Q (haiku): <conversation_so_far>
<user>
在TCGA肺腺癌研究中，EGFR突变的频率是多少？
</user>

<assistant>
在 Lung Adenocarcinoma (TCGA, PanCancer Atlas) 中，566 个检测样本中有 70 个（12.4%）携带 EGFR 突变。
</assistant>
</conversation_so_far>

Continue this conversation: reply to the user's new message.

<user>
那 KRAS 呢？
</user>

▶ read_guide
{
 "uri": "cbioportal://mutation-frequency-guide"
}

◀ result
# Mutation Frequency Analysis Guide

## IMPORTANT: Reporting Mutation Frequencies
- **ALWAYS report frequencies as percentages**, not raw counts: `frequency = (altered_samples / total_profiled_samples) × 100`
- For quick frequency lookups, **prefer the TCGA Pan-Cancer Atlas study first**, then offer to expand to other studies
- When reporting across multiple studies, show **ranges** (e.g., "TP53 is mutated in 30–60% of samples") rather than a single average
- **NEVER** sum mutation events across studies to compute an aggregate frequency — this can exceed 100% due to double-counting
- Warn users that samples may overlap across cohorts (e.g., MSK studies may share patients)
- **Choose and state the counting unit**: use patient-level frequencies for prevalence/rate questions unless the user explicitly asks for samples; use sample-level frequencies when the user asks about samples.
- **For "across cancer types" questions**, jump to the [Cross-Cancer-Type Mutation Frequency](#cross-cancer-type-mutation-frequency) section below — there is one correct recipe and several common wrong ones.

## Counting Unit: Samples vs Patients

Before answering any mutation count or frequency question, decide whether the unit is samples or patients and state that choice in the answer.

| User wording | Counting unit |
|--------------|---------------|
| "prevalence", "rate", "fraction of patients", "patients with", "how common is" | Patient-level: `COUNT(DISTINCT patient_unique_id)` |
| "samples", "specimens", "biopsies", sample-level cohort composition | Sample-level: `COUNT(DISTINCT sample_unique_id)` |
| Ambiguous | Ask, or default to patient-level for prevalence/rate language and say so |

### Cross-study sample-count caveat

When an answer touches more than one study and reports a sample count, prepend a one-line caveat:

> Sample IDs are unique within cBioPortal study prefixes, not guaranteed biological-sample identifiers across studies; overlapping cohorts can count the same patient/sample more than once.

Prefer one of these safer approaches:

- Use a shipped `cancer_study_query_preferences` cohort such as `pan_cancer_tcga` or `all_studies_non_redundant`.
- Restrict to one named study.
- Aggregate by `patient_unique_id` when the biological question is patient prevalence.

## STOP rule: a frequency above 100% means your query is wrong

If your query returns a frequency over 100%, **do not try to debug or explain the data inconsistency to the user**. The cause is always one of these query bugs:

- Summing mutation events instead of `COUNT(DISTINCT sample_unique_id)` for the numerator
- Using a study-wide sample count as the denominator instead of the gene-specific profiled count
- Cross-study aggregation where the same biological sample appears under multiple `sample_unique_id` values (e.g., MSK-IMPACT and MSK-CHORD share patients)
- **Joining the profiled CTE through `gene_panel` / `gene_panel_list` without a WES branch.** `gene_panel_id = 'WES'` is *not* a row in … (35166 more chars)

▶ clickhouse_run_select_query
{
 "query": "
SELECT *
FROM gene_mutation_frequency_in_study(
    study = 'luad_tcga_pan_can_atlas_2018',
    gene = 'KRAS'
)
"
}

✗ error
Error POSTing to endpoint: {"jsonrpc":"2.0","id":5,"error":{"code":-32600,"message":"Anthropic Proxy: Invalid content from server","data":null}}

▶ clickhouse_run_select_query
{
 "query": "
SELECT hugo_gene_symbol, altered_samples, profiled_samples, frequency_pct
FROM gene_mutation_variants_in_study(
    study = 'luad_tcga_pan_can_atlas_2018',
    gene = 'KRAS'
)
LIMIT 1
"
}

✗ error
Error POSTing to endpoint: {"jsonrpc":"2.0","id":6,"error":{"code":-32600,"message":"Anthropic Proxy: Invalid content from server","data":null}}

▶ clickhouse_run_select_query
{
 "query": "
SELECT 
    COUNT(DISTINCT sample_unique_id) as altered_samples,
    hugo_gene_symbol
FROM genomic_event_derived
WHERE cancer_study_identifier = 'luad_tcga_pan_can_atlas_2018'
  AND hugo_gene_symbol = 'KRAS'
  AND variant_type = 'mutation'
  AND mutation_status != 'UNCALLED'
GROUP BY hugo_gene_symbol
"
}

◀ result
{"rows":[{"altered_samples":168,"hugo_gene_symbol":"KRAS"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT COUNT(DISTINCT stgp.sample_unique_id) as profiled_samples
FROM sample_to_gene_panel_derived stgp
WHERE stgp.cancer_study_identifier = 'luad_tcga_pan_can_atlas_2018'
  AND stgp.alteration_type = 'MUTATION_EXTENDED'
"
}

◀ result
{"rows":[{"profiled_samples":566}]}

═ answer (success)
在 Lung Adenocarcinoma (TCGA, PanCancer Atlas) 中，**KRAS 突变的频率是 29.7%**（168 个样本中有 168 个携带 KRAS 突变，共 566 个检测样本）。

对比一下：
- **EGFR**：70/566 = 12.4%
- **KRAS**：168/566 = 29.7%

KRAS 在 TCGA 肺腺癌中的突变频率明显高于 EGFR，这与临床观察一致——在非吸烟者中 EGFR 突变更常见，而在吸烟者中 KRAS 突变更为常见。