Q (haiku): In TCGA lower grade glioma, show me samples that are TP53 mutant or EGFR amplified.

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

▶ list_tables
{}

◀ 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)

✗ error
<tool_use_error>Error: No such tool available: mcp__claude_ai_cBioPortal_MCP__list_tables</tool_use_error>

▶ clickhouse_list_tables
{}

◀ result
{"tables":[{"name":"allele_specific_copy_number"},{"name":"alteration_driver_annotation"},{"name":"cancer_study"},{"name":"cancer_study_query_preferences"},{"name":"cancer_study_tags"},{"name":"cbioportal_sequence_state"},{"name":"clinical_attribute_counts"},{"name":"clinical_attribute_meta"},{"name":"clinical_data_derived"},{"name":"clinical_event"},{"name":"clinical_event_data"},{"name":"clinical_event_data_derived"},{"name":"clinical_event_derived"},{"name":"clinical_patient"},{"name":"clinical_sample"},{"name":"cna_event"},{"name":"cna_panel_gene_coverage"},{"name":"cna_wes_coverage"},{"name":"co_altered_genes_in_study"},{"name":"copy_number_seg"},{"name":"copy_number_seg_file"},{"name":"gene"},{"name":"gene_alias"},{"name":"gene_alteration_frequency_by_cancer_type"},{"name":"gene_cna_distribution_in_study"},{"name":"gene_mutation_frequency_by_cancer_type"},{"name":"gene_mutation_frequency_in_studies"},{"name":"gene_mutation_frequency_in_study"},{"name":"gene_mutation_variants_in_study"},{"name":"gene_pair_coexpression"},{"name":"gene_panel"},{"name":"gene_panel_list"},{"name":"gene_panel_to_gene_derived"},{"name":"generic_assay_data_derived"},{"name":"generic_assay_meta_derived"},{"name":"generic_assay_profile_entity_derived"},{"name":"generic_entity_properties"},{"name":"geneset"},{"name":"geneset_gene"},{"name":"geneset_hierarchy_leaf"},{"name":"geneset_hierarchy_node"},{"name":"genetic_alteration"},{"name":"genetic_alteration_derived"},{"name":"genetic_entity"},{"name":"genetic_profile"},{"name":"genetic_profile_link"},{"name":"genetic_profile_samples"},{"name":"genomic_event_derived"},{"name":"gistic"},{"name":"gistic_to_gene"},{"name":"info"},{"name":"mut_sig"},{"name":"mutation"},{"name":"mutation_count_by_keyword"},{"name":"mutation_derived"},{"name":"mutation_event"},{"name":"mutation_panel_gene_coverage"},{"name":"mutation_wes_coverage"},{"name":"patient"},{"name":"reference_genome"},{"name":"reference_genome_gene"},{"name":"resource_definition"},{"name":"resource_patient"},{"name":"resource_sample"},{"name":"resource_study"},{"name":"sample"},{"name":"sample_cna_event"},{"name":"sample_derived"},{"name":"sample_list"},{"name":"sample_list_list"},{"name":"sample_profile"},{"name":"sample_to_gene_panel_derived"},{"name":"structural_variant"},{"name":"sv_panel_gene_coverage"},{"name":"sv_wes_coverage"},{"name":"top_cna_genes_in_study"},{"name":"top_mutated_genes_in_cohort"},{"name":"top_mutated_genes_in_study"},{"name":"top_sv_genes_in_study"},{"name":"treatment_counts_in_study"},{"name":"treatment_regimens_in_study"},{"name":"type_of_cancer"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT
    gd.sample_id,
    gd.patient_id,
    gd.hugo_gene_symbol,
    gd.alteration_type,
    CASE WHEN gd.alteration_type = 'mutation' THEN gd.protein_change ELSE gd.cna_value END AS alteration_detail,
    gd.cancer_study_identifier
FROM genomic_event_derived gd
WHERE gd.cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018'
  AND (
    (gd.hugo_gene_symbol = 'TP53' AND gd.alteration_type = 'mutation')
    OR
    (gd.hugo_gene_symbol = 'EGFR' AND gd.alteration_type = 'cna' AND gd.cna_value IN ('AMP', 'GAIN'))
  )
ORDER BY gd.hugo_gene_symbol, gd.sample_id
LIMIT 200
",
 "max_rows": 200
}

◀ 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 'gd.sample_id' cannot be resolved from table with name gd. In scope SELECT DISTINCT gd.sample_id, gd.patient_id, gd.hugo_gene_symbol, gd.alteration_type, multiIf(gd.alteration_type = 'mutation', gd.protein_change, gd.cna_value) AS alteration_detail, gd.cancer_study_identifier FROM genomic_event_derived AS gd WHERE (gd.cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018') AND (((gd.hugo_gene_symbol = 'TP53') AND (gd.alteration_type = 'mutation')) OR ((gd.hugo_gene_symbol = 'EGFR') AND (gd.alteration_type = 'cna') AND (gd.cna_value IN ('AMP', 'GAIN')))) ORDER BY gd.hugo_gene_symbol ASC, gd.sample_id ASC LIMIT 200. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_list_table_columns
{
 "table": "genomic_event_derived"
}

◀ 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 DISTINCT
    gd.sample_unique_id,
    gd.patient_unique_id,
    gd.hugo_gene_symbol,
    gd.variant_type,
    CASE 
      WHEN gd.variant_type = 'mutation' THEN gd.mutation_variant
      WHEN gd.variant_type = 'cna' AND gd.cna_alteration = 2 THEN 'AMP'
      WHEN gd.variant_type = 'cna' AND gd.cna_alteration = -2 THEN 'HOMDEL'
      ELSE 'Other'
    END AS alteration_detail,
    gd.cancer_study_identifier
FROM genomic_event_derived gd
WHERE gd.cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018'
  AND (
    (gd.hugo_gene_symbol = 'TP53' AND gd.variant_type = 'mutation')
    OR
    (gd.hugo_gene_symbol = 'EGFR' AND gd.variant_type = 'cna' AND gd.cna_alteration IN (2))
  )
ORDER BY gd.hugo_gene_symbol, gd.sample_unique_id
LIMIT 200
",
 "max_rows": 200
}

◀ result
<persisted-output>
Output too large (51.8KB). Full output saved to: /home/ino/.claude-cbioportal-team/projects/-tmp-mcp-qa-claude-491rduy0/b8ff9d30-f639-41b8-ac4d-cca9e9ef4a58/tool-results/toolu_01FvC368AknaeCAB8isxUkjX.txt

Preview (first 2KB):
{"rows":[{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-CS-4941-01","patient_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-CS-4941","hugo_gene_symbol":"EGFR","variant_type":"cna","alteration_detail":"AMP","cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-CS-5393-01","patient_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-CS-5393","hugo_gene_symbol":"EGFR","variant_type":"cna","alteration_detail":"AMP","cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-CS-6188-01","patient_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-CS-6188","hugo_gene_symbol":"EGFR","variant_type":"cna","alteration_detail":"AMP","cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DH-5142-01","patient_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DH-5142","hugo_gene_symbol":"EGFR","variant_type":"cna","alteration_detail":"AMP","cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-5852-01","patient_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-5852","hugo_gene_symbol":"EGFR","variant_type":"cna","alteration_detail":"AMP","cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-5854-01","patient_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-5854","hugo_gene_symbol":"EGFR","variant_type":"cna","alteration_detail":"AMP","cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-6403-01","patient_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-6403","hugo_gene_symbol":"EGFR","variant_type":"cna","alteration_detail":"AMP","cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018"},{"sample_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-6405-01","patient_unique_id":"lgg_tcga_pan_can_atlas_2018_TCGA-DU-6405","hugo_gene_symbol":"EGFR","variant_type":"cna","a
...
</persisted-output>

▶ clickhouse_run_select_query
{
 "query": "
SELECT
    gd.hugo_gene_symbol,
    COUNT(DISTINCT gd.sample_unique_id) AS sample_count
FROM genomic_event_derived gd
WHERE gd.cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018'
  AND (
    (gd.hugo_gene_symbol = 'TP53' AND gd.variant_type = 'mutation')
    OR
    (gd.hugo_gene_symbol = 'EGFR' AND gd.variant_type = 'cna' AND gd.cna_alteration IN (2))
  )
GROUP BY gd.hugo_gene_symbol
",
 "max_rows": 10
}

◀ result
{"rows":[{"hugo_gene_symbol":"EGFR","sample_count":39},{"hugo_gene_symbol":"TP53","sample_count":249}]}

▶ navigate_to_results_view
{
 "studyIds": [
  "lgg_tcga_pan_can_atlas_2018"
 ],
 "genes": [
  "TP53",
  "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=TP53%0AEGFR&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=TP53%0AEGFR&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":["TP53","EGFR"],"caseSetId":"lgg_tcga_pan_can_atlas_2018_all","pageDescription":"Visual summary of alterations in queried genes across samples."}}

═ answer (success)
## Results

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

**Samples with TP53 mutations or EGFR amplifications:**
- **TP53 mutant:** 249 samples (48.4%)
- **EGFR amplified (AMP):** 39 samples (7.6%)

[View OncoPrint with TP53 and EGFR alterations](https://www.cbioportal.org/results/oncoprint?cancer_study_list=lgg_tcga_pan_can_atlas_2018&gene_list=TP53%0AEGFR&case_set_id=lgg_tcga_pan_can_atlas_2018_all)

The OncoPrint visualization shows the spatial distribution of these alterations across all samples. Note that TP53 is frequently mutated in lower grade glioma, while EGFR amplifications are less common but represent a distinct subgroup.