Q (haiku): compare egfr mutations between lung and brain cancer

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

▶ search_oncotree
{
 "search_term": "lung"
}

▶ search_oncotree
{
 "search_term": "brain"
}

◀ 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)

◀ result
{"result":[{"code":"LUNG","name":"Lung","score":100,"mainType":"Lung Cancer","tissue":"Lung","hierarchy":"LUNG"},{"code":"LAIS","name":"Lung Adenocarcinoma In Situ","score":60,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > LAIS"},{"code":"LNET","name":"Lung Neuroendocrine Tumor","score":60,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > LNET"},{"code":"LUAD","name":"Lung Adenocarcinoma","score":60,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > LUAD"},{"code":"LUAS","name":"Lung Adenosquamous Carcinoma","score":60,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > LUAS"},{"code":"LUCA","name":"Lung Carcinoid","score":60,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > LNET > LUCA"},{"code":"LUSC","name":"Lung Squamous Cell Carcinoma","score":60,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > LUSC"},{"code":"ALUCA","name":"Atypical Lung Carcinoid","score":50,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > LNET > ALUCA"},{"code":"BLCLC","name":"Basaloid Large Cell Carcinoma of the Lung","score":50,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > LCLC > BLCLC"},{"code":"CCLC","name":"Clear Cell Carcinoma of the Lung","score":50,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > LCLC > CCLC"},{"code":"CMPT","name":"Ciliated Muconodular Papillary Tumor of the Lung","score":50,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > CMPT"},{"code":"CSCLC","name":"Combined Small Cell Lung Carcinoma","score":50,"mainType":"Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > CSCLC"},{"code":"GCLC","name":"Giant Cell Carcinoma of the Lung","score":50,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > LCLC > GCLC"},{"code":"IMTL","name":"Inflammatory Myofibroblastic Lung Tumor","score":50,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > IMTL"},{"code":"LCLC","name":"Large Cell Lung Carcinoma","score":50,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > LCLC"},{"code":"LECLC","name":"Lymphoepithelioma-like Carcinoma of the Lung","score":50,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > LCLC > LECLC"},{"code":"LUACC","name":"Adenoid Cystic Carcinoma of the Lung","score":50,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > SGTTL > LUACC"},{"code":"LUMEC","name":"Mucoepidermoid Carcinoma of the Lung","score":50,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > SGTTL > LUMEC"},{"code":"LUPC","name":"Pleomorphic Carcinoma of the Lung","score":50,"mainType":"Non-Small Cell Lung Cancer","tissue":"Lung","hierarchy":"LUNG > NSCLC > LUPC"},{"code":"NSCLC","na … (947 more chars)

◀ result
{"result":[{"code":"BRAIN","name":"CNS/Brain","score":100,"mainType":"CNS/Brain Cancer","tissue":"CNS/Brain","hierarchy":"BRAIN"},{"code":"BGCT","name":"Germ Cell Tumor, Brain","score":50,"mainType":"Germ Cell Tumor","tissue":"CNS/Brain","hierarchy":"BRAIN > BGCT"},{"code":"MBT","name":"Miscellaneous Brain Tumor","score":50,"mainType":"Miscellaneous Brain Tumor","tissue":"CNS/Brain","hierarchy":"BRAIN > MBT"},{"code":"PBT","name":"Primary Brain Tumor","score":50,"mainType":"Miscellaneous Brain Tumor","tissue":"CNS/Brain","hierarchy":"BRAIN > MBT > PBT"},{"code":"HGNET","name":"High-Grade Neuroepithelial Tumor","score":45,"mainType":"Miscellaneous Brain Tumor","tissue":"CNS/Brain","hierarchy":"BRAIN > MBT > HGNET"},{"code":"HMBL","name":"Hemangioblastoma","score":45,"mainType":"Miscellaneous Brain Tumor","tissue":"CNS/Brain","hierarchy":"BRAIN > MBT > HMBL"},{"code":"LGNET","name":"Polymorphous Low-Grade Neuroepithelial Tumor of the Young","score":45,"mainType":"Miscellaneous Brain Tumor","tissue":"CNS/Brain","hierarchy":"BRAIN > DIFG > PDIFLG > LGNET"},{"code":"MCHSCNS","name":"Mesenchymal Chondrosarcoma of the CNS","score":45,"mainType":"Miscellaneous Brain Tumor","tissue":"CNS/Brain","hierarchy":"BRAIN > MBT > MCHSCNS"},{"code":"MLYM","name":"Malignant Lymphoma","score":45,"mainType":"Miscellaneous Brain Tumor","tissue":"CNS/Brain","hierarchy":"BRAIN > MBT > MLYM"},{"code":"MT","name":"Malignant Tumor","score":45,"mainType":"Miscellaneous Brain Tumor","tissue":"CNS/Brain","hierarchy":"BRAIN > MBT > MT"},{"code":"PRNET","name":"Primary Neuroepithelial Tumor","score":45,"mainType":"Miscellaneous Brain Tumor","tissue":"CNS/Brain","hierarchy":"BRAIN > MBT > PRNET"},{"code":"ACPG","name":"Craniopharyngioma, Adamantinomatous Type","score":40,"mainType":"Sellar Tumor","tissue":"CNS/Brain","hierarchy":"BRAIN > SELT > ACPG"},{"code":"ACPP","name":"Atypical Choroid Plexus Papilloma","score":40,"mainType":"Choroid Plexus Tumor","tissue":"CNS/Brain","hierarchy":"BRAIN > CPT > ACPP"},{"code":"ADIFG","name":"Adult-Type Diffuse Glioma","score":40,"mainType":"Gliomas, Glioneuronal Tumors, and Neuronal Tumors","tissue":"CNS/Brain","hierarchy":"BRAIN > DIFG > ADIFG"},{"code":"AGNG","name":"Anaplastic Ganglioglioma","score":40,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > ENCG > AGNG"},{"code":"AMBL","name":"Large Cell/Anaplastic Medulloblastoma","score":40,"mainType":"Embryonal Tumor","tissue":"CNS/Brain","hierarchy":"BRAIN > EMBT > AMBL"},{"code":"AMBLNOS","name":"Anaplastic Medulloblastoma, NOS","score":40,"mainType":"Large Cell/Anaplastic Medulloblastoma","tissue":"CNS/Brain","hierarchy":"BRAIN > EMBT > AMBL > AMBLNOS"},{"code":"AMBLNWS","name":"Anaplastic Medulloblastoma, Non-WNT, Non-SHH","score":40,"mainType":"Large Cell/Anaplastic Medulloblastoma","tissue":"CNS/Brain","hierarchy":"BRAIN > EMBT > AMBL > AMBLNWS"},{"code":"AMBLNWSG3","name":"Anaplastic Medulloblastoma, Group 3","score":40,"mainType":"Large Cell/Anaplastic Medulloblastoma","t … (1062 more chars)

▶ clickhouse_run_select_query
{
 "query": "
SELECT *
FROM gene_mutation_frequency_by_cancer_type(
    preference = 'pan_cancer_tcga',
    gene = 'EGFR'
)
WHERE cancer_type IN ('Non-Small Cell Lung Cancer', 'CNS/Brain Cancer')
ORDER BY frequency_pct DESC
"
}

◀ result
{"rows":[{"cancer_type":"Non-Small Cell Lung Cancer","altered_samples":84,"profiled_samples":1050,"frequency_pct":8}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT cancer_type
FROM clinical_data_derived cd
JOIN cancer_study_query_preferences csp 
  ON cd.cancer_study_identifier = csp.cancer_study_identifier
WHERE csp.preference_name = 'pan_cancer_tcga'
  AND cd.attribute_name = 'CANCER_TYPE'
ORDER BY cancer_type
",
 "max_rows": 100
}

◀ 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 identifier `cancer_type` in scope SELECT DISTINCT cancer_type FROM clinical_data_derived AS cd INNER JOIN cancer_study_query_preferences AS csp ON cd.cancer_study_identifier = csp.cancer_study_identifier WHERE (csp.preference_name = 'pan_cancer_tcga') AND (cd.attribute_name = 'CANCER_TYPE') ORDER BY cancer_type ASC. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT attribute_value AS cancer_type
FROM clinical_data_derived cd
JOIN cancer_study_query_preferences csp 
  ON cd.cancer_study_identifier = csp.cancer_study_identifier
WHERE csp.preference_name = 'pan_cancer_tcga'
  AND cd.attribute_name = 'CANCER_TYPE'
ORDER BY cancer_type
",
 "max_rows": 100
}

◀ result
{"rows":[{"cancer_type":"Adrenocortical Carcinoma"},{"cancer_type":"Bladder Cancer"},{"cancer_type":"Breast Cancer"},{"cancer_type":"Cervical Cancer"},{"cancer_type":"Cholangiocarcinoma"},{"cancer_type":"Colorectal Cancer"},{"cancer_type":"Endometrial Cancer"},{"cancer_type":"Esophagogastric Cancer"},{"cancer_type":"Glioblastoma"},{"cancer_type":"Glioma"},{"cancer_type":"Head and Neck Cancer"},{"cancer_type":"Hepatobiliary Cancer"},{"cancer_type":"Leukemia"},{"cancer_type":"Mature B-Cell Neoplasms"},{"cancer_type":"Melanoma"},{"cancer_type":"Miscellaneous Neuroepithelial Tumor"},{"cancer_type":"Non-Seminomatous Germ Cell Tumor"},{"cancer_type":"Non-Small Cell Lung Cancer"},{"cancer_type":"Ocular Melanoma"},{"cancer_type":"Ovarian Epithelial Tumor"},{"cancer_type":"Pancreatic Cancer"},{"cancer_type":"Pheochromocytoma"},{"cancer_type":"Pleural Mesothelioma"},{"cancer_type":"Prostate Cancer"},{"cancer_type":"Renal Clear Cell Carcinoma"},{"cancer_type":"Renal Non-Clear Cell Carcinoma"},{"cancer_type":"Sarcoma"},{"cancer_type":"Seminoma"},{"cancer_type":"Thymic Epithelial Tumor"},{"cancer_type":"Thyroid Cancer"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT *
FROM gene_mutation_frequency_by_cancer_type(
    preference = 'pan_cancer_tcga',
    gene = 'EGFR'
)
WHERE cancer_type IN ('Non-Small Cell Lung Cancer', 'Glioblastoma', 'Glioma')
ORDER BY frequency_pct DESC
"
}

◀ result
{"rows":[{"cancer_type":"Glioblastoma","altered_samples":94,"profiled_samples":397,"frequency_pct":23.7},{"cancer_type":"Non-Small Cell Lung Cancer","altered_samples":84,"profiled_samples":1050,"frequency_pct":8},{"cancer_type":"Glioma","altered_samples":35,"profiled_samples":514,"frequency_pct":6.8}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT cancer_study_identifier
FROM cancer_study_query_preferences
WHERE preference_name = 'pan_cancer_tcga'
ORDER BY cancer_study_identifier
",
 "max_rows": 100
}

◀ result
{"rows":[{"cancer_study_identifier":"acc_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"blca_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"cesc_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"chol_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"coadread_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"dlbc_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"esca_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"gbm_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"hnsc_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"kich_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"kirc_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"kirp_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"laml_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"lihc_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"luad_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"lusc_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"meso_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"ov_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"paad_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"pcpg_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"prad_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"sarc_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"skcm_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"stad_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"tgct_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"thca_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"thym_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"ucec_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"ucs_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"uvm_tcga_pan_can_atlas_2018"}]}

▶ resolve_and_route
{
 "studyIds": [
  "gbm_tcga_pan_can_atlas_2018",
  "lgg_tcga_pan_can_atlas_2018",
  "luad_tcga_pan_can_atlas_2018",
  "lusc_tcga_pan_can_atlas_2018"
 ]
}

◀ result
{"success":true,"message":"Found 4 matching studies. Pick the best match (prefer TCGA → prefer PanCancer Atlas), use its metadata to call the appropriate navigation tool(s) and generate URLs immediately. Present other studies as alternatives.","data":{"totalCount":4,"studiesWithMetadata":[{"studyId":"gbm_tcga_pan_can_atlas_2018","name":"Glioblastoma Multiforme (TCGA, PanCancer Atlas)","sampleCount":592,"studyViewUrl":"https://www.cbioportal.org/study?id=gbm_tcga_pan_can_atlas_2018","metadata":{"clinicalAttributeIds":["AGE","AJCC_PATHOLOGIC_TUMOR_STAGE","AJCC_STAGING_EDITION","ANEUPLOIDY_SCORE","BUFFA_HYPOXIA_SCORE","CANCER_TYPE","CANCER_TYPE_ACRONYM","CANCER_TYPE_DETAILED","DAYS_LAST_FOLLOWUP","DAYS_TO_BIRTH","DAYS_TO_INITIAL_PATHOLOGIC_DIAGNOSIS","DFS_MONTHS","DFS_STATUS","DSS_MONTHS","DSS_STATUS","ETHNICITY","FORM_COMPLETION_DATE","FRACTION_GENOME_ALTERED","GENETIC_ANCESTRY_LABEL","GRADE","HISTORY_NEOADJUVANT_TRTYN","ICD_10","ICD_O_3_HISTOLOGY","ICD_O_3_SITE","INFORMED_CONSENT_VERIFIED","IN_PANCANPATHWAYS_FREEZE","MSI_SCORE_MANTIS","MSI_SENSOR_SCORE","MUTATION_COUNT","NEW_TUMOR_EVENT_AFTER_INITIAL_TREATMENT","ONCOTREE_CODE","OS_MONTHS","OS_STATUS","OTHER_PATIENT_ID","PATH_M_STAGE","PATH_N_STAGE","PATH_T_STAGE","PERSON_NEOPLASM_CANCER_STATUS","PFS_MONTHS","PFS_STATUS","PRIMARY_LYMPH_NODE_PRESENTATION_ASSESSMENT","PRIOR_DX","RACE","RADIATION_THERAPY","RAGNUM_HYPOXIA_SCORE","SAMPLE_COUNT","SAMPLE_TYPE","SEX","SOMATIC_STATUS","SUBTYPE","TBL_SCORE","TISSUE_PROSPECTIVE_COLLECTION_INDICATOR","TISSUE_RETROSPECTIVE_COLLECTION_INDICATOR","TISSUE_SOURCE_SITE","TISSUE_SOURCE_SITE_CODE","TMB_NONSYNONYMOUS","TUMOR_TISSUE_SITE","TUMOR_TYPE","WEIGHT","WINTER_HYPOXIA_SCORE"],"molecularProfileIds":["gbm_tcga_pan_can_atlas_2018_gistic","gbm_tcga_pan_can_atlas_2018_log2CNA","gbm_tcga_pan_can_atlas_2018_mutations","gbm_tcga_pan_can_atlas_2018_rna_seq_v2_mrna","gbm_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","gbm_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","gbm_tcga_pan_can_atlas_2018_rppa","gbm_tcga_pan_can_atlas_2018_rppa_Zscores","gbm_tcga_pan_can_atlas_2018_structural_variants"],"genericAssayProfiles":["gbm_tcga_pan_can_atlas_2018_armlevel_cna","gbm_tcga_pan_can_atlas_2018_genetic_ancestry","gbm_tcga_pan_can_atlas_2018_methylation_hm27_hm450_merge","gbm_tcga_pan_can_atlas_2018_methylation_hm450"],"heatmapProfileIds":["gbm_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","gbm_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","gbm_tcga_pan_can_atlas_2018_rppa_Zscores"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations","mrna","protein","generic_assay_armlevel_cna","generic_assay_genetic_ancestry","generic_assay_methylation"]}},{"studyId":"lgg_tcga_pan_can_atlas_2018","name":"Brain Lower Grade Glioma (TCGA, PanCancer Atlas)","sampleCount":514,"studyViewUrl":"https://www.cbioportal.org/study?id=lgg_tcga_pan_can_atlas_2018","metadata":{"clinicalAttributeIds":["AGE","AJCC_PATH … (7506 more chars)

▶ navigate_to_results_view
{
 "studyIds": [
  "gbm_tcga_pan_can_atlas_2018",
  "lgg_tcga_pan_can_atlas_2018",
  "luad_tcga_pan_can_atlas_2018",
  "lusc_tcga_pan_can_atlas_2018"
 ],
 "genes": [
  "EGFR"
 ],
 "tab": "oncoprint"
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/results/oncoprint?cancer_study_list=gbm_tcga_pan_can_atlas_2018%2Clgg_tcga_pan_can_atlas_2018%2Cluad_tcga_pan_can_atlas_2018%2Clusc_tcga_pan_can_atlas_2018&gene_list=EGFR&case_set_id=all","url":"https://www.cbioportal.org/results/oncoprint?cancer_study_list=gbm_tcga_pan_can_atlas_2018%2Clgg_tcga_pan_can_atlas_2018%2Cluad_tcga_pan_can_atlas_2018%2Clusc_tcga_pan_can_atlas_2018&gene_list=EGFR&case_set_id=all","data":{"studyIds":["gbm_tcga_pan_can_atlas_2018","lgg_tcga_pan_can_atlas_2018","luad_tcga_pan_can_atlas_2018","lusc_tcga_pan_can_atlas_2018"],"studies":[{"studyId":"gbm_tcga_pan_can_atlas_2018","name":"Glioblastoma Multiforme (TCGA, PanCancer Atlas)","sampleCount":592},{"studyId":"lgg_tcga_pan_can_atlas_2018","name":"Brain Lower Grade Glioma (TCGA, PanCancer Atlas)","sampleCount":514},{"studyId":"luad_tcga_pan_can_atlas_2018","name":"Lung Adenocarcinoma (TCGA, PanCancer Atlas)","sampleCount":566},{"studyId":"lusc_tcga_pan_can_atlas_2018","name":"Lung Squamous Cell Carcinoma (TCGA, PanCancer Atlas)","sampleCount":487}],"genes":["EGFR"],"caseSetId":"all","pageDescription":"Visual summary of alterations in queried genes across samples."}}

═ answer (success)
Perfect! Here are the results:

## EGFR Mutation Frequency Comparison: Lung vs Brain Cancer

**Counting unit: Sample-level frequencies across TCGA Pan-Cancer Atlas**

| Cancer Type | EGFR-Mutated Samples | Total Profiled | Frequency |
|---|---|---|---|
| **Glioblastoma** | 94 | 397 | **23.7%** |
| **Non-Small Cell Lung Cancer** | 84 | 1,050 | **8.0%** |
| **Glioma (Lower Grade)** | 35 | 514 | **6.8%** |

### Key Findings

**EGFR mutations are significantly more frequent in glioblastoma than in lung cancers** — nearly **3-fold higher** in GBM (23.7%) compared to non-small cell lung cancer (8.0%). This is noteworthy because EGFR mutations are considered a hallmark driver in lung adenocarcinoma. The discrepancy reflects differences in EGFR's role across these malignancies:

- **Glioblastoma**: EGFR amplification and mutations are common driver events (~25% mutation rate)
- **Lung adenocarcinoma**: EGFR mutations are activating drivers in ~10% overall, though higher in Asian cohorts and never-smokers
- **Lower-grade glioma**: Similar to lung cancers (~7% mutated)

### Interactive Analysis

[View EGFR alterations across lung and brain cancers (OncoPrint)](https://www.cbioportal.org/results/oncoprint?cancer_study_list=gbm_tcga_pan_can_atlas_2018%2Clgg_tcga_pan_can_atlas_2018%2Cluad_tcga_pan_can_atlas_2018%2Clusc_tcga_pan_can_atlas_2018&gene_list=EGFR&case_set_id=all)

This links directly to an OncoPrint visualization showing EGFR-mutated samples (blue bars) across all four studies, with patient sample IDs and mutation details on click.