Q (sonnet): show me cholangio with idh1 mutations other than r132

▶ 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 … (36467 more chars)

▶ list_studies
{
 "search": "cholangiocarcinoma"
}

▶ search_oncotree
{
 "search_term": "cholangiocarcinoma"
}

◀ result
{"result":[{"cancer_study_identifier":"chol_icgc_2017","name":"Cholangiocarcinoma (ICGC, Cancer Discov 2017)","type_of_cancer_id":"chol","sample_count":489,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=chol_icgc_2017"},{"cancer_study_identifier":"ihch_msk_2021","name":"Intrahepatic Cholangiocarcinoma (MSK, Hepatology 2021)","type_of_cancer_id":"ihch","sample_count":412,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=ihch_msk_2021"},{"cancer_study_identifier":"ihch_mskcc_2020","name":"Intrahepatic Cholangiocarcinoma (MSK, Clin Cancer Res 2021)","type_of_cancer_id":"ihch","sample_count":219,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=ihch_mskcc_2020"},{"cancer_study_identifier":"chol_msk_2018","name":"Cholangiocarcinoma (MSK, Clin Cancer Res 2018)","type_of_cancer_id":"chol","sample_count":195,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=chol_msk_2018"},{"cancer_study_identifier":"hccihch_pku_2019","name":"Combined Hepatocellular and Intrahepatic Cholangiocarcinoma (Peking University, Cancer Cell 2019)","type_of_cancer_id":"hccihch","sample_count":173,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=hccihch_pku_2019"},{"cancer_study_identifier":"ihch_smmu_2014","name":"Intrahepatic Cholangiocarcinoma (Shanghai, Nat Commun 2014)","type_of_cancer_id":"ihch","sample_count":103,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=ihch_smmu_2014"},{"cancer_study_identifier":"chol_tcga_gdc","name":"Cholangiocarcinoma (TCGA GDC, 2025)","type_of_cancer_id":"chol","sample_count":51,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=chol_tcga_gdc"},{"cancer_study_identifier":"chol_tcga","name":"Cholangiocarcinoma (TCGA, Firehose Legacy)","type_of_cancer_id":"chol","sample_count":51,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=chol_tcga"},{"cancer_study_identifier":"chol_jhu_2013","name":"Intrahepatic Cholangiocarcinoma (JHU, Nat Genet 2013)","type_of_cancer_id":"chol","sample_count":40,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=chol_jhu_2013"},{"cancer_study_identifier":"chol_tcga_pan_can_atlas_2018","name":"Cholangiocarcinoma (TCGA, PanCancer Atlas)","type_of_cancer_id":"chol","sample_count":36,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=chol_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"chol_nccs_2013","name":"Cholangiocarcinoma (National Cancer Centre of Singapore, Nat Genet 2013)","type_of_cancer_id":"chol","sample_count":15,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=chol_nccs_2013"},{"cancer_study_identifier":"ihch_ismms_2015","name":"Intrahepatic Cholangiocarcinoma (Mount Sinai 2015)","type_of_cancer_id":"ihch","sample_count":8,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=ihch_ismms_2015"},{"cancer_study_identifier":"chol_nus_2012","name":"Cholangiocarcinoma (National Universit … (163 more chars)

◀ result
{"result":[{"code":"CHOL","name":"Cholangiocarcinoma","score":80,"mainType":"Hepatobiliary Cancer","tissue":"Biliary Tract","hierarchy":"BILIARY_TRACT > IPN > CHOL"},{"code":"EHCH","name":"Extrahepatic Cholangiocarcinoma","score":50,"mainType":"Hepatobiliary Cancer","tissue":"Biliary Tract","hierarchy":"BILIARY_TRACT > IPN > CHOL > EHCH"},{"code":"HCCIHCH","name":"Hepatocellular Carcinoma plus Intrahepatic Cholangiocarcinoma","score":50,"mainType":"Hepatobiliary Cancer","tissue":"Liver","hierarchy":"LIVER > HCCIHCH"},{"code":"IHCH","name":"Intrahepatic Cholangiocarcinoma","score":50,"mainType":"Hepatobiliary Cancer","tissue":"Biliary Tract","hierarchy":"BILIARY_TRACT > IPN > CHOL > IHCH"},{"code":"PHCH","name":"Perihilar Cholangiocarcinoma","score":50,"mainType":"Hepatobiliary Cancer","tissue":"Biliary Tract","hierarchy":"BILIARY_TRACT > IPN > CHOL > PHCH"}]}

═ answer (success)
There are many cholangiocarcinoma cohorts in cBioPortal. Since "cholangio" matches multiple studies of different sizes and origins (broad CHOL vs. intrahepatic-only IHCH cohorts), I want to confirm scope before running the query across all of them.

**Matching studies:**
| Study | ID | Samples |
|---|---|---|
| [Cholangiocarcinoma (ICGC, Cancer Discov 2017)](https://www.cbioportal.org/study/summary?id=chol_icgc_2017) | `chol_icgc_2017` | 489 |
| [Intrahepatic Cholangiocarcinoma (MSK, Hepatology 2021)](https://www.cbioportal.org/study/summary?id=ihch_msk_2021) | `ihch_msk_2021` | 412 |
| [Intrahepatic Cholangiocarcinoma (MSK, Clin Cancer Res 2021)](https://www.cbioportal.org/study/summary?id=ihch_mskcc_2020) | `ihch_mskcc_2020` | 219 |
| [Cholangiocarcinoma (MSK, Clin Cancer Res 2018)](https://www.cbioportal.org/study/summary?id=chol_msk_2018) | `chol_msk_2018` | 195 |
| [Combined HCC + Intrahepatic Cholangio (Peking Univ, Cancer Cell 2019)](https://www.cbioportal.org/study/summary?id=hccihch_pku_2019) | `hccihch_pku_2019` | 173 |
| [Intrahepatic Cholangiocarcinoma (Shanghai, Nat Commun 2014)](https://www.cbioportal.org/study/summary?id=ihch_smmu_2014) | `ihch_smmu_2014` | 103 |
| [Cholangiocarcinoma (TCGA GDC, 2025)](https://www.cbioportal.org/study/summary?id=chol_tcga_gdc) | `chol_tcga_gdc` | 51 |
| [Cholangiocarcinoma (TCGA, Firehose Legacy)](https://www.cbioportal.org/study/summary?id=chol_tcga) | `chol_tcga` | 51 |
| [Intrahepatic Cholangiocarcinoma (JHU, Nat Genet 2013)](https://www.cbioportal.org/study/summary?id=chol_jhu_2013) | `chol_jhu_2013` | 40 |
| [Cholangiocarcinoma (TCGA, PanCancer Atlas)](https://www.cbioportal.org/study/summary?id=chol_tcga_pan_can_atlas_2018) | `chol_tcga_pan_can_atlas_2018` | 36 |
| [Cholangiocarcinoma (NCC Singapore, Nat Genet 2013)](https://www.cbioportal.org/study/summary?id=chol_nccs_2013) | `chol_nccs_2013` | 15 |
| [Intrahepatic Cholangiocarcinoma (Mount Sinai 2015)](https://www.cbioportal.org/study/summary?id=ihch_ismms_2015) | `ihch_ismms_2015` | 8 |
| [Cholangiocarcinoma (NUS Singapore, Nat Genet 2012)](https://www.cbioportal.org/study/summary?id=chol_nus_2012) | `chol_nus_2012` | 8 |

Since IDH1 mutations occur almost exclusively in the **intrahepatic** subtype, would you like me to:

1. Run this across **all** cholangiocarcinoma studies listed above (largest, most comprehensive — recommended, since IDH1 hits are sparse per-cohort), or
2. Restrict to a specific study/subset (e.g., just the MSK intrahepatic cohorts, or just TCGA)?

Let me know, or say "all of them" and I'll pull IDH1 mutation variants excluding R132* across every cholangio cohort above.