alteration_value = '-1'
",
 "max_rows": 10
}

◀ result
{"rows":[{"samples_with_shallow_deletion":111}]}

▶ clickhouse_run_select_query
{
 "query": "
WITH smarca4_samples AS (
    SELECT DISTINCT sample_unique_id
    FROM genetic_alteration_derived
    WHERE 
        cancer_study_identifier = 'pog570_bcgsc_2020'
        AND hugo_gene_symbol = 'SMARCA4'
        AND profile_type = 'gistic'
        AND alteration_value = '-1'
)
SELECT 
    COUNT(DISTINCT patient_unique_id) as patient_count,
    COUNT(DISTINCT sample_unique_id) as sample_count
FROM clinical_data_derived
WHERE 
    cancer_study_identifier = 'pog570_bcgsc_2020'
    AND sample_unique_id IN (SELECT sample_unique_id FROM smarca4_samples)
",
 "max_rows": 10
}

◀ result
{"rows":[{"patient_count":111,"sample_count":111}]}

═ answer (success)
Perfect! Now I have the answer. Let me provide the result:

## Answer

**111 patients** in the POG (Pan-cancer Analysis of Advanced and Metastatic Tumors) study have a shallow deletion (−1 copy) for **SMARCA4**.

**Study:** Pan-cancer Analysis of Advanced and Metastatic Tumors (BCGSC, Nature Cancer 2020) - 570 total samples

**Shallow deletion definition:** In the gistic CNA profile, alteration value = −1 represents heterozygous loss (shallow deletion).