Q (haiku): are there cdkn2a het losses in gbm tcga study? ▶ resolve_and_route { "studyKeywords": [ "GBM", "TCGA" ] } ◀ result {"success":true,"message":"Found 6 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":6,"studiesWithMetadata":[{"studyId":"lgggbm_tcga_pub","name":"Merged Cohort of LGG and GBM (TCGA, Cell 2016)","sampleCount":1122,"studyViewUrl":"https://www.cbioportal.org/study?id=lgggbm_tcga_pub","metadata":{"clinicalAttributeIds":["ABSOLUTE_EXTRACT_PLOIDY","AGE","ATRX_STATUS","BCR_STATUS","BRAF_KIAA1549_FUSION","BRAF_V600E_STATUS","CANCER_TYPE","CANCER_TYPE_DETAILED","CHR_19_20_CO_GAIN","CHR_7_GAIN_CHR_10_LOSS","DAXX_STATUS","ESTIMATE_COMBINED_SCORE","ESTIMATE_IMMUNE_SCORE","ESTIMATE_STROMAL_SCORE","GRADE","HISTOLOGICAL_DIAGNOSIS","HM27","HM450","IDH_1P19Q_SUBTYPE","IDH_CODEL_SUBTYPE","IDH_SPECIFIC_DNA_METHYLATION_CLUSTER","IDH_SPECIFIC_RNA_EXPRESSION_CLUSTER","IDH_STATUS","KARNOFSKY_PERFORMANCE_SCORE","MGMT_PROMOTER_STATUS","MUTATION_COUNT","ONCOTREE_CODE","ORIGINAL_SUBTYPE","OS_MONTHS","OS_STATUS","PAN_GLIOMA_DNA_METHYLATION_CLUSTER","PAN_GLIOMA_RNA_EXPRESSION_CLUSTER","PERCENT_ANEUPLOIDY","PURITY_ABSOLUTE","RANDOM_FOREST_STURM_CLUSTER","RNASEQ_DATA","RPPA","RPPA_CLUSTER","SAMPLE_COUNT","SEX","SNP6","SOMATIC_STATUS","STUDY","SUPERVISED_DNA_METHYLATION_CLUSTER","TELOMERE_LENGTH_ESTIMATE_IN_BLOOD_NORMAL_KB","TELOMERE_LENGTH_ESTIMATE_IN_TUMOR_KB","TELOMERE_MAINTENANCE","TERT_EXPRESSION_LOG2","TERT_EXPRESSION_STATUS","TERT_PROMOTER_STATUS","TISSUE_SOURCE_SITE","TMB_NONSYNONYMOUS","TRANSCRIPTOME_SUBTYPE","U133A","WHOLE_EXOME_SEQUENCING","WHOLE_GENOME_SEQUENCING"],"molecularProfileIds":["lgggbm_tcga_pub_gistic","lgggbm_tcga_pub_log2CNA","lgggbm_tcga_pub_mutations"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations"]}},{"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","PHARMAC … (6641 more chars) ▶ clickhouse_run_select_query { "query": " SELECT COUNT(DISTINCT CASE WHEN alteration_type = 'HETLOSS' THEN sample_stable_id END) AS hetloss_samples, COUNT(DISTINCT sample_stable_id) AS total_cna_profiled, ROUND(100.0 * COUNT(DISTINCT CASE WHEN alteration_type = 'HETLOSS' THEN sample_stable_id END) / COUNT(DISTINCT sample_stable_id), 2) AS hetloss_pct FROM genomic_event_derived WHERE cancer_study_identifier = 'gbm_tcga' AND hugo_gene_symbol = 'CDKN2A' AND profile_type = 'cna' ", "max_rows": 10 } ◀ 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 or function identifier `alteration_type` in scope SELECT COUNTDistinct(multiIf(alteration_type = 'HETLOSS', sample_stable_id, NULL)) AS hetloss_samples, COUNTDistinct(sample_stable_id) AS total_cna_profiled, ROUND((100. * COUNTDistinct(multiIf(alteration_type = 'HETLOSS', sample_stable_id, NULL))) / COUNTDistinct(sample_stable_id), 2) AS hetloss_pct FROM genomic_event_derived WHERE (cancer_study_identifier = 'gbm_tcga') AND (hugo_gene_symbol = 'CDKN2A') AND (profile_type = 'cna'). Maybe you meant: ['mutation_type']. (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 COUNT(DISTINCT CASE WHEN alteration_value = '-1' THEN sample_unique_id END) AS hetloss_samples, COUNT(DISTINCT sample_unique_id) AS total_cna_profiled, ROUND(100.0 * COUNT(DISTINCT CASE WHEN alteration_value = '-1' THEN sample_unique_id END) / COUNT(DISTINCT sample_unique_id), 2) AS hetloss_pct FROM genetic_alteration_derived WHERE cancer_study_identifier = 'gbm_tcga' AND hugo_gene_symbol = 'CDKN2A' AND profile_type = 'gistic' ", "max_rows": 10 } ◀ result {"rows":[{"hetloss_samples":107,"total_cna_profiled":577,"hetloss_pct":18.54}]} ▶ navigate_to_study_view { "studyIds": [ "gbm_tcga" ], "filterJson": { "genomicDataFilters": [ { "hugoGeneSymbol": "CDKN2A", "profileType": "gistic", "values": [ [ { "value": "-1" } ] ] } ] } } ✗ 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": [ "gbm_tcga" ], "filterJson": { "genomicDataFilters": [ { "hugoGeneSymbol": "CDKN2A", "profileType": "gistic", "values": [ { "value": "-1" } ] } ] } } ◀ result {"success":true,"message":"Navigating to https://www.cbioportal.org/study/summary?id=gbm_tcga#filterJson=%7B%22genomicDataFilters%22%3A%5B%7B%22hugoGeneSymbol%22%3A%22CDKN2A%22%2C%22profileType%22%3A%22gistic%22%2C%22values%22%3A%5B%7B%22value%22%3A%22-1%22%7D%5D%7D%5D%7D","url":"https://www.cbioportal.org/study/summary?id=gbm_tcga#filterJson=%7B%22genomicDataFilters%22%3A%5B%7B%22hugoGeneSymbol%22%3A%22CDKN2A%22%2C%22profileType%22%3A%22gistic%22%2C%22values%22%3A%5B%7B%22value%22%3A%22-1%22%7D%5D%7D%5D%7D","data":{"studyIds":["gbm_tcga"],"studies":[{"studyId":"gbm_tcga","name":"Glioblastoma Multiforme (TCGA, Firehose Legacy)","sampleCount":619}],"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) [View GBM TCGA cohort filtered to CDKN2A HETLOSS](https://www.cbioportal.org/study/summary?id=gbm_tcga#filterJson=%7B%22genomicDataFilters%22%3A%5B%7B%22hugoGeneSymbol%22%3A%22CDKN2A%22%2C%22profileType%22%3A%22gistic%22%2C%22values%22%3A%5B%7B%22value%22%3A%22-1%22%7D%5D%7D%5D%7D)