Q (haiku): show me gbm with mgmt hypermethylation ▶ resolve_and_route { "studyKeywords": [ "GBM", "glioblastoma" ] } ▶ list_studies { "search": "GBM", "limit": "20", "verbose": "true" } ◀ result {"success":true,"message":"Found 8 matching studies (top 5 with full metadata, rest with basic info). 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":8,"studiesWithMetadata":[{"studyId":"gbm_tcga","name":"Glioblastoma Multiforme (TCGA, Firehose Legacy)","sampleCount":619,"studyViewUrl":"https://www.cbioportal.org/study?id=gbm_tcga","metadata":{"clinicalAttributeIds":["AGE","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","ETHNICITY","FORM_COMPLETION_DATE","FRACTION_GENOME_ALTERED","HISTOLOGICAL_DIAGNOSIS","HISTORY_LGG_DX_OF_BRAIN_TISSUE","HISTORY_NEOADJUVANT_TRTYN","HISTORY_OTHER_MALIGNANCY","ICD_10","ICD_O_3_HISTOLOGY","ICD_O_3_SITE","INFORMED_CONSENT_VERIFIED","INITIAL_PATHOLOGIC_DX_YEAR","IS_FFPE","KARNOFSKY_PERFORMANCE_SCORE","LONGEST_DIMENSION","METHOD_OF_INITIAL_SAMPLE_PROCUREMENT","METHOD_OF_INITIAL_SAMPLE_PROCUREMENT_OTHER","METHOD_OF_SAMPLE_PROCUREMENT","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_TIMING","PHARMACEUTICAL_TX_ADJUVANT","PRIMARY_SITE_PATIENT","PROJECT_CODE","PROSPECTIVE_COLLECTION","RACE","RADIATION_TREATMENT_ADJUVANT","RETROSPECTIVE_COLLECTION","SAMPLE_COUNT","SAMPLE_INITIAL_WEIGHT","SAMPLE_TYPE","SAMPLE_TYPE_ID","SEX","SHORTEST_DIMENSION","SITE_OF_TUMOR_TISSUE","SOMATIC_STATUS","SPECIMEN_CURRENT_WEIGHT","SPECIMEN_FREEZING_METHOD","SPECIMEN_SECOND_LONGEST_DIMENSION","TIME_BETWEEN_CLAMPING_AND_FREEZING","TIME_BETWEEN_EXCISION_AND_FREEZING","TISSUE_SOURCE_SITE","TMB_NONSYNONYMOUS","TREATMENT_OUTCOME_FIRST_COURSE","TUMOR_STATUS","VIAL_NUMBER"],"molecularProfileIds":["gbm_tcga_gistic","gbm_tcga_linear_CNA","gbm_tcga_methylation_hm27","gbm_tcga_methylation_hm450","gbm_tcga_mrna","gbm_tcga_mrna_U133","gbm_tcga_mrna_U133_Zscores","gbm_tcga_mrna_U133_all_sample_Zscores","gbm_tcga_mrna_median_Zscores","gbm_tcga_mrna_median_all_sample_Zscores","gbm_tcga_mutations","gbm_tcga_rna_seq_v2_mrna","gbm_tcga_rna_seq_v2_mrna_median_Zscores","gbm_tcga_rna_seq_v2_mrna_median_all_sample_Zscores","gbm_tcga_rppa","gbm_tcga_rppa_Zscores"],"heatmapProfileIds":["gbm_tcga_methylation_hm27","gbm_tcga_methylation_hm450","gbm_tcga_mrna_U133_Zscores","gbm_tcga_mrna_U133_all_sample_Zscores","gbm_tcga_mrna_median_Zscores","gbm_tcga_mrna_median_all_sample_Zscores","gbm_tcga_rna_seq_v2_mrna_median_Zscores","gbm_tcga_rna_seq_v2_mrna_median_all_sample_Zscores","gbm_tcga_rppa_Zscores"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations","mrna","protein","dna_methylation"]}},{"studyId":"gbm_tcga_gdc","name":"Glioblastoma Multif … (6771 more chars) ✗ error Error: No such tool available: mcp__navigator__list_studies ▶ clickhouse_run_select_query { "query": " SELECT s.stable_id, p.patient_id, c.attribute_value AS mgmt_methylation_status, COUNT(*) as count FROM sample s LEFT JOIN patient p ON s.patient_id = p.internal_id LEFT JOIN clinical_data_derived c ON s.internal_id = c.sample_id AND c.attribute_id = 'MGMT_STATUS' WHERE s.cancer_study_id = (SELECT cancer_study_id FROM cancer_study WHERE cancer_study_identifier = 'gbm_tcga_pan_can_atlas_2018') AND c.attribute_value != '' GROUP BY s.stable_id, p.patient_id, c.attribute_value LIMIT 100 ", "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: Identifier 'c.sample_id' cannot be resolved from table with name c. In scope SELECT s.stable_id, p.patient_id, c.attribute_value AS mgmt_methylation_status, COUNT(*) AS count FROM sample AS s LEFT JOIN patient AS p ON s.patient_id = p.internal_id LEFT JOIN clinical_data_derived AS c ON (s.internal_id = c.sample_id) AND (c.attribute_id = 'MGMT_STATUS') WHERE (s.cancer_study_id = (SELECT cancer_study_id FROM cancer_study WHERE cancer_study_identifier = 'gbm_tcga_pan_can_atlas_2018')) AND (c.attribute_value != '') GROUP BY s.stable_id, p.patient_id, c.attribute_value LIMIT 100. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"} ▶ clickhouse_list_table_columns { "table": "clinical_data_derived" } ▶ clickhouse_list_table_columns { "table": "sample" } ◀ result {"columns":[{"name":"internal_id","type":"Int32"},{"name":"sample_unique_id","type":"String","comment":"Globally unique sample ID: cancer_study_identifier + \"_\" + sample.stable_id. Empty for patient-level attributes. Use this for sample filtering and joins."},{"name":"patient_unique_id","type":"String","comment":"Globally unique patient ID: cancer_study_identifier + \"_\" + patient.stable_id. Present for both sample and patient-level attributes."},{"name":"attribute_name","type":"LowCardinality(String)","comment":"Clinical attribute name (e.g., SAMPLE_TYPE, CANCER_TYPE, AGE, OS_MONTHS). Use with attribute_value for filtering. AGE may be floored or capped for de-identification (e.g. all children recorded as 18, or everyone 89+ recorded as 89 or 90): before age statistics check for a pile-up at the min/max, and if present compute age from DAYS_TO_BIRTH (-days / 365.25)."},{"name":"attribute_value","type":"String","comment":"Value of the clinical attribute (String). For SAMPLE_TYPE: Primary, Metastasis, Local Recurrence, Unknown. Missing values are empty strings, so use toFloat64OrNull(attribute_value) for numeric comparisons — CAST fails on them."},{"name":"cancer_study_identifier","type":"LowCardinality(String)"},{"name":"type","type":"LowCardinality(String)","comment":"Data level: \"sample\" for sample-level attributes (e.g., SAMPLE_TYPE), \"patient\" for patient-level attributes (e.g., AGE, OS_MONTHS)."}]} ◀ result {"columns":[{"name":"internal_id","type":"Int64","comment":"Primary key. Unique internal identifier for the sample."},{"name":"stable_id","type":"String","comment":"Stable identifier for the sample within the study. Combined with cancer_study_identifier forms sample_unique_id."},{"name":"patient_id","type":"Int64","comment":"Foreign key to patient.internal_id. Links sample to its patient."}]} ▶ clickhouse_run_select_query { "query": " SELECT c.sample_unique_id, c.patient_unique_id, c.attribute_value AS mgmt_status, COUNT(*) as sample_count FROM clinical_data_derived c WHERE c.cancer_study_identifier = 'gbm_tcga_pan_can_atlas_2018' AND c.attribute_name = 'MGMT_STATUS' AND c.attribute_value != '' GROUP BY c.sample_unique_id, c.patient_unique_id, c.attribute_value ORDER BY c.attribute_value LIMIT 200 ", "max_rows": 200 } ◀ result {"rows":[]} ▶ clickhouse_run_select_query { "query": " SELECT DISTINCT attribute_name FROM clinical_data_derived WHERE cancer_study_identifier = 'gbm_tcga_pan_can_atlas_2018' ORDER BY attribute_name ", "max_rows": 100 } ◀ result {"rows":[{"attribute_name":"AGE"},{"attribute_name":"AJCC_PATHOLOGIC_TUMOR_STAGE"},{"attribute_name":"AJCC_STAGING_EDITION"},{"attribute_name":"ANEUPLOIDY_SCORE"},{"attribute_name":"BUFFA_HYPOXIA_SCORE"},{"attribute_name":"CANCER_TYPE"},{"attribute_name":"CANCER_TYPE_ACRONYM"},{"attribute_name":"CANCER_TYPE_DETAILED"},{"attribute_name":"DAYS_LAST_FOLLOWUP"},{"attribute_name":"DAYS_TO_BIRTH"},{"attribute_name":"DAYS_TO_INITIAL_PATHOLOGIC_DIAGNOSIS"},{"attribute_name":"DFS_MONTHS"},{"attribute_name":"DFS_STATUS"},{"attribute_name":"DSS_MONTHS"},{"attribute_name":"DSS_STATUS"},{"attribute_name":"ETHNICITY"},{"attribute_name":"FORM_COMPLETION_DATE"},{"attribute_name":"FRACTION_GENOME_ALTERED"},{"attribute_name":"GENETIC_ANCESTRY_LABEL"},{"attribute_name":"GRADE"},{"attribute_name":"HISTORY_NEOADJUVANT_TRTYN"},{"attribute_name":"ICD_10"},{"attribute_name":"ICD_O_3_HISTOLOGY"},{"attribute_name":"ICD_O_3_SITE"},{"attribute_name":"INFORMED_CONSENT_VERIFIED"},{"attribute_name":"IN_PANCANPATHWAYS_FREEZE"},{"attribute_name":"MSI_SCORE_MANTIS"},{"attribute_name":"MSI_SENSOR_SCORE"},{"attribute_name":"MUTATION_COUNT"},{"attribute_name":"NEW_TUMOR_EVENT_AFTER_INITIAL_TREATMENT"},{"attribute_name":"ONCOTREE_CODE"},{"attribute_name":"OS_MONTHS"},{"attribute_name":"OS_STATUS"},{"attribute_name":"OTHER_PATIENT_ID"},{"attribute_name":"PATH_M_STAGE"},{"attribute_name":"PATH_N_STAGE"},{"attribute_name":"PATH_T_STAGE"},{"attribute_name":"PERSON_NEOPLASM_CANCER_STATUS"},{"attribute_name":"PFS_MONTHS"},{"attribute_name":"PFS_STATUS"},{"attribute_name":"PRIMARY_LYMPH_NODE_PRESENTATION_ASSESSMENT"},{"attribute_name":"PRIOR_DX"},{"attribute_name":"RACE"},{"attribute_name":"RADIATION_THERAPY"},{"attribute_name":"RAGNUM_HYPOXIA_SCORE"},{"attribute_name":"SAMPLE_COUNT"},{"attribute_name":"SAMPLE_TYPE"},{"attribute_name":"SEX"},{"attribute_name":"SOMATIC_STATUS"},{"attribute_name":"SUBTYPE"},{"attribute_name":"TBL_SCORE"},{"attribute_name":"TISSUE_PROSPECTIVE_COLLECTION_INDICATOR"},{"attribute_name":"TISSUE_RETROSPECTIVE_COLLECTION_INDICATOR"},{"attribute_name":"TISSUE_SOURCE_SITE"},{"attribute_name":"TISSUE_SOURCE_SITE_CODE"},{"attribute_name":"TMB_NONSYNONYMOUS"},{"attribute_name":"TUMOR_TISSUE_SITE"},{"attribute_name":"TUMOR_TYPE"},{"attribute_name":"WEIGHT"},{"attribute_name":"WINTER_HYPOXIA_SCORE"}]} ▶ clickhouse_run_select_query { "query": " SELECT c.sample_unique_id, c.patient_unique_id, c.attribute_value AS mgmt_status, COUNT(*) as count FROM clinical_data_derived c WHERE c.cancer_study_identifier IN ('gbm_tcga_pub2013', 'gbm_tcga') AND c.attribute_name = 'MGMT_STATUS' AND c.attribute_value != '' GROUP BY c.cancer_study_identifier, c.sample_unique_id, c.patient_unique_id, c.attribute_value ORDER BY c.cancer_study_identifier, c.attribute_value ", "max_rows": 300 } ◀ result {"rows":[{"sample_unique_id":"gbm_tcga_pub2013_TCGA-12-0818-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-12-0818","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-06-1802-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-06-1802","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-06-1804-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-06-1804","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-06-0128-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-06-0128","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-06-5410-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-06-5410","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-27-1830-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-27-1830","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-02-0033-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-02-0033","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-06-1084-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-06-1084","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-32-4208-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-32-4208","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-28-5219-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-28-5219","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-12-3646-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-12-3646","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-14-1401-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-14-1401","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-28-1756-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-28-1756","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-19-2631-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-19-2631","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-28-2509-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-28-2509","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-06-2570-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-06-2570","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-19-1387-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-19-1387","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-06-6389-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-06-6389","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-32-4209-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-32-4209","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-19-5955-01","patient_unique_id":"gbm_tcga_pub2013_TCGA-19-5955","mgmt_status":"METHYLATED","count":1},{"sample_unique_id":"gbm_tcga_pub2013_TCGA-06-5412-01","patient_unique_id":"gbm_tcga_pub201 … (41063 more chars) ▶ clickhouse_run_select_query { "query": " SELECT c.cancer_study_identifier, c.attribute_value AS mgmt_status, COUNT(DISTINCT c.patient_unique_id) as num_patients, COUNT(DISTINCT c.sample_unique_id) as num_samples FROM clinical_data_derived c WHERE c.cancer_study_identifier IN ('gbm_tcga_pub2013', 'gbm_tcga') AND c.attribute_name = 'MGMT_STATUS' AND c.attribute_value != '' GROUP BY c.cancer_study_identifier, c.attribute_value ORDER BY c.cancer_study_identifier, c.attribute_value ", "max_rows": 20 } ◀ result {"rows":[{"cancer_study_identifier":"gbm_tcga_pub2013","mgmt_status":"METHYLATED","num_patients":170,"num_samples":170},{"cancer_study_identifier":"gbm_tcga_pub2013","mgmt_status":"UNMETHYLATED","num_patients":180,"num_samples":180}]} ▶ navigate_to_study_view { "studyIds": [ "gbm_tcga_pub2013" ], "filterJson": { "clinicalDataFilters": [ { "attributeId": "MGMT_STATUS", "values": [ { "value": "METHYLATED" } ] } ] } } ◀ result {"success":true,"message":"Navigating to https://www.cbioportal.org/study/summary?id=gbm_tcga_pub2013#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22MGMT_STATUS%22%2C%22values%22%3A%5B%7B%22value%22%3A%22METHYLATED%22%7D%5D%7D%5D%7D","url":"https://www.cbioportal.org/study/summary?id=gbm_tcga_pub2013#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22MGMT_STATUS%22%2C%22values%22%3A%5B%7B%22value%22%3A%22METHYLATED%22%7D%5D%7D%5D%7D","data":{"studyIds":["gbm_tcga_pub2013"],"studies":[{"studyId":"gbm_tcga_pub2013","name":"Glioblastoma (TCGA, Cell 2013)","sampleCount":577}],"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_group_comparison { "studyIds": [ "gbm_tcga_pub2013" ], "groups": [ { "name": "MGMT Methylated", "studyViewFilter": { "clinicalDataFilters": [ { "attributeId": "MGMT_STATUS", "values": [ { "value": "METHYLATED" } ] } ] } }, { "name": "MGMT Unmethylated", "studyViewFilter": { "clinicalDataFilters": [ { "attributeId": "MGMT_STATUS", "values": [ { "value": "UNMETHYLATED" } ] } ] } } ], "tab": "clinical" } ◀ result {"success":true,"message":"Navigating to https://www.cbioportal.org/comparison/clinical?comparisonId=6ab4301ac2115c492d884961","url":"https://www.cbioportal.org/comparison/clinical?comparisonId=6ab4301ac2115c492d884961","data":{"description":"Group comparison (2 custom groups)","studies":["gbm_tcga_pub2013"],"totalGroups":2,"groups":[{"name":"MGMT Methylated","sampleCount":170},{"name":"MGMT Unmethylated","sampleCount":180}],"studyViewUrl":"https://www.cbioportal.org/study?id=gbm_tcga_pub2013","groupUrls":[{"groupName":"MGMT Methylated","url":"https://www.cbioportal.org/study?id=gbm_tcga_pub2013#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22MGMT_STATUS%22%2C%22values%22%3A%5B%7B%22value%22%3A%22METHYLATED%22%7D%5D%7D%5D%7D"},{"groupName":"MGMT Unmethylated","url":"https://www.cbioportal.org/study?id=gbm_tcga_pub2013#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22MGMT_STATUS%22%2C%22values%22%3A%5B%7B%22value%22%3A%22UNMETHYLATED%22%7D%5D%7D%5D%7D"}],"pageDescription":"Clinical attribute distributions compared across MGMT Methylated (170) vs MGMT Unmethylated (180)."}} ═ answer (success) ## GBM with MGMT Hypermethylation **Study:** [Glioblastoma (TCGA, Cell 2013)](https://www.cbioportal.org/study/summary?id=gbm_tcga_pub2013) — 577 total GBM samples ### MGMT Status Distribution | MGMT Status | Patients | Samples | |---|---|---| | **Methylated** | 170 | 170 | | **Unmethylated** | 180 | 180 | The study contains 170 GBM samples with **MGMT hypermethylation** (MGMT methylated promoter), which is associated with improved response to alkylating chemotherapy. ### View the Data **[View MGMT-methylated GBM samples](https://www.cbioportal.org/study/summary?id=gbm_tcga_pub2013#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22MGMT_STATUS%22%2C%22values%22%3A%5B%7B%22value%22%3A%22METHYLATED%22%7D%5D%7D%5D%7D)** — Cohort overview and clinical data for the 170 methylated samples **[Compare MGMT-methylated vs unmethylated](https://www.cbioportal.org/comparison/clinical?comparisonId=6ab4301ac2115c492d884961)** — Clinical attribute comparison between the two groups (survival, demographics, genomics)