Q (sonnet): "What percentage of glioblastoma patients have alterations in RB pathway genes (CDKN2A, CDK4, RB1)?" ▶ read_guide { "uri": "cbioportal://mutation-frequency-guide" } ▶ list_studies { "search": "glioblastoma" } ▶ search_oncotree { "search_term": "glioblastoma" } ◀ result # Mutation Frequency Analysis Guide ## IMPORTANT: Reporting Mutation Frequencies - **ALWAYS report frequencies as percentages**, not raw counts: `frequency = (altered_samples / total_profiled_samples) × 100` - For quick frequency lookups, **prefer the TCGA Pan-Cancer Atlas study first**, then offer to expand to other studies - When reporting across multiple studies, show **ranges** (e.g., "TP53 is mutated in 30–60% of samples") rather than a single average - **NEVER** sum mutation events across studies to compute an aggregate frequency — this can exceed 100% due to double-counting - Warn users that samples may overlap across cohorts (e.g., MSK studies may share patients) - **Choose and state the counting unit**: use patient-level frequencies for prevalence/rate questions unless the user explicitly asks for samples; use sample-level frequencies when the user asks about samples. - **For "across cancer types" questions**, jump to the [Cross-Cancer-Type Mutation Frequency](#cross-cancer-type-mutation-frequency) section below — there is one correct recipe and several common wrong ones. ## Counting Unit: Samples vs Patients Before answering any mutation count or frequency question, decide whether the unit is samples or patients and state that choice in the answer. | User wording | Counting unit | |--------------|---------------| | "prevalence", "rate", "fraction of patients", "patients with", "how common is" | Patient-level: `COUNT(DISTINCT patient_unique_id)` | | "samples", "specimens", "biopsies", sample-level cohort composition | Sample-level: `COUNT(DISTINCT sample_unique_id)` | | Ambiguous | Ask, or default to patient-level for prevalence/rate language and say so | ### Cross-study sample-count caveat When an answer touches more than one study and reports a sample count, prepend a one-line caveat: > Sample IDs are unique within cBioPortal study prefixes, not guaranteed biological-sample identifiers across studies; overlapping cohorts can count the same patient/sample more than once. Prefer one of these safer approaches: - Use a shipped `cancer_study_query_preferences` cohort such as `pan_cancer_tcga` or `all_studies_non_redundant`. - Restrict to one named study. - Aggregate by `patient_unique_id` when the biological question is patient prevalence. ## STOP rule: a frequency above 100% means your query is wrong If your query returns a frequency over 100%, **do not try to debug or explain the data inconsistency to the user**. The cause is always one of these query bugs: - Summing mutation events instead of `COUNT(DISTINCT sample_unique_id)` for the numerator - Using a study-wide sample count as the denominator instead of the gene-specific profiled count - Cross-study aggregation where the same biological sample appears under multiple `sample_unique_id` values (e.g., MSK-IMPACT and MSK-CHORD share patients) - **Joining the profiled CTE through `gene_panel` / `gene_panel_list` without a WES branch.** `gene_panel_id = 'WES'` is *not* a row in … (36467 more chars) ◀ result {"result":[{"cancer_study_identifier":"gbm_tcga","name":"Glioblastoma Multiforme (TCGA, Firehose Legacy)","type_of_cancer_id":"difg","sample_count":619,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=gbm_tcga"},{"cancer_study_identifier":"gbm_tcga_gdc","name":"Glioblastoma Multiforme (TCGA GDC, 2025)","type_of_cancer_id":"difg","sample_count":611,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=gbm_tcga_gdc"},{"cancer_study_identifier":"gbm_tcga_pan_can_atlas_2018","name":"Glioblastoma Multiforme (TCGA, PanCancer Atlas)","type_of_cancer_id":"difg","sample_count":592,"has_guide":true,"url":"https://www.cbioportal.org/study/summary?id=gbm_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"gbm_tcga_pub2013","name":"Glioblastoma (TCGA, Cell 2013)","type_of_cancer_id":"difg","sample_count":577,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=gbm_tcga_pub2013"},{"cancer_study_identifier":"gbm_tcga_pub","name":"Glioblastoma (TCGA, Nature 2008)","type_of_cancer_id":"difg","sample_count":206,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=gbm_tcga_pub"},{"cancer_study_identifier":"gbm_cptac_2021","name":"Glioblastoma (CPTAC, Cell 2021)","type_of_cancer_id":"difg","sample_count":99,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=gbm_cptac_2021"},{"cancer_study_identifier":"gbm_columbia_2019","name":"Glioblastoma (Columbia, Nat Med. 2019)","type_of_cancer_id":"difg","sample_count":42,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=gbm_columbia_2019"},{"cancer_study_identifier":"gbm_iatlas_prins_2019","name":"Glioblastoma (Randomized Clinical Trial, Nat Med. 2019) - iAtlas Harmonized","type_of_cancer_id":"adifg","sample_count":30,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=gbm_iatlas_prins_2019"}]} ◀ result {"result":[{"code":"GB","name":"Glioblastoma, IDH-Wildtype","score":60,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > DIFG > ADIFG > GB","replacedCodes":["GBM"]},{"code":"SCGBM","name":"Small Cell Glioblastoma","score":50,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > DIFG > ADIFG > GB > SCGBM"}]} ▶ clickhouse_run_select_query { "query": " WITH cs AS ( SELECT concat('gbm_tcga_pan_can_atlas_2018_', s.stable_id) AS sid FROM sample_list_list sll JOIN sample_list sl ON sl.list_id = sll.list_id JOIN sample s ON s.internal_id = sll.sample_id WHERE sl.stable_id = 'gbm_tcga_pan_can_atlas_2018_cnaseq' ) SELECT (SELECT count() FROM cs) AS n_samples, uniqExact(sample_unique_id) AS altered_samples, round(altered_samples * 100.0 / (SELECT count() FROM cs), 1) AS pct FROM genomic_event_derived WHERE cancer_study_identifier = 'gbm_tcga_pan_can_atlas_2018' AND hugo_gene_symbol IN ('CDKN2A', 'CDK4', 'RB1') AND ((variant_type = 'mutation' AND mutation_status != 'UNCALLED') OR (variant_type = 'cna' AND cna_alteration IN (2, -2))) AND sample_unique_id IN (SELECT sid FROM cs); " } ◀ result {"rows":[{"n_samples":378,"altered_samples":304,"pct":80.4}]} ▶ clickhouse_run_select_query { "query": " WITH cs AS ( SELECT concat('gbm_tcga_pan_can_atlas_2018_', s.stable_id) AS sid FROM sample_list_list sll JOIN sample_list sl ON sl.list_id = sll.list_id JOIN sample s ON s.internal_id = sll.sample_id WHERE sl.stable_id = 'gbm_tcga_pan_can_atlas_2018_cnaseq' ) SELECT hugo_gene_symbol, variant_type, CASE WHEN variant_type='cna' THEN toString(cna_alteration) ELSE mutation_type END AS event_subtype, uniqExact(sample_unique_id) AS n FROM genomic_event_derived WHERE cancer_study_identifier = 'gbm_tcga_pan_can_atlas_2018' AND hugo_gene_symbol IN ('CDKN2A', 'CDK4', 'RB1') AND ((variant_type = 'mutation' AND mutation_status != 'UNCALLED') OR (variant_type = 'cna' AND cna_alteration IN (2, -2))) AND sample_unique_id IN (SELECT sid FROM cs) GROUP BY hugo_gene_symbol, variant_type, event_subtype ORDER BY hugo_gene_symbol, n DESC; " } ◀ result {"rows":[{"hugo_gene_symbol":"CDK4","variant_type":"cna","event_subtype":"2","n":60},{"hugo_gene_symbol":"CDKN2A","variant_type":"cna","event_subtype":"-2","n":213},{"hugo_gene_symbol":"CDKN2A","variant_type":"mutation","event_subtype":"Nonsense_Mutation","n":2},{"hugo_gene_symbol":"CDKN2A","variant_type":"mutation","event_subtype":"Missense_Mutation","n":1},{"hugo_gene_symbol":"CDKN2A","variant_type":"mutation","event_subtype":"Frame_Shift_Del","n":1},{"hugo_gene_symbol":"RB1","variant_type":"mutation","event_subtype":"Nonsense_Mutation","n":16},{"hugo_gene_symbol":"RB1","variant_type":"mutation","event_subtype":"Frame_Shift_Del","n":10},{"hugo_gene_symbol":"RB1","variant_type":"cna","event_subtype":"-2","n":10},{"hugo_gene_symbol":"RB1","variant_type":"mutation","event_subtype":"Splice_Site","n":8},{"hugo_gene_symbol":"RB1","variant_type":"mutation","event_subtype":"Missense_Mutation","n":4},{"hugo_gene_symbol":"RB1","variant_type":"mutation","event_subtype":"In_Frame_Del","n":1}]} ▶ resolve_and_route { "studyIds": [ "gbm_tcga_pan_can_atlas_2018" ] } ◀ result {"success":true,"message":"Found 1 study. Use the metadata to call the appropriate navigation tool(s).","data":{"totalCount":1,"studiesWithMetadata":[{"studyId":"gbm_tcga_pan_can_atlas_2018","name":"Glioblastoma Multiforme (TCGA, PanCancer Atlas)","sampleCount":592,"studyViewUrl":"https://www.cbioportal.org/study?id=gbm_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":["gbm_tcga_pan_can_atlas_2018_gistic","gbm_tcga_pan_can_atlas_2018_log2CNA","gbm_tcga_pan_can_atlas_2018_mutations","gbm_tcga_pan_can_atlas_2018_rna_seq_v2_mrna","gbm_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","gbm_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","gbm_tcga_pan_can_atlas_2018_rppa","gbm_tcga_pan_can_atlas_2018_rppa_Zscores","gbm_tcga_pan_can_atlas_2018_structural_variants"],"genericAssayProfiles":["gbm_tcga_pan_can_atlas_2018_armlevel_cna","gbm_tcga_pan_can_atlas_2018_genetic_ancestry","gbm_tcga_pan_can_atlas_2018_methylation_hm27_hm450_merge","gbm_tcga_pan_can_atlas_2018_methylation_hm450"],"heatmapProfileIds":["gbm_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","gbm_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","gbm_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"]}}]}} ▶ navigate_to_results_view { "studyIds": [ "gbm_tcga_pan_can_atlas_2018" ], "genes": [ "CDKN2A: MUT AMP HOMDEL", "CDK4: MUT AMP HOMDEL", "RB1: MUT AMP HOMDEL" ], "tab": "oncoprint", "caseSetId": "gbm_tcga_pan_can_atlas_2018_cnaseq" } ◀ result {"success":true,"message":"Navigating to https://www.cbioportal.org/results/oncoprint?cancer_study_list=gbm_tcga_pan_can_atlas_2018&gene_list=CDKN2A%3A+MUT+AMP+HOMDEL%0ACDK4%3A+MUT+AMP+HOMDEL%0ARB1%3A+MUT+AMP+HOMDEL&case_set_id=gbm_tcga_pan_can_atlas_2018_cnaseq","url":"https://www.cbioportal.org/results/oncoprint?cancer_study_list=gbm_tcga_pan_can_atlas_2018&gene_list=CDKN2A%3A+MUT+AMP+HOMDEL%0ACDK4%3A+MUT+AMP+HOMDEL%0ARB1%3A+MUT+AMP+HOMDEL&case_set_id=gbm_tcga_pan_can_atlas_2018_cnaseq","data":{"studyIds":["gbm_tcga_pan_can_atlas_2018"],"studies":[{"studyId":"gbm_tcga_pan_can_atlas_2018","name":"Glioblastoma Multiforme (TCGA, PanCancer Atlas)","sampleCount":592}],"genes":["CDKN2A","CDK4","RB1"],"caseSetId":"gbm_tcga_pan_can_atlas_2018_cnaseq","pageDescription":"Visual summary of alterations in queried genes across samples."}} ▶ navigate_to_study_view { "studyIds": [ "gbm_tcga_pan_can_atlas_2018" ], "filterJson": { "geneFilters": [ { "molecularProfileIds": [ "gbm_tcga_pan_can_atlas_2018_mutations", "gbm_tcga_pan_can_atlas_2018_gistic" ], "geneQueries": [ [ { "hugoGeneSymbol": "CDKN2A", "alterations": [ "AMP", "HOMDEL" ] }, { "hugoGeneSymbol": "CDK4", "alterations": [ "AMP", "HOMDEL" ] }, { "hugoGeneSymbol": "RB1", "alterations": [ "AMP", "HOMDEL" ] } ] ] } ] } } ◀ result {"success":true,"message":"Navigating to https://www.cbioportal.org/study/summary?id=gbm_tcga_pan_can_atlas_2018#filterJson=%7B%22geneFilters%22%3A%5B%7B%22geneQueries%22%3A%5B%5B%7B%22alterations%22%3A%5B%22AMP%22%2C%22HOMDEL%22%5D%2C%22hugoGeneSymbol%22%3A%22CDKN2A%22%7D%2C%7B%22alterations%22%3A%5B%22AMP%22%2C%22HOMDEL%22%5D%2C%22hugoGeneSymbol%22%3A%22CDK4%22%7D%2C%7B%22alterations%22%3A%5B%22AMP%22%2C%22HOMDEL%22%5D%2C%22hugoGeneSymbol%22%3A%22RB1%22%7D%5D%5D%2C%22molecularProfileIds%22%3A%5B%22gbm_tcga_pan_can_atlas_2018_gistic%22%2C%22gbm_tcga_pan_can_atlas_2018_mutations%22%5D%7D%5D%7D","url":"https://www.cbioportal.org/study/summary?id=gbm_tcga_pan_can_atlas_2018#filterJson=%7B%22geneFilters%22%3A%5B%7B%22geneQueries%22%3A%5B%5B%7B%22alterations%22%3A%5B%22AMP%22%2C%22HOMDEL%22%5D%2C%22hugoGeneSymbol%22%3A%22CDKN2A%22%7D%2C%7B%22alterations%22%3A%5B%22AMP%22%2C%22HOMDEL%22%5D%2C%22hugoGeneSymbol%22%3A%22CDK4%22%7D%2C%7B%22alterations%22%3A%5B%22AMP%22%2C%22HOMDEL%22%5D%2C%22hugoGeneSymbol%22%3A%22RB1%22%7D%5D%5D%2C%22molecularProfileIds%22%3A%5B%22gbm_tcga_pan_can_atlas_2018_gistic%22%2C%22gbm_tcga_pan_can_atlas_2018_mutations%22%5D%7D%5D%7D","data":{"studyIds":["gbm_tcga_pan_can_atlas_2018"],"studies":[{"studyId":"gbm_tcga_pan_can_atlas_2018","name":"Glioblastoma Multiforme (TCGA, PanCancer Atlas)","sampleCount":592}],"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) **Explore further:** - [OncoPrint: RB pathway alterations in GBM](https://www.cbioportal.org/results/oncoprint?cancer_study_list=gbm_tcga_pan_can_atlas_2018&gene_list=CDKN2A%3A+MUT+AMP+HOMDEL%0ACDK4%3A+MUT+AMP+HOMDEL%0ARB1%3A+MUT+AMP+HOMDEL&case_set_id=gbm_tcga_pan_can_atlas_2018_cnaseq) — visual per-sample view of which alterations co-occur - [Study View: GBM cohort filtered to RB pathway–altered samples](https://www.cbioportal.org/study/summary?id=gbm_tcga_pan_can_atlas_2018#filterJson=%7B%22geneFilters%22%3A%5B%7B%22geneQueries%22%3A%5B%5B%7B%22alterations%22%3A%5B%22AMP%22%2C%22HOMDEL%22%5D%2C%22hugoGeneSymbol%22%3A%22CDKN2A%22%7D%2C%7B%22alterations%22%3A%5B%22AMP%22%2C%22HOMDEL%22%5D%2C%22hugoGeneSymbol%22%3A%22CDK4%22%7D%2C%7B%22alterations%22%3A%5B%22AMP%22%2C%22HOMDEL%22%5D%2C%22hugoGeneSymbol%22%3A%22RB1%22%7D%5D%5D%2C%22molecularProfileIds%22%3A%5B%22gbm_tcga_pan_can_atlas_2018_gistic%22%2C%22gbm_tcga_pan_can_atlas_2018_mutations%22%5D%7D%5D%7D) — explore clinical characteristics of these patients