Q (sonnet): What are the EGFR mutation frequencies across cancer types in the MSK-IMPACT 50K study?

▶ 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_by_cancer_type(preference = 'large_genomic_cohort', gene = 'EGFR') ORDER BY frequency_pct DESC",
 "max_rows": 100
}

◀ result
{"rows":[{"cancer_type":"Non-Small Cell Lung Cancer","altered_samples":2060,"profiled_samples":7867,"frequency_pct":26.2},{"cancer_type":"Glioma","altered_samples":353,"profiled_samples":2322,"frequency_pct":15.2},{"cancer_type":"Small Cell Lung Cancer","altered_samples":42,"profiled_samples":466,"frequency_pct":9},{"cancer_type":"Melanoma","altered_samples":131,"profiled_samples":1831,"frequency_pct":7.2},{"cancer_type":"Skin Cancer, Non-Melanoma","altered_samples":26,"profiled_samples":455,"frequency_pct":5.7},{"cancer_type":"Miscellaneous Brain Tumor","altered_samples":3,"profiled_samples":58,"frequency_pct":5.2},{"cancer_type":"Endometrial Cancer","altered_samples":105,"profiled_samples":2445,"frequency_pct":4.3},{"altered_samples":2,"profiled_samples":50,"frequency_pct":4},{"cancer_type":"Bladder Cancer","altered_samples":87,"profiled_samples":2526,"frequency_pct":3.4},{"cancer_type":"Cancer of Unknown Primary","altered_samples":41,"profiled_samples":1581,"frequency_pct":2.6},{"cancer_type":"Colorectal Cancer","altered_samples":135,"profiled_samples":5277,"frequency_pct":2.6},{"cancer_type":"Small Bowel Cancer","altered_samples":4,"profiled_samples":161,"frequency_pct":2.5},{"cancer_type":"Adrenocortical Carcinoma","altered_samples":2,"profiled_samples":88,"frequency_pct":2.3},{"cancer_type":"Anal Cancer","altered_samples":3,"profiled_samples":143,"frequency_pct":2.1},{"cancer_type":"Esophagogastric Cancer","altered_samples":38,"profiled_samples":1834,"frequency_pct":2.1},{"cancer_type":"Head and Neck Cancer","altered_samples":12,"profiled_samples":657,"frequency_pct":1.8},{"cancer_type":"Breast Cancer","altered_samples":100,"profiled_samples":6807,"frequency_pct":1.5},{"cancer_type":"Uterine Sarcoma","altered_samples":5,"profiled_samples":344,"frequency_pct":1.5},{"cancer_type":"Ampullary Cancer","altered_samples":2,"profiled_samples":134,"frequency_pct":1.5},{"cancer_type":"Hepatobiliary Cancer","altered_samples":17,"profiled_samples":1431,"frequency_pct":1.2},{"cancer_type":"Salivary Gland Cancer","altered_samples":4,"profiled_samples":411,"frequency_pct":1},{"cancer_type":"Cervical Cancer","altered_samples":3,"profiled_samples":351,"frequency_pct":0.9},{"cancer_type":"Prostate Cancer","altered_samples":30,"profiled_samples":3324,"frequency_pct":0.9},{"cancer_type":"Sellar Tumor","altered_samples":1,"profiled_samples":106,"frequency_pct":0.9},{"cancer_type":"Germ Cell Tumor","altered_samples":6,"profiled_samples":725,"frequency_pct":0.8},{"cancer_type":"Ovarian Cancer","altered_samples":18,"profiled_samples":2140,"frequency_pct":0.8},{"cancer_type":"Appendiceal Cancer","altered_samples":2,"profiled_samples":274,"frequency_pct":0.7},{"cancer_type":"Thyroid Cancer","altered_samples":6,"profiled_samples":867,"frequency_pct":0.7},{"cancer_type":"Pancreatic Cancer","altered_samples":16,"profiled_samples":2851,"frequency_pct":0.6},{"cancer_type":"Renal Cell Carcinoma","altered_samples":7,"profiled_samples":1209,"frequency_pct":0.6},{"cancer_typ … (404 more chars)

▶ resolve_and_route
{
 "studyIds": [
  "msk_impact_50k_2026"
 ]
}

◀ result
{"success":true,"message":"Found 1 study. Use the metadata to call the appropriate navigation tool(s).","data":{"totalCount":1,"studiesWithMetadata":[{"studyId":"msk_impact_50k_2026","name":"MSK-IMPACT 50K Clinical Sequencing Cohort (MSK, Cancer Cell 2026)","sampleCount":54331,"studyViewUrl":"https://www.cbioportal.org/study?id=msk_impact_50k_2026","metadata":{"clinicalAttributeIds":["AGE_AT_DX","ANCESTRY_LABEL","CANCER_TYPE","CANCER_TYPE_DETAILED","DISEASE_STATUS","FACETS_PLOIDY","FACETS_PURITY","FACETS_QC","FACETS_SUITE_VERSION","FACETS_WGD","FRACTION_GENOME_ALTERED","GENE_PANEL","HLA-A1","HLA-A2","HLA-B1","HLA-B2","HLA-C1","HLA-C2","HLA_A1_LOH","HLA_A2_LOH","HLA_B1_LOH","HLA_B2_LOH","HLA_C1_LOH","HLA_C2_LOH","HLA_GENOTYPE_AVAILABLE","METASTATIC_SITE","MSI_SCORE","MSI_TYPE","MUTATION_COUNT","N_OTHER_CANCER_TYPES","ONCOTREE_CODE","OS_MONTHS","OS_STATUS","PRIMARY_SITE","PURITY_ESTIMATE_FROM_MUTATIONS","SAMPLE_COUNT","SAMPLE_COVERAGE","SAMPLE_TYPE","SEX","SOMATIC_STATUS","TMB_SCORE","TUMOR_PURITY"],"molecularProfileIds":["msk_impact_50k_2026_gistic","msk_impact_50k_2026_mutations","msk_impact_50k_2026_structural_variants"],"genericAssayProfiles":["msk_impact_50k_2026_armlevel_cna","msk_impact_50k_2026_loh_hla","msk_impact_50k_2026_mutational_signatures_contribution_v2"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations","generic_assay_armlevel_cna","generic_assay_loh_hla","generic_assay_mutational_signature"]}}]}}

▶ navigate_to_study_view
{
 "studyIds": [
  "msk_impact_50k_2026"
 ],
 "filterJson": {
  "geneFilters": [
   {
    "molecularProfileIds": [
     "msk_impact_50k_2026_mutations"
    ],
    "geneQueries": [
     [
      {
       "hugoGeneSymbol": "EGFR"
      }
     ]
    ]
   }
  ]
 }
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/study/summary?id=msk_impact_50k_2026#filterJson=%7B%22geneFilters%22%3A%5B%7B%22geneQueries%22%3A%5B%5B%7B%22hugoGeneSymbol%22%3A%22EGFR%22%7D%5D%5D%2C%22molecularProfileIds%22%3A%5B%22msk_impact_50k_2026_mutations%22%5D%7D%5D%7D","url":"https://www.cbioportal.org/study/summary?id=msk_impact_50k_2026#filterJson=%7B%22geneFilters%22%3A%5B%7B%22geneQueries%22%3A%5B%5B%7B%22hugoGeneSymbol%22%3A%22EGFR%22%7D%5D%5D%2C%22molecularProfileIds%22%3A%5B%22msk_impact_50k_2026_mutations%22%5D%7D%5D%7D","data":{"studyIds":["msk_impact_50k_2026"],"studies":[{"studyId":"msk_impact_50k_2026","name":"MSK-IMPACT 50K Clinical Sequencing Cohort (MSK, Cancer Cell 2026)","sampleCount":54331}],"tab":"summary","hasFilters":true,"hasPlotsConfig":false,"pageDescription":"Overview of all study data displayed as interactive charts summarizing available clinical and genomic data. Click within a chart to filter. Additional charts may be available in the Charts menu."}}

▶ navigate_to_results_view
{
 "studyIds": [
  "msk_impact_50k_2026"
 ],
 "genes": [
  "EGFR"
 ],
 "tab": "cancerTypesSummary"
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/results/cancerTypesSummary?cancer_study_list=msk_impact_50k_2026&gene_list=EGFR&case_set_id=msk_impact_50k_2026_all","url":"https://www.cbioportal.org/results/cancerTypesSummary?cancer_study_list=msk_impact_50k_2026&gene_list=EGFR&case_set_id=msk_impact_50k_2026_all","data":{"studyIds":["msk_impact_50k_2026"],"studies":[{"studyId":"msk_impact_50k_2026","name":"MSK-IMPACT 50K Clinical Sequencing Cohort (MSK, Cancer Cell 2026)","sampleCount":54331}],"genes":["EGFR"],"caseSetId":"msk_impact_50k_2026_all","pageDescription":"Alteration frequencies for queried genes by cancer type."}}

═ answer (success)
**Navigation links:**

- [View EGFR-mutant samples in Study View](https://www.cbioportal.org/study/summary?id=msk_impact_50k_2026#filterJson=%7B%22geneFilters%22%3A%5B%7B%22geneQueries%22%3A%5B%5B%7B%22hugoGeneSymbol%22%3A%22EGFR%22%7D%5D%5D%2C%22molecularProfileIds%22%3A%5B%22msk_impact_50k_2026_mutations%22%5D%7D%5D%7D) — cohort overview filtered to EGFR-mutant samples (MSK-IMPACT 50K, 54,331 samples total)
- [EGFR Alteration Frequency by Cancer Type](https://www.cbioportal.org/results/cancerTypesSummary?cancer_study_list=msk_impact_50k_2026&gene_list=EGFR&case_set_id=msk_impact_50k_2026_all) — Cancer Types Summary tab showing alteration frequencies for EGFR across all cancer types in this study