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

▶ list_guides
{}

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

◀ result
{"result":[{"uri":"cbioportal://mutation-frequency-guide","description":"Comprehensive guide for calculating gene mutation frequencies with gene-specific profiling denominators"},{"uri":"cbioportal://clinical-data-guide","description":"Guide for querying clinical data including patient vs sample level considerations"},{"uri":"cbioportal://sample-filtering-guide","description":"Guide for filtering samples and studies in cBioPortal queries"},{"uri":"cbioportal://common-pitfalls","description":"Guide to avoid common mistakes when querying cBioPortal data. If you already know which numbered pitfall applies, fetch just that section via read_guide(\"cbioportal://common-pitfalls#<number>\") (e.g. #16) instead of the full guide"},{"uri":"cbioportal://treatment-guide","description":"Guide for querying treatment/clinical event data including drug agents, timelines, and linking to genomic data"},{"uri":"cbioportal://faq-guide","description":"General cBioPortal FAQ: history, how to cite, data types, reference genome, abbreviations, GISTIC thresholds, API access"},{"uri":"cbioportal://statistical-tests-guide","description":"Statistical test selection guide — decision matrix for choosing Fisher's exact, Wilcoxon, chi-squared, t-test, ANOVA, etc. based on data type and group count"},{"uri":"cbioportal://gene-expression-guide","description":"Gene expression / copy-number / methylation analysis. Covers genetic_alteration_derived, profile_type discovery, and the gene_pair_coexpression view for Spearman correlation between two genes"},{"uri":"cbioportal://external-resources-guide","description":"Guide for finding external linked resources such as imaging, pathology, Minerva, HTAN, or other resource_* table links before declaring data unavailable"},{"uri":"cbioportal://gene-resolution-guide","description":"Guide for resolving ambiguous gene symbols, aliases, gene families, and shorthand such as CD3 before querying expression or alteration data"},{"uri":"cbioportal://study-resolution-guide","description":"Guide for resolving requested studies, avoiding silent substitute cohorts, and redirecting to known external cBioPortal instances when data is not in this deployment"},{"uri":"cbioportal://germline-guide","description":"Guide for querying germline variant data — storage columns, study discovery, query patterns, and somatic vs germline considerations"},{"uri":"cbioportal://study-guide/{study_id}","description":"Dynamic study-specific guide - use get_study_guide(study_id) tool to generate"}]}

◀ 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)

▶ get_studyviewfilter_options
{
 "studyId": "lgg_tcga_pan_can_atlas_2018",
 "geneSpecificQueries": [
  {
   "hugoGeneSymbol": "EGFR",
   "profileType": "gistic"
  }
 ]
}

▶ clickhouse_list_table_columns
{
 "table": "genomic_event_derived"
}

◀ result
{"success":true,"message":"Successfully retrieved StudyView filter options","data":{"studyId":"lgg_tcga_pan_can_atlas_2018","geneSpecificCounts":[{"hugoGeneSymbol":"EGFR","profileType":"gistic","counts":[{"value":"NA","label":"NA","count":3},{"value":"2","label":"Amplified","count":39},{"value":"-1","label":"Heterozygously deleted","count":4},{"value":"0","label":"Diploid","count":381},{"value":"1","label":"Gained","count":87}]}]}}

◀ result
{"columns":[{"name":"sample_unique_id","type":"String"},{"name":"hugo_gene_symbol","type":"String","comment":"HUGO gene symbol (e.g., TP53, KRAS, BRAF). Use for gene-specific queries."},{"name":"entrez_gene_id","type":"Int32"},{"name":"gene_panel_stable_id","type":"LowCardinality(String)"},{"name":"cancer_study_identifier","type":"LowCardinality(String)"},{"name":"genetic_profile_stable_id","type":"LowCardinality(String)"},{"name":"variant_type","type":"LowCardinality(String)","comment":"Type of genomic event: \"mutation\" for SNVs/indels, \"cna\" for copy number alterations, \"structural_variant\" for SVs. Always filter by this."},{"name":"mutation_variant","type":"String","comment":"Protein change notation (e.g., p.V600E, p.R175H). Use for specific variant queries. \"NA\" for non-mutation events."},{"name":"mutation_type","type":"LowCardinality(String)"},{"name":"mutation_status","type":"LowCardinality(String)","comment":"For mutations: Somatic, Germline, UNKNOWN, or UNCALLED. Filter mutation_status != \"UNCALLED\" to exclude uncertain calls. Include all other statuses."},{"name":"driver_filter","type":"LowCardinality(String)"},{"name":"driver_filter_annotation","type":"String"},{"name":"driver_tiers_filter","type":"LowCardinality(String)"},{"name":"driver_tiers_filter_annotation","type":"String"},{"name":"cna_alteration","type":"Nullable(Int8)","comment":"Copy number alteration: only 2 = amplification (AMP) and -2 = deep deletion (HOMDEL) are stored. Shallow deletion (-1), diploid (0) and gain (1) are not in this table; query genetic_alteration_derived WHERE profile_type = 'gistic' (alteration_value is a String, e.g. '-1'). NULL for non-CNA events."},{"name":"cna_cytoband","type":"String"},{"name":"sv_event_info","type":"String"},{"name":"patient_unique_id","type":"String"},{"name":"off_panel","type":"Bool","comment":"Boolean: 1 = mutation outside gene panel coverage (off-panel), 0 = within panel (on-panel). Filter off_panel = 0 for reliable frequency calculations."}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT
    ga.sample_unique_id,
    s.stable_id AS sample_id,
    ga.alteration_value
FROM genetic_alteration_derived ga
JOIN sample s ON s.internal_id = ga.sample_id
WHERE ga.cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018'
  AND ga.hugo_gene_symbol = 'EGFR'
  AND ga.profile_type = 'gistic'
  AND ga.alteration_value = '1'
ORDER BY sample_id
",
 "max_rows": 100
}

✗ error
The operation timed out.

▶ clickhouse_list_table_columns
{
 "table": "genetic_alteration_derived"
}

◀ 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 sample_unique_id, alteration_value
FROM genetic_alteration_derived
WHERE cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018'
  AND hugo_gene_symbol = 'EGFR'
  AND profile_type = 'gistic'
  AND alteration_value = '1'
ORDER BY sample_unique_id
",
 "max_rows": 100
}

◀ result
{"rows":[{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-CS-4942-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-CS-5395-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-CS-5396-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-CS-5397-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-CS-6186-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-CS-6665-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-CS-6670-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DB-5270-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DB-5277-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DB-A4X9-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DB-A4XE-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DB-A64O-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DH-A669-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DH-A66G-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DH-A7UT-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DH-A7UV-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-6392-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-6395-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-6400-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-6402-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-6404-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-6407-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-6410-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-7006-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-7011-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-7012-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-7014-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-7015-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-8161-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-8163-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-8165-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-8166-01","alteration_value":"1"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-A5TR-01","alteration_value":"1"},{"sample_unique_id":" … (4840 more chars)

▶ navigate_to_study_view
{
 "studyIds": [
  "lgg_tcga_pan_can_atlas_2018"
 ],
 "filterJson": {
  "genomicDataFilters": [
   {
    "hugoGeneSymbol": "EGFR",
    "profileType": "gistic",
    "values": [
     {
      "value": "1"
     }
    ]
   }
  ]
 }
}

◀ 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%221%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%221%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."}}

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

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/results/oncoprint?cancer_study_list=lgg_tcga_pan_can_atlas_2018&gene_list=EGFR&case_set_id=lgg_tcga_pan_can_atlas_2018_all","url":"https://www.cbioportal.org/results/oncoprint?cancer_study_list=lgg_tcga_pan_can_atlas_2018&gene_list=EGFR&case_set_id=lgg_tcga_pan_can_atlas_2018_all","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}],"genes":["EGFR"],"caseSetId":"lgg_tcga_pan_can_atlas_2018_all","pageDescription":"Visual summary of alterations in queried genes across samples."}}

═ answer (success)
## Summary

**Study:** Brain Lower Grade Glioma (TCGA, PanCancer Atlas) — `lgg_tcga_pan_can_atlas_2018`, 514 samples

**EGFR copy-number gain (GISTIC level = +1, low-level amplification):** **87/514 samples (16.9%)**

(For context, the full EGFR CNA distribution: Diploid 381, Gained 87, Amplified 39, Heterozygously deleted 4, NA 3.)

**Links:**

- [View Study Cohort Filtered by EGFR Gain](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%221%22%7D%5D%7D%5D%7D) — StudyView pre-filtered to the 87 EGFR-gained samples; overview of all study data displayed as interactive charts.
- [View EGFR OncoPrint](https://www.cbioportal.org/results/oncoprint?cancer_study_list=lgg_tcga_pan_can_atlas_2018&gene_list=EGFR&case_set_id=lgg_tcga_pan_can_atlas_2018_all) — visual summary of all EGFR alterations (mutations + CNA) across the full cohort; use the CNA track color legend to distinguish Gain (light blue) from Amplification (red).

Note: "Gain" (GISTIC +1) is a low-level copy-number increase, distinct from high-level amplification (GISTIC +2, 39 samples). I did not query driver/oncogenicity annotations, so no claims are made about functional significance of these gains.