Q (haiku): In TCGA lower grade glioma, show me samples with EGFR gains.

▶ read_guide
{
 "uri": "cbioportal://gene-expression-guide"
}

▶ resolve_and_route
{
 "studyKeywords": [
  "TCGA",
  "lower grade glioma"
 ]
}

◀ result
# Gene Expression Analysis Guide

This guide covers continuous-value genomic data: gene **expression**, **copy number** values, **methylation**, and related profile types. Mutation/CNA/SV *frequency* analysis lives in `cbioportal://mutation-frequency-guide`.

## Where this data lives

Continuous per-sample-per-gene values are stored in `genetic_alteration_derived`:

| Column | Description |
|---|---|
| `sample_unique_id` | `<study>_<sample_stable_id>` |
| `cancer_study_identifier` | study scope |
| `hugo_gene_symbol` | gene |
| `profile_type` | which assay/normalization (see below) |
| `alteration_value` | the actual value — stored as Nullable(String); cast with `toFloat64OrNull` |

`alteration_value` is a string because the same column hosts many different value scales. The `''` and `'NA'` sentinels mean "missing"; always filter them out and use `toFloat64OrNull(alteration_value) IS NOT NULL` for downstream math.

## Discovering profile types for a study

Different studies expose different profile types depending on what assays were run and how the data was normalized. Always check what a specific study supports before picking one:

```sql
SELECT DISTINCT profile_type
FROM genetic_alteration_derived
WHERE cancer_study_identifier = 'brca_metabric'
ORDER BY profile_type;
```

Common values across the public portal:

| Family | Profile types |
|---|---|
| mRNA expression | `rna_seq_v2_mrna`, `rna_seq_v2_mrna_median_Zscores`, `rna_seq_v2_mrna_median_all_sample_Zscores` (TCGA PanCancer Atlas), `mrna`, `mrna_median_Zscores`, `mrna_seq_v2_rsem`, `mrna_seq_v2_rsem_Zscores`, `mrna_seq_cpm`, `mrna_seq_fpkm`, `mrna_U133`, `mrna_outliers` |
| Copy number (continuous) | `cna`, `linear_CNA`, `log2CNA`, `cna_consensus`, `cna_rae`, `gistic` |
| Methylation | `methylation_hm27`, `methylation_hm450`, `methylation_epic`, `methylation_promoters_rrbs` |
| miRNA | `mirna`, `mirna_median_Zscores` |
| Protein | `protein_quantification`, `protein_level`, `RPPA` |

**Z-score vs raw choice.** When the user asks "is X correlated with Y", either works for Spearman (rank-based) — Pearson would care. Default to the non-Z-score variant if both exist, and call out which one in the response.

## Canonical recipe — Spearman correlation between two genes

```sql
SELECT *
FROM gene_pair_coexpression(
    study        = 'brca_metabric',
    gene_a       = 'TP53',
    gene_b       = 'MYC',
    profile_type = 'mrna'
);
```

Returns one row: `(gene_a, gene_b, profile_type, spearman_correlation, num_samples)`.

- `spearman_correlation` in [−1, 1]; `NULL` when fewer than 3 valid paired samples.
- Mirrors cbioportal-backend's `ClickhouseCoExpressionMapper.getCoExpressions`, simplified to a pair lookup (the backend computes one ref gene vs ALL other genes for the coexpression page; here the agent asks about a specific pair).

### Verified examples

| Study | gene_a | gene_b | profile_type | spearman | n |
|---|---|---|---|---|---|
| `brca_metabric` | TP53 | MYC | `mrna` | 0.118 | 1980 |
|  … (4931 more chars)

◀ result
{"success":true,"message":"Found 2 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":2,"studiesWithMetadata":[{"studyId":"lgg_tcga","name":"Brain Lower Grade Glioma (TCGA, Firehose Legacy)","sampleCount":530,"studyViewUrl":"https://www.cbioportal.org/study?id=lgg_tcga","metadata":{"clinicalAttributeIds":["AGE","ANIMAL_INSECT_ALLERGY_AGE","ANIMAL_INSECT_ALLERGY_HIST","ASTHMA_ECZEMA_ALLERGY_FIRST_DIAGNOSIS","ASTHMA_HISTORY","CANCER_TYPE","CANCER_TYPE_DETAILED","DAYS_TO_COLLECTION","DAYS_TO_INITIAL_PATHOLOGIC_DIAGNOSIS","DAYS_TO_SPECIMEN_COLLECTION","DFS_MONTHS","DFS_STATUS","DISEASE_CODE","ECOG_SCORE","ECZEMA_HISTORY","ETHNICITY","FAMILY_HISTORY_OF_CANCER","FAMILY_HISTORY_OF_PRIMARY_BRAIN_TUMOR","FIRST_SYMPTOM_LONGEST_DURATION","FOOD_ALLERGY_AGE","FOOD_ALLERGY_HISTORY","FOOD_ALLERGY_TYPES","FORM_COMPLETION_DATE","FRACTION_GENOME_ALTERED","GRADE","HAY_FEVER_HISTORY","HEADACHE_HISTORY","HISTOLOGICAL_DIAGNOSIS","HISTORY_IONIZING_RT_TO_HEAD","HISTORY_NEOADJUVANT_MEDICATION","HISTORY_NEOADJUVANT_STEROID_TX","HISTORY_NEOADJUVANT_TRTYN","HISTORY_OTHER_MALIGNANCY","ICD_10","ICD_O_3_HISTOLOGY","ICD_O_3_SITE","IDH1_MUTATION","IDH1_MUTATION_TEST_INDICATOR","IDH1_MUTATION_TEST_METHOD","INFORMED_CONSENT_VERIFIED","INHERITED_GENETIC_SYNDROME_INDICATOR","INHERITED_GENETIC_SYNDROME_SPECIFIED","INITIAL_PATHOLOGIC_DX_YEAR","IS_FFPE","KARNOFSKY_PERFORMANCE_SCORE","LATERALITY","LONGEST_DIMENSION","METHOD_OF_SAMPLE_PROCUREMENT","MOLD_OR_DUST_ALLERGY_HISTORY","MUTATION_COUNT","NEW_TUMOR_EVENT_AFTER_INITIAL_TREATMENT","OCT_EMBEDDED","ONCOTREE_CODE","OS_MONTHS","OS_STATUS","OTHER_METHOD_OF_SAMPLE_PROCUREMENT","OTHER_PATIENT_ID","OTHER_SAMPLE_ID","PATHOLOGY_REPORT_FILE_NAME","PATHOLOGY_REPORT_UUID","PERFORMANCE_STATUS_DAYS_TO","PERFORMANCE_STATUS_TIMING","PROJECT_CODE","PROSPECTIVE_COLLECTION","RACE","RADIATION_TREATMENT_ADJUVANT","RELATED_SYMPTOM_FIRST_PRESENT","RETROSPECTIVE_COLLECTION","SAMPLE_COUNT","SAMPLE_INITIAL_WEIGHT","SAMPLE_TYPE","SAMPLE_TYPE_ID","SEIZURE_HISTORY","SEX","SHORTEST_DIMENSION","SITE_OF_TUMOR_TISSUE","SOMATIC_STATUS","SPECIMEN_CURRENT_WEIGHT","SPECIMEN_FREEZING_METHOD","SPECIMEN_SECOND_LONGEST_DIMENSION","SUPRATENTORIAL_LOCALIZATION","SYMP_CHANGES_MENTAL_STATUS","SYMP_CHANGES_MOTOR_MOVEMENT","SYMP_CHANGES_SENSORY","SYMP_CHANGES_VISUAL","TARGETED_MOLECULAR_THERAPY","TIME_BETWEEN_CLAMPING_AND_FREEZING","TIME_BETWEEN_EXCISION_AND_FREEZING","TISSUE_SOURCE_SITE","TMB_NONSYNONYMOUS","TREATMENT_OUTCOME_FIRST_COURSE","TUMOR_SITE","TUMOR_STATUS","VIAL_NUMBER"],"molecularProfileIds":["lgg_tcga_gistic","lgg_tcga_linear_CNA","lgg_tcga_methylation_hm450","lgg_tcga_mrna","lgg_tcga_mrna_median_Zscores","lgg_tcga_mrna_median_all_sample_Zscores","lgg_tcga_mutations","lgg_tcga_rna_seq_v2_mrna","lgg_tcga_rna_seq_v2_mrna_median_Zscores","lgg_tcga_rna_seq_v2_mrna_median_all_sample_Zscores","lg … (2867 more chars)

▶ clickhouse_run_select_query
{
 "query": "
SELECT 
    DISTINCT s.sample_stable_id,
    s.patient_id,
    round(toFloat64OrNull(g.alteration_value), 2) AS egfr_cna_value,
    s.sample_type
FROM genetic_alteration_derived g
JOIN sample_derived s ON g.sample_unique_id = s.sample_unique_id
WHERE g.cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018'
  AND g.hugo_gene_symbol = 'EGFR'
  AND g.profile_type IN ('gistic', 'log2CNA')
  AND g.alteration_value NOT IN ('', 'NA')
  AND toFloat64OrNull(g.alteration_value) IS NOT NULL
  AND toFloat64OrNull(g.alteration_value) > 0
ORDER BY toFloat64OrNull(g.alteration_value) DESC, s.sample_stable_id
LIMIT 100
",
 "max_rows": 100
}

▶ resolve_and_route
{
 "studyIds": [
  "lgg_tcga_pan_can_atlas_2018"
 ]
}

◀ 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 's.patient_id' cannot be resolved from table with name s. In scope SELECT DISTINCT s.sample_stable_id, s.patient_id, round(toFloat64OrNull(g.alteration_value), 2) AS egfr_cna_value, s.sample_type FROM genetic_alteration_derived AS g INNER JOIN sample_derived AS s ON g.sample_unique_id = s.sample_unique_id WHERE (g.cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018') AND (g.hugo_gene_symbol = 'EGFR') AND (g.profile_type IN ('gistic', 'log2CNA')) AND (g.alteration_value NOT IN ('', 'NA')) AND (toFloat64OrNull(g.alteration_value) IS NOT NULL) AND (toFloat64OrNull(g.alteration_value) > 0) ORDER BY toFloat64OrNull(g.alteration_value) DESC, s.sample_stable_id ASC LIMIT 100. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}

◀ result
{"success":true,"message":"Found 1 study. Use the metadata to call the appropriate navigation tool(s).","data":{"totalCount":1,"studiesWithMetadata":[{"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_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":["lgg_tcga_pan_can_atlas_2018_gistic","lgg_tcga_pan_can_atlas_2018_log2CNA","lgg_tcga_pan_can_atlas_2018_mutations","lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna","lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","lgg_tcga_pan_can_atlas_2018_rppa","lgg_tcga_pan_can_atlas_2018_rppa_Zscores","lgg_tcga_pan_can_atlas_2018_structural_variants"],"genericAssayProfiles":["lgg_tcga_pan_can_atlas_2018_armlevel_cna","lgg_tcga_pan_can_atlas_2018_genetic_ancestry","lgg_tcga_pan_can_atlas_2018_methylation_hm27_hm450_merge","lgg_tcga_pan_can_atlas_2018_methylation_hm450"],"heatmapProfileIds":["lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","lgg_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"]}}]}}

▶ clickhouse_list_table_columns
{
 "table": "sample_derived"
}

▶ clickhouse_list_table_columns
{
 "table": "genetic_alteration_derived"
}

◀ result
{"columns":[{"name":"sample_unique_id","type":"String"},{"name":"sample_unique_id_base64","type":"String"},{"name":"sample_stable_id","type":"String"},{"name":"patient_unique_id","type":"String"},{"name":"patient_unique_id_base64","type":"String"},{"name":"patient_stable_id","type":"String"},{"name":"cancer_study_identifier","type":"LowCardinality(String)"},{"name":"internal_id","type":"Int32"},{"name":"patient_internal_id","type":"Int32"},{"name":"sample_type","type":"String"},{"name":"sequenced","type":"Int32"},{"name":"copy_number_segment_present","type":"Int32"}]}

◀ 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 
    DISTINCT s.sample_stable_id,
    s.patient_stable_id,
    round(toFloat64OrNull(g.alteration_value), 2) AS egfr_cna_value,
    s.sample_type
FROM genetic_alteration_derived g
JOIN sample_derived s ON g.sample_unique_id = s.sample_unique_id
WHERE g.cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018'
  AND g.hugo_gene_symbol = 'EGFR'
  AND g.profile_type IN ('gistic', 'log2CNA')
  AND g.alteration_value NOT IN ('', 'NA')
  AND toFloat64OrNull(g.alteration_value) IS NOT NULL
  AND toFloat64OrNull(g.alteration_value) > 0
ORDER BY toFloat64OrNull(g.alteration_value) DESC, s.sample_stable_id
LIMIT 100
",
 "max_rows": 100
}

◀ result
{"rows":[{"sample_stable_id":"TCGA-CS-4941-01","patient_stable_id":"TCGA-CS-4941","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-CS-6188-01","patient_stable_id":"TCGA-CS-6188","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-DU-5852-01","patient_stable_id":"TCGA-DU-5852","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-DU-5854-01","patient_stable_id":"TCGA-DU-5854","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-DU-6403-01","patient_stable_id":"TCGA-DU-6403","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-DU-6405-01","patient_stable_id":"TCGA-DU-6405","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-DU-6406-01","patient_stable_id":"TCGA-DU-6406","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-DU-7013-01","patient_stable_id":"TCGA-DU-7013","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-DU-7292-01","patient_stable_id":"TCGA-DU-7292","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-DU-A5TY-01","patient_stable_id":"TCGA-DU-A5TY","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-DU-A7TD-01","patient_stable_id":"TCGA-DU-A7TD","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-DU-A7TJ-01","patient_stable_id":"TCGA-DU-A7TJ","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-E1-A7YD-01","patient_stable_id":"TCGA-E1-A7YD","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-E1-A7YJ-01","patient_stable_id":"TCGA-E1-A7YJ","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-E1-A7YQ-01","patient_stable_id":"TCGA-E1-A7YQ","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-FG-6688-01","patient_stable_id":"TCGA-FG-6688","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-FG-6692-01","patient_stable_id":"TCGA-FG-6692","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-FG-A4MU-01","patient_stable_id":"TCGA-FG-A4MU","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-FG-A4MW-01","patient_stable_id":"TCGA-FG-A4MW","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-FG-A70Z-01","patient_stable_id":"TCGA-FG-A70Z","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-FG-A87Q-01","patient_stable_id":"TCGA-FG-A87Q","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-HT-8104-01","patient_stable_id":"TCGA-HT-8104","egfr_cna_value":3.66,"sample_type":"Primary Solid Tumor"},{"sample_stable_id":"TCGA-HT-8110-01","patient_stable_id":"TCGA-HT-8110","egfr_cna_valu … (10036 more chars)

▶ navigate_to_study_view
{
 "studyIds": [
  "lgg_tcga_pan_can_atlas_2018"
 ],
 "filterJson": {
  "genomicDataFilters": [
   {
    "hugoGeneSymbol": "EGFR",
    "profileType": "gistic",
    "values": [
     [
      {
       "value": "2"
      }
     ]
    ]
   }
  ]
 }
}

✗ error
MCP error -32602: Input validation error: Invalid arguments for tool navigate_to_study_view: [
  {
    "code": "invalid_union",
    "errors": [
      [
        {
          "expected": "object",
          "code": "invalid_type",
          "path": [],
          "message": "Invalid input: expected object, received array"
        }
      ],
      [
        {
          "expected": "object",
          "code": "invalid_type",
          "path": [],
          "message": "Invalid input: expected object, received array"
        }
      ]
    ],
    "path": [
      "filterJson",
      "genomicDataFilters",
      0,
      "values",
      0
    ],
    "message": "Invalid input"
  }
]

▶ navigate_to_study_view
{
 "studyIds": [
  "lgg_tcga_pan_can_atlas_2018"
 ],
 "filterJson": {
  "genomicDataFilters": [
   {
    "hugoGeneSymbol": "EGFR",
    "profileType": "gistic",
    "values": [
     {
      "value": "2"
     }
    ]
   }
  ]
 }
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/study/summary?id=lgg_tcga_pan_can_atlas_2018#filterJson=%7B%22genomicDataFilters%22%3A%5B%7B%22hugoGeneSymbol%22%3A%22EGFR%22%2C%22profileType%22%3A%22gistic%22%2C%22values%22%3A%5B%7B%22value%22%3A%222%22%7D%5D%7D%5D%7D","url":"https://www.cbioportal.org/study/summary?id=lgg_tcga_pan_can_atlas_2018#filterJson=%7B%22genomicDataFilters%22%3A%5B%7B%22hugoGeneSymbol%22%3A%22EGFR%22%2C%22profileType%22%3A%22gistic%22%2C%22values%22%3A%5B%7B%22value%22%3A%222%22%7D%5D%7D%5D%7D","data":{"studyIds":["lgg_tcga_pan_can_atlas_2018"],"studies":[{"studyId":"lgg_tcga_pan_can_atlas_2018","name":"Brain Lower Grade Glioma (TCGA, PanCancer Atlas)","sampleCount":514}],"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."}}

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

## EGFR Gain Samples in TCGA Lower Grade Glioma

**Study:** [Brain Lower Grade Glioma (TCGA, PanCancer Atlas)](https://www.cbioportal.org/study/summary?id=lgg_tcga_pan_can_atlas_2018) — 514 samples

**EGFR Gain Count:** 99 unique samples with positive copy number values

### Summary
- **35 samples** with GISTIC gain score = 2 (high-level amplification)
- **1 sample** (TCGA-DU-8162) with GISTIC gain score = 3.44
- **35 samples** with GISTIC gain score = 3.66 (highest level)
- **Additional samples** with lower-level gains (log2CNA values 1.0–1.77)

All samples are **Primary Solid Tumors**.

### Top Samples by Amplification Level
| Sample | Patient | EGFR CNA Value |
|--------|---------|-----------------|
| TCGA-CS-4941-01 | TCGA-CS-4941 | 3.66 |
| TCGA-CS-6188-01 | TCGA-CS-6188 | 3.66 |
| TCGA-DU-5852-01 | TCGA-DU-5852 | 3.66 |
| TCGA-DU-5854-01 | TCGA-DU-5854 | 3.66 |
| TCGA-DU-6403-01 | TCGA-DU-6403 | 3.66 |
| (… 30 more at 3.66) | | |
| TCGA-DU-8162-01 | TCGA-DU-8162 | 3.44 |

### Explore in cBioPortal
[View filtered cohort with EGFR gains](https://www.cbioportal.org/study/summary?id=lgg_tcga_pan_can_atlas_2018#filterJson=%7B%22genomicDataFilters%22%3A%5B%7B%22hugoGeneSymbol%22%3A%22EGFR%22%2C%22profileType%22%3A%22gistic%22%2C%22values%22%3A%5B%7B%22value%22%3A%222%22%7D%5D%7D%5D%7D) — Opens the study overview with the EGFR-amplified samples highlighted.