Q (sonnet-5.5): what's the frequency of different idh1 mutations in glioma vs cholangio vs chndrosarcoma? Give me a link to compare the frequency of the specific IDH1 mutations in those cancer types. ▶ read_guide { "uri": "cbioportal://mutation-frequency-guide" } ▶ search_oncotree { "search_term": "glioma" } ◀ 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":[{"code":"AGNG","name":"Anaplastic Ganglioglioma","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > ENCG > AGNG"},{"code":"APXA","name":"Anaplastic Pleomorphic Xanthoastrocytoma","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > ENCG > APXA"},{"code":"ASTR","name":"Astrocytoma, IDH-Mutant","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > DIFG > ADIFG > ASTR","replacedCodes":["AASTR"]},{"code":"DASTR","name":"Diffuse Astrocytoma, MYB- or MYBL1-Altered","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > DIFG > PDIFLG > DASTR"},{"code":"DIFG","name":"Diffuse Glioma","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > DIFG"},{"code":"DNT","name":"Dysembryoplastic Neuroepithelial Tumor","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > ENCG > DNT"},{"code":"ENCG","name":"Encapsulated Glioma","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > ENCG"},{"code":"EPM","name":"Ependymoma","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > EPMT > EPM"},{"code":"GB","name":"Glioblastoma, IDH-Wildtype","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > DIFG > ADIFG > GB","replacedCodes":["GBM"]},{"code":"GNC","name":"Gangliocytoma","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > ENCG > GNC"},{"code":"GNG","name":"Ganglioglioma","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > ENCG > GNG"},{"code":"GNOS","name":"Glioma, NOS","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > DIFG > GNOS","replacedCodes":["AOAST","OAST"]},{"code":"GSARC","name":"Gliosarcoma","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > DIFG > ADIFG > GB > GSARC"},{"code":"HGGNOS","name":"High-Grade Glioma, NOS","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > DIFG > HGGNOS"},{"code":"LGGNOS","name":"Low-Grade Glioma, NOS","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > ENCG > LGGNOS"},{"code":"ODG","name":"Oligodendroglioma, IDH-mutant, and 1p/19q-Codeleted","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > DIFG > ADIFG > ODG","replacedCodes":["AODG"]},{"code":"PAST","name":"Pilocytic Astrocytoma","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > ENCG > PAST"},{"code":"PMA","name":"Pilomyxoid Astrocytoma","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > ENCG > PMA"},{"code":"PXA","name":"Pleomorphic Xanthoastrocytoma","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > ENCG > PXA"},{"code":"SCGBM","name":"Small Cell Glioblastoma","score":65,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > DIFG > ADIFG > GB > SCGBM"},{"code":"ADIFG","name":"Adult-Type Diffuse Glioma","score":50,"mainType":"Gliomas, Glioneuronal Tumors, and Neuronal Tumors","t … (782 more chars) ▶ search_oncotree { "search_term": "cholangiocarcinoma" } ▶ search_oncotree { "search_term": "chondrosarcoma" } ◀ result {"result":[{"code":"CHOL","name":"Cholangiocarcinoma","score":80,"mainType":"Hepatobiliary Cancer","tissue":"Biliary Tract","hierarchy":"BILIARY_TRACT > IPN > CHOL"},{"code":"EHCH","name":"Extrahepatic Cholangiocarcinoma","score":50,"mainType":"Hepatobiliary Cancer","tissue":"Biliary Tract","hierarchy":"BILIARY_TRACT > IPN > CHOL > EHCH"},{"code":"HCCIHCH","name":"Hepatocellular Carcinoma plus Intrahepatic Cholangiocarcinoma","score":50,"mainType":"Hepatobiliary Cancer","tissue":"Liver","hierarchy":"LIVER > HCCIHCH"},{"code":"IHCH","name":"Intrahepatic Cholangiocarcinoma","score":50,"mainType":"Hepatobiliary Cancer","tissue":"Biliary Tract","hierarchy":"BILIARY_TRACT > IPN > CHOL > IHCH"},{"code":"PHCH","name":"Perihilar Cholangiocarcinoma","score":50,"mainType":"Hepatobiliary Cancer","tissue":"Biliary Tract","hierarchy":"BILIARY_TRACT > IPN > CHOL > PHCH"}]} ◀ result {"result":[{"code":"CHS","name":"Chondrosarcoma","score":80,"mainType":"Bone Cancer","tissue":"Bone","hierarchy":"BONE > CHS"},{"code":"DDCHS","name":"Dedifferentiated Chondrosarcoma","score":50,"mainType":"Bone Cancer","tissue":"Bone","hierarchy":"BONE > CHS > DDCHS"},{"code":"EMCHS","name":"Extraskeletal Myxoid Chondrosarcoma","score":50,"mainType":"Bone Cancer","tissue":"Bone","hierarchy":"BONE > CHS > EMCHS"},{"code":"MCHS","name":"Mesenchymal Chondrosarcoma","score":50,"mainType":"Bone Cancer","tissue":"Bone","hierarchy":"BONE > CHS > MCHS"},{"code":"MCHSCNS","name":"Mesenchymal Chondrosarcoma of the CNS","score":50,"mainType":"Miscellaneous Brain Tumor","tissue":"CNS/Brain","hierarchy":"BRAIN > MBT > MCHSCNS"},{"code":"MYCHS","name":"Myxoid Chondrosarcoma","score":50,"mainType":"Bone Cancer","tissue":"Bone","hierarchy":"BONE > CHS > MYCHS"}]} ▶ clickhouse_run_select_query { "query": "SELECT attribute_name, attribute_value, uniqExact(sample_unique_id) n FROM clinical_data_derived WHERE cancer_study_identifier='msk_impact_50k_2026' AND ((attribute_name='CANCER_TYPE' AND attribute_value IN ('Glioma','Bone Cancer','Hepatobiliary Cancer')) OR (attribute_name='CANCER_TYPE_DETAILED' AND (attribute_value ILIKE '%chondrosarcoma%' OR attribute_value ILIKE '%cholangiocarcinoma%'))) GROUP BY 1,2 ORDER BY 1,3 DESC" } ◀ result {"rows":[{"attribute_name":"CANCER_TYPE","attribute_value":"Glioma","n":2322},{"attribute_name":"CANCER_TYPE","attribute_value":"Hepatobiliary Cancer","n":1431},{"attribute_name":"CANCER_TYPE","attribute_value":"Bone Cancer","n":590},{"attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Intrahepatic Cholangiocarcinoma","n":525},{"attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Cholangiocarcinoma","n":169},{"attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Extrahepatic Cholangiocarcinoma","n":116},{"attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Chondrosarcoma","n":67},{"attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Perihilar Cholangiocarcinoma","n":21},{"attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Hepatocellular Carcinoma plus Intrahepatic Cholangiocarcinoma","n":19},{"attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Dedifferentiated Chondrosarcoma","n":18},{"attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Extraskeletal Myxoid Chondrosarcoma","n":15},{"attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Mesenchymal Chondrosarcoma","n":7},{"attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Myxoid Chondrosarcoma","n":5}]} ▶ clickhouse_run_select_query { "query": "WITH grp AS ( SELECT sample_unique_id, multiIf(attribute_name='CANCER_TYPE' AND attribute_value='Glioma','Glioma', attribute_value IN ('Intrahepatic Cholangiocarcinoma','Cholangiocarcinoma','Extrahepatic Cholangiocarcinoma','Perihilar Cholangiocarcinoma'),'Cholangiocarcinoma', attribute_value='Chondrosarcoma','Chondrosarcoma','') g FROM clinical_data_derived WHERE cancer_study_identifier='msk_impact_50k_2026' AND attribute_name IN ('CANCER_TYPE','CANCER_TYPE_DETAILED')), grp2 AS (SELECT DISTINCT sample_unique_id, g FROM grp WHERE g!=''), prof AS (SELECT sample_unique_id FROM mutation_panel_gene_coverage WHERE hugo_gene_symbol='IDH1' AND cancer_study_identifier='msk_impact_50k_2026' UNION ALL SELECT sample_unique_id FROM mutation_wes_coverage WHERE cancer_study_identifier='msk_impact_50k_2026'), den AS (SELECT g, uniqExact(sample_unique_id) profiled FROM grp2 WHERE sample_unique_id IN (SELECT sample_unique_id FROM prof) GROUP BY g), num AS (SELECT g, mutation_variant, uniqExact(e.sample_unique_id) n FROM genomic_event_derived e JOIN grp2 USING sample_unique_id WHERE e.cancer_study_identifier='msk_impact_50k_2026' AND variant_type='mutation' AND mutation_status!='UNCALLED' AND off_panel=0 AND hugo_gene_symbol='IDH1' GROUP BY g, mutation_variant), tot AS (SELECT g, uniqExact(e.sample_unique_id) n FROM genomic_event_derived e JOIN grp2 USING sample_unique_id WHERE e.cancer_study_identifier='msk_impact_50k_2026' AND variant_type='mutation' AND mutation_status!='UNCALLED' AND off_panel=0 AND hugo_gene_symbol='IDH1' GROUP BY g) SELECT num.g, mutation_variant, num.n altered, den.profiled, round(num.n*100/den.profiled,1) pct, tot.n any_idh1 FROM num JOIN den USING g JOIN tot USING g ORDER BY num.g, num.n DESC" } ◀ result {"rows":[{"num.g":"Cholangiocarcinoma","mutation_variant":"R132C","altered":105,"profiled":831,"pct":12.6,"any_idh1":149},{"num.g":"Cholangiocarcinoma","mutation_variant":"R132L","altered":25,"profiled":831,"pct":3,"any_idh1":149},{"num.g":"Cholangiocarcinoma","mutation_variant":"R132G","altered":11,"profiled":831,"pct":1.3,"any_idh1":149},{"num.g":"Cholangiocarcinoma","mutation_variant":"R132S","altered":6,"profiled":831,"pct":0.7,"any_idh1":149},{"num.g":"Cholangiocarcinoma","mutation_variant":"N349S","altered":1,"profiled":831,"pct":0.1,"any_idh1":149},{"num.g":"Cholangiocarcinoma","mutation_variant":"I5Sfs*7","altered":1,"profiled":831,"pct":0.1,"any_idh1":149},{"num.g":"Chondrosarcoma","mutation_variant":"R132C","altered":7,"profiled":67,"pct":10.4,"any_idh1":20},{"num.g":"Chondrosarcoma","mutation_variant":"R132H","altered":5,"profiled":67,"pct":7.5,"any_idh1":20},{"num.g":"Chondrosarcoma","mutation_variant":"R132G","altered":4,"profiled":67,"pct":6,"any_idh1":20},{"num.g":"Chondrosarcoma","mutation_variant":"R132L","altered":2,"profiled":67,"pct":3,"any_idh1":20},{"num.g":"Chondrosarcoma","mutation_variant":"R132I","altered":1,"profiled":67,"pct":1.5,"any_idh1":20},{"num.g":"Chondrosarcoma","mutation_variant":"R132S","altered":1,"profiled":67,"pct":1.5,"any_idh1":20},{"num.g":"Glioma","mutation_variant":"R132H","altered":535,"profiled":2322,"pct":23,"any_idh1":604},{"num.g":"Glioma","mutation_variant":"R132C","altered":26,"profiled":2322,"pct":1.1,"any_idh1":604},{"num.g":"Glioma","mutation_variant":"R132S","altered":18,"profiled":2322,"pct":0.8,"any_idh1":604},{"num.g":"Glioma","mutation_variant":"R132G","altered":16,"profiled":2322,"pct":0.7,"any_idh1":604},{"num.g":"Glioma","mutation_variant":"R132L","altered":3,"profiled":2322,"pct":0.1,"any_idh1":604},{"num.g":"Glioma","mutation_variant":"A307V","altered":2,"profiled":2322,"pct":0.1,"any_idh1":604},{"num.g":"Glioma","mutation_variant":"R100*","altered":1,"profiled":2322,"pct":0,"any_idh1":604},{"num.g":"Glioma","mutation_variant":"P118N","altered":1,"profiled":2322,"pct":0,"any_idh1":604},{"num.g":"Glioma","mutation_variant":"G339E","altered":1,"profiled":2322,"pct":0,"any_idh1":604},{"num.g":"Glioma","mutation_variant":"G161R","altered":1,"profiled":2322,"pct":0,"any_idh1":604},{"num.g":"Glioma","mutation_variant":"T75N","altered":1,"profiled":2322,"pct":0,"any_idh1":604},{"num.g":"Glioma","mutation_variant":"R49H","altered":1,"profiled":2322,"pct":0,"any_idh1":604},{"num.g":"Glioma","mutation_variant":"T311N","altered":1,"profiled":2322,"pct":0,"any_idh1":604},{"num.g":"Glioma","mutation_variant":"T142I","altered":1,"profiled":2322,"pct":0,"any_idh1":604}]} ▶ resolve_and_route { "studyIds": [ "msk_impact_50k_2026" ] } ◀ result {"success":true,"message":"Found 1 study. Use the metadata to call the appropriate navigation tool(s).","data":{"totalCount":1,"studiesWithMetadata":[{"studyId":"msk_impact_50k_2026","name":"MSK-IMPACT 50K Clinical Sequencing Cohort (MSK, Cancer Cell 2026)","sampleCount":54331,"studyViewUrl":"https://www.cbioportal.org/study?id=msk_impact_50k_2026","metadata":{"clinicalAttributeIds":["AGE_AT_DX","ANCESTRY_LABEL","CANCER_TYPE","CANCER_TYPE_DETAILED","DISEASE_STATUS","FACETS_PLOIDY","FACETS_PURITY","FACETS_QC","FACETS_SUITE_VERSION","FACETS_WGD","FRACTION_GENOME_ALTERED","GENE_PANEL","HLA-A1","HLA-A2","HLA-B1","HLA-B2","HLA-C1","HLA-C2","HLA_A1_LOH","HLA_A2_LOH","HLA_B1_LOH","HLA_B2_LOH","HLA_C1_LOH","HLA_C2_LOH","HLA_GENOTYPE_AVAILABLE","METASTATIC_SITE","MSI_SCORE","MSI_TYPE","MUTATION_COUNT","N_OTHER_CANCER_TYPES","ONCOTREE_CODE","OS_MONTHS","OS_STATUS","PRIMARY_SITE","PURITY_ESTIMATE_FROM_MUTATIONS","SAMPLE_COUNT","SAMPLE_COVERAGE","SAMPLE_TYPE","SEX","SOMATIC_STATUS","TMB_SCORE","TUMOR_PURITY"],"molecularProfileIds":["msk_impact_50k_2026_gistic","msk_impact_50k_2026_mutations","msk_impact_50k_2026_structural_variants"],"genericAssayProfiles":["msk_impact_50k_2026_armlevel_cna","msk_impact_50k_2026_loh_hla","msk_impact_50k_2026_mutational_signatures_contribution_v2"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations","generic_assay_armlevel_cna","generic_assay_loh_hla","generic_assay_mutational_signature"]}}]}} ▶ get_studyviewfilter_options { "studyId": "msk_impact_50k_2026", "attributeIds": [ "CANCER_TYPE", "CANCER_TYPE_DETAILED" ] } ◀ result {"success":true,"message":"Successfully retrieved StudyView filter options","data":{"studyId":"msk_impact_50k_2026","attributes":[{"attributeId":"CANCER_TYPE","displayName":"Cancer Type","description":"Cancer Type","datatype":"STRING","values":["Endometrial Cancer","Pheochromocytoma","Melanocytoma","Ampullary Cancer","Small Cell Lung Cancer","Colorectal Cancer","Mesothelioma","Embryonal Tumor","Hepatobiliary Cancer","Peripheral Nervous System","Cancer of Unknown Primary","Uterine Sarcoma","Thymic Tumor","Non-Small Cell Lung Cancer","Skin Cancer, Non-Melanoma","Miscellaneous Neuroepithelial Tumor","Malignant Glomus Tumor","Angiomatoid Fibrous Histiocytoma","Gastrointestinal Neuroendocrine Tumors of the Esophagus/Stomach","Parathyroid Cancer","Gestational Trophoblastic Disease","Breast Sarcoma","Renal Cell Carcinoma","Vaginal Cancer","Cervical Cancer","Rhabdoid Cancer","Melanoma","Adrenocortical Carcinoma","Head and Neck Cancer","Soft Tissue Sarcoma","Pancreatic Cancer","Nerve Sheath Tumor","Clear Cell Sarcoma of Kidney","NA","Peritoneal Cancer, NOS","Anal Cancer","Retinoblastoma","Lacrimal Gland Tumor","Esophagogastric Cancer","CNS Cancer","Salivary Gland Cancer","Sex Cord Stromal Tumor","Undifferentiated Embryonal Sarcoma of the Liver","Primary CNS Melanocytic Tumors","Small Bowel Cancer","Germ Cell Tumor","Ovarian Cancer","Choroid Plexus Tumor","Soft Tissue Cancer","Appendiceal Cancer","Penile Cancer","Sellar Tumor","Adrenocortical Adenoma","Gastrointestinal Neuroendocrine Tumor","Bladder Cancer","Gastrointestinal Stromal Tumor","Breast Cancer","Miscellaneous Brain Tumor","Adenocarcinoma In Situ","Pineal Tumor","Bone Cancer","Glioma","Tubular Adenoma of the Colon","Thyroid Cancer","Prostate Cancer","Wilms Tumor"]},{"attributeId":"CANCER_TYPE_DETAILED","displayName":"Cancer Type Detailed","description":"Cancer Type Detailed","datatype":"STRING","values":["Malignant Phyllodes Tumor of the Breast","Testicular Mesothelioma","Epithelioid Hemangioendothelioma","Pleomorphic Carcinoma of the Lung","Desmoplastic/Nodular Medulloblastoma","Pituicytoma","Ovarian Cancer, Other","Adenomyoepithelioma of the Breast","Basal Cell Carcinoma","Solitary Fibrous Tumor of the Central Nervous System","Gastrointestinal Neuroendocrine Tumors of the Esophagus/Stomach","Breast Sarcoma","Pituitary Adenoma","Esophageal Squamous Cell Carcinoma","Cutaneous Melanoma","Mucosal Melanoma of the Urethra","Mucinous Adenocarcinoma of the Appendix","Oligodendroglioma, IDH-mutant, and 1p/19q-Codeleted","Mixed Germ Cell Tumor","Chondroblastic Osteosarcoma","Pilocytic Astrocytoma","Nerve Sheath Tumor","Uterine Serous Carcinoma/Uterine Papillary Serous Carcinoma","Metaplastic Carcinosarcoma","Pineoblastoma","Medulloblastoma","Fibrothecoma","Low-Grade Serous Ovarian Cancer","Intraductal Oncocytic Papillary Neoplasm","Well-Differentiated Neuroendocrine Tumors of the Stomach","Olfactory Neuroblastoma","Dysgerminoma","Primary Neuroepithelial Tumor","Telangiectatic Osteosarcoma","Mixed Cervica … (14038 more chars) ▶ navigate_to_group_comparison { "studyIds": [ "msk_impact_50k_2026" ], "groups": [ { "name": "Glioma", "studyViewFilter": { "clinicalDataFilters": [ { "attributeId": "CANCER_TYPE", "values": [ { "value": "Glioma" } ] } ] } }, { "name": "Cholangiocarcinoma", "studyViewFilter": { "clinicalDataFilters": [ { "attributeId": "CANCER_TYPE_DETAILED", "values": [ { "value": "Intrahepatic Cholangiocarcinoma" }, { "value": "Cholangiocarcinoma" }, { "value": "Extrahepatic Cholangiocarcinoma" }, { "value": "Perihilar Cholangiocarcinoma" } ] } ] } }, { "name": "Chondrosarcoma", "studyViewFilter": { "clinicalDataFilters": [ { "attributeId": "CANCER_TYPE_DETAILED", "values": [ { "value": "Chondrosarcoma" } ] } ] } } ], "tab": "mutations", "selectedGene": "IDH1" } ◀ result {"success":true,"message":"Navigating to https://www.cbioportal.org/comparison/mutations?comparisonId=6abb42c8e497aad53593ca53&selectedGene=IDH1","url":"https://www.cbioportal.org/comparison/mutations?comparisonId=6abb42c8e497aad53593ca53&selectedGene=IDH1","data":{"description":"Group comparison (3 custom groups)","studies":["msk_impact_50k_2026"],"totalGroups":3,"groups":[{"name":"Glioma","sampleCount":2322},{"name":"Cholangiocarcinoma","sampleCount":831},{"name":"Chondrosarcoma","sampleCount":67}],"studyViewUrl":"https://www.cbioportal.org/study?id=msk_impact_50k_2026","groupUrls":[{"groupName":"Glioma","url":"https://www.cbioportal.org/study?id=msk_impact_50k_2026#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CANCER_TYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22Glioma%22%7D%5D%7D%5D%7D"},{"groupName":"Cholangiocarcinoma","url":"https://www.cbioportal.org/study?id=msk_impact_50k_2026#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CANCER_TYPE_DETAILED%22%2C%22values%22%3A%5B%7B%22value%22%3A%22Intrahepatic%20Cholangiocarcinoma%22%7D%2C%7B%22value%22%3A%22Cholangiocarcinoma%22%7D%2C%7B%22value%22%3A%22Extrahepatic%20Cholangiocarcinoma%22%7D%2C%7B%22value%22%3A%22Perihilar%20Cholangiocarcinoma%22%7D%5D%7D%5D%7D"},{"groupName":"Chondrosarcoma","url":"https://www.cbioportal.org/study?id=msk_impact_50k_2026#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CANCER_TYPE_DETAILED%22%2C%22values%22%3A%5B%7B%22value%22%3A%22Chondrosarcoma%22%7D%5D%7D%5D%7D"}],"pageDescription":"Mutation frequency (protein change) compared across Glioma (2322) vs Cholangiocarcinoma (831) vs Chondrosarcoma (67)."}} ═ answer (success) **IDH1 mutation frequency by variant in glioma, cholangiocarcinoma and chondrosarcoma** The counting unit is samples, in the MSK-IMPACT 50K Clinical Sequencing Cohort (MSK, Cancer Cell 2026). All samples in each group were sequenced for IDH1. TCGA has no chondrosarcoma or cholangiocarcinoma subtypes, so I used this cohort. Each cell shows altered samples, then the percentage of profiled samples. | IDH1 variant | Glioma (n=2,322) | Cholangiocarcinoma (n=831) | Chondrosarcoma (n=67) | |---|---|---|---| | R132H | 535 (23.0%) | 0 | 5 (7.5%) | | R132C | 26 (1.1%) | 105 (12.6%) | 7 (10.4%) | | R132G | 16 (0.7%) | 11 (1.3%) | 4 (6.0%) | | R132S | 18 (0.8%) | 6 (0.7%) | 1 (1.5%) | | R132L | 3 (0.1%) | 25 (3.0%) | 2 (3.0%) | | R132I | 0 | 0 | 1 (1.5%) | | **Any IDH1 mutation** | **604 (26.0%)** | **149 (17.9%)** | **20 (29.9%)** | - **Glioma:** R132H accounts for 535 of the 604 IDH1-mutant samples. The rest are a long tail of rare variants, each in 1–2 samples. They include A307V (2 samples), R100*, P118N, G339E, G161R, T75N, R49H, T311N and T142I. - **Cholangiocarcinoma:** R132C is the dominant variant, and no R132H was found. There were also single samples with N349S and an I5Sfs*7 frameshift. - **Chondrosarcoma:** IDH1 mutations are spread across R132C, R132H, R132G, R132L, R132S and R132I. This group is small (n=67), so the percentages are imprecise. **How I defined the groups** - **Glioma:** all samples with cancer type "Glioma" (astrocytoma, oligodendroglioma, glioblastoma and others). The overall glioma rate is diluted by IDH-wildtype tumors such as glioblastoma. - **Cholangiocarcinoma:** intrahepatic, extrahepatic, perihilar and NOS combined. - **Chondrosarcoma:** the conventional "Chondrosarcoma" subtype only. It excludes the dedifferentiated, mesenchymal, myxoid and extraskeletal myxoid subtypes. I haven't run a statistical test. The comparison page below can test differences between the groups. [Compare IDH1 mutations across Glioma, Cholangiocarcinoma and Chondrosarcoma](https://www.cbioportal.org/comparison/mutations?comparisonId=6abb42c8e497aad53593ca53&selectedGene=IDH1) The page compares mutation frequency by protein change across Glioma (2,322), Cholangiocarcinoma (831) and Chondrosarcoma (67), with IDH1 preselected. You can also [explore the full cohort in Study View](https://www.cbioportal.org/study?id=msk_impact_50k_2026).