Q (sonnet): is there a relationship between cic mutation and 19q del in lgg? ▶ read_guide { "uri": "cbioportal://statistical-tests-guide" } ▶ list_studies { "search": "low grade glioma" } ◀ result Statistical Test Selection Guide ================================ Purpose ------- This guide ensures the correct statistical test is selected before performing any group comparison, matching cBioPortal's own Group Comparison defaults. HARD RULES — NEVER FABRICATE A STATISTIC ---------------------------------------- ClickHouse cannot run statistical tests. The agent therefore must NEVER produce a derived statistic that is not a literal column value from a SQL result. Specifically: 1. **Never invent a p-value.** Not "p < 0.001", not "p ≈ 0.05", not any p-value. If the user asks "what is the p-value?", the answer is *"I can't compute that — here is the 2x2 contingency table (or group statistics). Run it in cBioPortal's Group Comparison tab, in R with `fisher.test(...)` / `wilcox.test(...)`, or in Python with `scipy.stats.fisher_exact(...)` / `mannwhitneyu(...)`."* 2. **Never claim mutual exclusivity (or co-occurrence) from a contingency table alone.** A 2x2 table is not a test. The shape "altered/not altered × group A/group B" needs Fisher's exact + a defined direction (odds ratio < 1 with significant p). Without that test, the agent presents the table and stops. Descriptive phrasing is also a claim: "largely/mostly mutually exclusive", "rarely co-occur", "tend to co-occur" are forbidden without the test — point to cBioPortal's Mutual Exclusivity tab instead. 3. **Never report a "median" that came from `AVG(...)` or any non-median aggregate.** "Median" and "mean" are different statistics; for skewed clinical distributions (especially survival) they differ substantially. Use ClickHouse's `quantile(0.5)(...)` for actual median, and label arithmetic averages as "mean", never "median". 4. **Never report a hazard ratio, odds ratio, risk ratio, or relative risk** that wasn't computed by an external tool. These require regression / model fitting that ClickHouse does not do. 5. **Never report median overall survival from `AVG(OS_MONTHS)` or even `quantile(0.5)(OS_MONTHS)`.** Median OS requires Kaplan-Meier estimation, which handles censoring (`OS_STATUS = 0:LIVING` means the event hasn't happened yet). Naive medians/means over `OS_MONTHS` ignore censoring and are systematically wrong. The correct handoff: return the raw `(OS_MONTHS, OS_STATUS)` pairs (or descriptive counts: N events, N censored, follow-up range) and tell the user to run KM in R (`survival::survfit`) or Python (`lifelines.KaplanMeierFitter`), or use cBioPortal's Survival comparison. If asked to do any of (1)–(5), respond with the appropriate handoff template from the "Approved Response Templates" section below — do not produce the number. Ambiguous-Term Clarification (before any analysis) -------------------------------------------------- If the user's question uses an ambiguous term, ask before computing anything. Examples: - **"aggressive"** → could mean shorter overall survival, higher metastasis rate, higher grade/stage, higher TMB, or specific molecular features. Ask which definit … (9984 more chars) ◀ result {"result":[{"cancer_study_identifier":"lgg_tcga","name":"Brain Lower Grade Glioma (TCGA, Firehose Legacy)","type_of_cancer_id":"difg","sample_count":530,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=lgg_tcga"},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018","name":"Brain Lower Grade Glioma (TCGA, PanCancer Atlas)","type_of_cancer_id":"difg","sample_count":514,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=lgg_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"brain_cptac_2020","name":"Pediatric Brain Cancer (CPTAC/CHOP, Cell 2020)","type_of_cancer_id":"brain","sample_count":218,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=brain_cptac_2020"},{"cancer_study_identifier":"difg_msk_2023","name":"IDH-mutated Diffuse Glioma (MSK, Clin Cancer Res 2024)","type_of_cancer_id":"difg","sample_count":73,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=difg_msk_2023"},{"cancer_study_identifier":"lgg_ucsf_2014","name":"Low-Grade Gliomas (UCSF, Science 2014)","type_of_cancer_id":"difg","sample_count":61,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=lgg_ucsf_2014"},{"cancer_study_identifier":"lgg_ctf_synodos_2025","name":"Pediatric Low-Grade Glioma (CTF, Acta Neuropathol 2021)","type_of_cancer_id":"difg","sample_count":31,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=lgg_ctf_synodos_2025"}]} ▶ 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_list_table_columns { "table": "genetic_alteration_derived" } ▶ clickhouse_list_tables {} ◀ result {"columns":[{"name":"sample_unique_id","type":"String"},{"name":"cancer_study_identifier","type":"LowCardinality(String)"},{"name":"hugo_gene_symbol","type":"String"},{"name":"profile_type","type":"LowCardinality(String)"},{"name":"alteration_value","type":"Nullable(String)"}]} ◀ 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 attribute_name, count(*) FROM clinical_data_derived WHERE cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018' AND (lower(attribute_name) LIKE '%19q%' OR lower(attribute_name) LIKE '%codel%' OR lower(attribute_name) LIKE '%1p%') GROUP BY attribute_name" } ◀ result {"rows":[]} ▶ clickhouse_run_select_query { "query": "SELECT DISTINCT attribute_name FROM clinical_data_derived WHERE cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018' ORDER BY attribute_name", "max_rows": 200 } ◀ 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 DISTINCT attribute_name FROM clinical_data_derived WHERE cancer_study_identifier = 'lgg_tcga' ORDER BY attribute_name", "max_rows": 200 } ◀ result {"rows":[{"attribute_name":"AGE"},{"attribute_name":"ANIMAL_INSECT_ALLERGY_AGE"},{"attribute_name":"ANIMAL_INSECT_ALLERGY_HIST"},{"attribute_name":"ASTHMA_ECZEMA_ALLERGY_FIRST_DIAGNOSIS"},{"attribute_name":"ASTHMA_HISTORY"},{"attribute_name":"CANCER_TYPE"},{"attribute_name":"CANCER_TYPE_DETAILED"},{"attribute_name":"DAYS_TO_COLLECTION"},{"attribute_name":"DAYS_TO_INITIAL_PATHOLOGIC_DIAGNOSIS"},{"attribute_name":"DAYS_TO_SPECIMEN_COLLECTION"},{"attribute_name":"DFS_MONTHS"},{"attribute_name":"DFS_STATUS"},{"attribute_name":"DISEASE_CODE"},{"attribute_name":"ECOG_SCORE"},{"attribute_name":"ECZEMA_HISTORY"},{"attribute_name":"ETHNICITY"},{"attribute_name":"FAMILY_HISTORY_OF_CANCER"},{"attribute_name":"FAMILY_HISTORY_OF_PRIMARY_BRAIN_TUMOR"},{"attribute_name":"FIRST_SYMPTOM_LONGEST_DURATION"},{"attribute_name":"FOOD_ALLERGY_AGE"},{"attribute_name":"FOOD_ALLERGY_HISTORY"},{"attribute_name":"FOOD_ALLERGY_TYPES"},{"attribute_name":"FORM_COMPLETION_DATE"},{"attribute_name":"FRACTION_GENOME_ALTERED"},{"attribute_name":"GRADE"},{"attribute_name":"HAY_FEVER_HISTORY"},{"attribute_name":"HEADACHE_HISTORY"},{"attribute_name":"HISTOLOGICAL_DIAGNOSIS"},{"attribute_name":"HISTORY_IONIZING_RT_TO_HEAD"},{"attribute_name":"HISTORY_NEOADJUVANT_MEDICATION"},{"attribute_name":"HISTORY_NEOADJUVANT_STEROID_TX"},{"attribute_name":"HISTORY_NEOADJUVANT_TRTYN"},{"attribute_name":"HISTORY_OTHER_MALIGNANCY"},{"attribute_name":"ICD_10"},{"attribute_name":"ICD_O_3_HISTOLOGY"},{"attribute_name":"ICD_O_3_SITE"},{"attribute_name":"IDH1_MUTATION"},{"attribute_name":"IDH1_MUTATION_TEST_INDICATOR"},{"attribute_name":"IDH1_MUTATION_TEST_METHOD"},{"attribute_name":"INFORMED_CONSENT_VERIFIED"},{"attribute_name":"INHERITED_GENETIC_SYNDROME_INDICATOR"},{"attribute_name":"INHERITED_GENETIC_SYNDROME_SPECIFIED"},{"attribute_name":"INITIAL_PATHOLOGIC_DX_YEAR"},{"attribute_name":"IS_FFPE"},{"attribute_name":"KARNOFSKY_PERFORMANCE_SCORE"},{"attribute_name":"LATERALITY"},{"attribute_name":"LONGEST_DIMENSION"},{"attribute_name":"METHOD_OF_SAMPLE_PROCUREMENT"},{"attribute_name":"MOLD_OR_DUST_ALLERGY_HISTORY"},{"attribute_name":"MUTATION_COUNT"},{"attribute_name":"NEW_TUMOR_EVENT_AFTER_INITIAL_TREATMENT"},{"attribute_name":"OCT_EMBEDDED"},{"attribute_name":"ONCOTREE_CODE"},{"attribute_name":"OS_MONTHS"},{"attribute_name":"OS_STATUS"},{"attribute_name":"OTHER_METHOD_OF_SAMPLE_PROCUREMENT"},{"attribute_name":"OTHER_PATIENT_ID"},{"attribute_name":"OTHER_SAMPLE_ID"},{"attribute_name":"PATHOLOGY_REPORT_FILE_NAME"},{"attribute_name":"PATHOLOGY_REPORT_UUID"},{"attribute_name":"PERFORMANCE_STATUS_DAYS_TO"},{"attribute_name":"PERFORMANCE_STATUS_TIMING"},{"attribute_name":"PROJECT_CODE"},{"attribute_name":"PROSPECTIVE_COLLECTION"},{"attribute_name":"RACE"},{"attribute_name":"RADIATION_TREATMENT_ADJUVANT"},{"attribute_name":"RELATED_SYMPTOM_FIRST_PRESENT"},{"attribute_name":"RETROSPECTIVE_COLLECTION"},{"attribute_name":"SAMPLE_COUNT"},{"attribute_name":"SAMPLE_INITIAL_WEIGHT"},{"attribute_name":"SAMPLE_TYPE"}, … (982 more chars) ▶ clickhouse_run_select_query { "query": "SELECT DISTINCT profile_type FROM genetic_alteration_derived WHERE cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018'" } ◀ result {"rows":[{"profile_type":"gistic"},{"profile_type":"log2CNA"},{"profile_type":"rna_seq_v2_mrna"},{"profile_type":"rna_seq_v2_mrna_median_Zscores"},{"profile_type":"rna_seq_v2_mrna_median_all_sample_Zscores"},{"profile_type":"rppa"},{"profile_type":"rppa_Zscores"}]} ▶ clickhouse_run_select_query { "query": " SELECT alteration_value, count(*) AS n FROM genetic_alteration_derived WHERE cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018' AND profile_type = 'gistic' AND hugo_gene_symbol = 'CIC' GROUP BY alteration_value ORDER BY alteration_value " } ▶ clickhouse_run_select_query { "query": " SELECT DISTINCT cna_cytoband FROM genomic_event_derived WHERE cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018' AND hugo_gene_symbol = 'CIC' " } ◀ result {"rows":[{"alteration_value":"-1","n":240},{"alteration_value":"-2","n":5},{"alteration_value":"0","n":241},{"alteration_value":"1","n":23},{"alteration_value":"2","n":2}]} ◀ result {"rows":[{"cna_cytoband":"19q13.2"},{}]} ▶ clickhouse_run_select_query { "query": " WITH mut AS ( SELECT DISTINCT sample_unique_id FROM genomic_event_derived WHERE cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018' AND hugo_gene_symbol = 'CIC' AND variant_type = 'mutation' AND mutation_status != 'UNCALLED' AND off_panel = FALSE ), loss AS ( SELECT DISTINCT sample_unique_id FROM genetic_alteration_derived WHERE cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018' AND profile_type = 'gistic' AND hugo_gene_symbol = 'CIC' AND alteration_value IN ('-1','-2') ), all_samples AS ( SELECT DISTINCT sample_unique_id FROM genetic_alteration_derived WHERE cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018' AND profile_type = 'gistic' AND hugo_gene_symbol = 'CIC' ) SELECT CASE WHEN m.sample_unique_id IS NOT NULL THEN 'CIC_MUT' ELSE 'CIC_WT' END AS mut_status, CASE WHEN l.sample_unique_id IS NOT NULL THEN '19q_LOSS' ELSE '19q_INTACT' END AS cn_status, count(*) AS n FROM all_samples a LEFT JOIN mut m ON a.sample_unique_id = m.sample_unique_id LEFT JOIN loss l ON a.sample_unique_id = l.sample_unique_id GROUP BY mut_status, cn_status ORDER BY mut_status, cn_status " } ◀ result {"rows":[{"mut_status":"CIC_MUT","cn_status":"19q_LOSS","n":511}]} ▶ clickhouse_run_select_query { "query": " WITH mut AS ( SELECT DISTINCT sample_unique_id FROM genomic_event_derived WHERE cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018' AND hugo_gene_symbol = 'CIC' AND variant_type = 'mutation' AND mutation_status != 'UNCALLED' AND off_panel = FALSE ), loss AS ( SELECT DISTINCT sample_unique_id FROM genetic_alteration_derived WHERE cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018' AND profile_type = 'gistic' AND hugo_gene_symbol = 'CIC' AND alteration_value IN ('-1','-2') ), all_samples AS ( SELECT DISTINCT sample_unique_id FROM genetic_alteration_derived WHERE cancer_study_identifier = 'lgg_tcga_pan_can_atlas_2018' AND profile_type = 'gistic' AND hugo_gene_symbol = 'CIC' ) SELECT count(*) AS total_profiled, countIf(sample_unique_id IN (SELECT sample_unique_id FROM mut) AND sample_unique_id IN (SELECT sample_unique_id FROM loss)) AS mut_and_loss, countIf(sample_unique_id IN (SELECT sample_unique_id FROM mut) AND sample_unique_id NOT IN (SELECT sample_unique_id FROM loss)) AS mut_and_intact, countIf(sample_unique_id NOT IN (SELECT sample_unique_id FROM mut) AND sample_unique_id IN (SELECT sample_unique_id FROM loss)) AS wt_and_loss, countIf(sample_unique_id NOT IN (SELECT sample_unique_id FROM mut) AND sample_unique_id NOT IN (SELECT sample_unique_id FROM loss)) AS wt_and_intact FROM all_samples " } ◀ result {"rows":[{"total_profiled":511,"mut_and_loss":107,"mut_and_intact":1,"wt_and_loss":138,"wt_and_intact":265}]} ▶ resolve_and_route { "studyIds": [ "lgg_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":"lgg_tcga_pan_can_atlas_2018","name":"Brain Lower Grade Glioma (TCGA, PanCancer Atlas)","sampleCount":514,"studyViewUrl":"https://www.cbioportal.org/study?id=lgg_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":["lgg_tcga_pan_can_atlas_2018_gistic","lgg_tcga_pan_can_atlas_2018_log2CNA","lgg_tcga_pan_can_atlas_2018_mutations","lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna","lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","lgg_tcga_pan_can_atlas_2018_rppa","lgg_tcga_pan_can_atlas_2018_rppa_Zscores","lgg_tcga_pan_can_atlas_2018_structural_variants"],"genericAssayProfiles":["lgg_tcga_pan_can_atlas_2018_armlevel_cna","lgg_tcga_pan_can_atlas_2018_genetic_ancestry","lgg_tcga_pan_can_atlas_2018_methylation_hm27_hm450_merge","lgg_tcga_pan_can_atlas_2018_methylation_hm450"],"heatmapProfileIds":["lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","lgg_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"]}}]}} ▶ get_studyviewfilter_options { "studyId": "lgg_tcga_pan_can_atlas_2018", "genericAssayProfileIds": [ "lgg_tcga_pan_can_atlas_2018_armlevel_cna" ], "entitySearch": "19q" } ◀ result {"success":false,"error":"Not Found","details":{"status":404,"response":{"req":{"method":"POST","url":"https://www.cbioportal.org/api/generic_assay_meta/fetch","data":{"molecularProfileIds":["lgg_tcga_pan_can_atlas_2018_armlevel_cna"]},"headers":{"user-agent":"node-superagent/3.8.3","accept":"application/json","content-type":"application/json"}},"header":{"cache-control":"no-cache, no-store, max-age=0, must-revalidate","content-encoding":"gzip","content-type":"application/json","date":"Sat, 26 Sep 2026 17:00:15 GMT","elapsed-time":"1","expires":"0","pragma":"no-cache","strict-transport-security":"max-age=31536000 ; includeSubDomains","vary":"origin,access-control-request-method,access-control-request-headers,accept-encoding","x-content-type-options":"nosniff","x-frame-options":"DENY","x-xss-protection":"0","connection":"close","transfer-encoding":"chunked"},"status":404,"text":"{\"timestamp\":1790442015278,\"status\":404,\"error\":\"Not Found\",\"path\":\"/api/generic_assay_meta/fetch\"}"}}} ▶ navigate_to_results_view { "studyIds": [ "lgg_tcga_pan_can_atlas_2018" ], "genes": [ "CIC: MUT" ], "tab": "comparison/generic_assay_armlevel_cna", "profileFilter": "mutations" } ✗ error MCP error -32602: Input validation error: Invalid arguments for tool navigate_to_results_view: [ { "code": "invalid_value", "values": [ "oncoprint", "mutations", "structuralVariants", "cancerTypesSummary", "mutualExclusivity", "plots", "survival", "coexpression", "comparison", "comparison/overlap", "comparison/survival", "comparison/clinical", "comparison/mrna", "comparison/protein", "comparison/dna_methylation", "comparison/alterations", "cnSegments", "pathways", "download" ], "path": [ "tab" ], "message": "Invalid option: expected one of \"oncoprint\"|\"mutations\"|\"structuralVariants\"|\"cancerTypesSummary\"|\"mutualExclusivity\"|\"plots\"|\"survival\"|\"coexpression\"|\"comparison\"|\"comparison/overlap\"|\"comparison/survival\"|\"comparison/clinical\"|\"comparison/mrna\"|\"comparison/protein\"|\"comparison/dna_methylation\"|\"comparison/alterations\"|\"cnSegments\"|\"pathways\"|\"download\"" } ] ▶ navigate_to_group_comparison { "studyIds": [ "lgg_tcga_pan_can_atlas_2018" ], "groups": [ { "name": "CIC mutant", "studyViewFilter": { "mutationDataFilters": [ { "hugoGeneSymbol": "CIC", "profileType": "mutations", "categorization": "MUTATED", "values": [ [ { "value": "Mutated" } ] ] } ] } }, { "name": "CIC wildtype", "isUnselected": true } ], "tab": "generic_assay_armlevel_cna" } ◀ result {"success":false,"error":"Internal Server Error","details":{"status":500,"response":{"req":{"method":"POST","url":"https://www.cbioportal.org/api/filtered-samples/fetch","data":{"mutationDataFilters":[{"hugoGeneSymbol":"CIC","profileType":"mutations","categorization":"MUTATED","values":[[{"value":"Mutated"}]]}],"studyIds":["lgg_tcga_pan_can_atlas_2018"]},"headers":{"user-agent":"node-superagent/3.8.3","accept":"application/json","content-type":"application/json"}},"header":{"cache-control":"no-cache, no-store, max-age=0, must-revalidate","content-encoding":"gzip","content-type":"application/json","date":"Sat, 26 Sep 2026 17:00:23 GMT","elapsed-time":"30","expires":"0","pragma":"no-cache","strict-transport-security":"max-age=31536000 ; 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If you are a maintainer of this instance, see logs for details.\"}"}}} ▶ get_studyviewfilter_options { "studyId": "lgg_tcga_pan_can_atlas_2018", "geneSpecificQueries": [ { "hugoGeneSymbol": "CIC", "profileType": "mutations" } ] } ◀ result {"success":true,"message":"Successfully retrieved StudyView filter options","data":{"studyId":"lgg_tcga_pan_can_atlas_2018","geneSpecificCounts":[{"hugoGeneSymbol":"CIC","profileType":"mutations","counts":[{"value":"Splice_Site","label":"Splice Site","count":4},{"value":"In_Frame_Del","label":"In Frame Del","count":4},{"value":"Nonsense_Mutation","label":"Nonsense Mutation","count":9},{"value":"Missense_Mutation","label":"Missense Mutation","count":64},{"value":"Frame_Shift_Del","label":"Frame Shift Del","count":36},{"value":"Frame_Shift_Ins","label":"Frame Shift Ins","count":13}]}]}} ▶ navigate_to_results_view { "studyIds": [ "lgg_tcga_pan_can_atlas_2018" ], "genes": [ "CIC: MUT" ], "tab": "comparison", "profileFilter": "mutations" } ◀ result {"success":true,"message":"Navigating to https://www.cbioportal.org/results/comparison?cancer_study_list=lgg_tcga_pan_can_atlas_2018&gene_list=CIC%3A+MUT&case_set_id=lgg_tcga_pan_can_atlas_2018_all&profileFilter=mutations","url":"https://www.cbioportal.org/results/comparison?cancer_study_list=lgg_tcga_pan_can_atlas_2018&gene_list=CIC%3A+MUT&case_set_id=lgg_tcga_pan_can_atlas_2018_all&profileFilter=mutations","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":["CIC"],"caseSetId":"lgg_tcga_pan_can_atlas_2018_all","pageDescription":"Compare groups of samples defined by query genes across data modalities including clinical, genomic, and survival."}} ═ answer (success) ## Summary **Study:** [Brain Lower Grade Glioma (TCGA, PanCancer Atlas)](https://www.cbioportal.org/study/summary?id=lgg_tcga_pan_can_atlas_2018) — 514 samples CIC sits at cytoband **19q13.2**, so I used copy-number loss at the CIC locus (shallow or deep deletion) as a proxy for 19q loss, since this database doesn't expose an explicit 1p/19q-codeletion clinical field (though the study *does* have true arm-level CNA data — see note below). **2×2 contingency table (511 samples with both mutation and CNA data at CIC):** | | 19q loss (CIC locus) | 19q intact | Total | |---|---|---|---| | **CIC mutated** | 107 | 1 | 108 | | **CIC wild-type** | 138 | 265 | 403 | | **Total** | 245 | 266 | 511 | - 99% (107/108) of CIC-mutant tumors show concurrent 19q loss at the CIC locus. - Only 34% (138/403) of CIC-wildtype tumors show that same loss. This pattern is consistent with the well-known two-hit mechanism in 1p/19q-codeleted oligodendrogliomas (a point mutation on one CIC allele, whole-arm 19q deletion of the other) — but I can't confirm statistical significance or an odds ratio from this table alone. The appropriate test is **Fisher's exact (two-tailed)**: - R: `fisher.test(matrix(c(107, 1, 138, 265), nrow=2))` - Python: `scipy.stats.fisher_exact([[107, 1], [138, 265]])` **Caveat:** this uses gene-locus CNA as a 19q proxy, not a validated whole-arm call. The study actually has a dedicated **arm-level CNA** data track that reports true 19q arm status directly — I wasn't able to pull its exact values through this session (API error), but you can inspect it yourself in the Comparison view below by adding the "Copy Number (Arm-level)" generic assay track for 19q. [View CIC-mutant vs. CIC-wildtype comparison](https://www.cbioportal.org/results/comparison?cancer_study_list=lgg_tcga_pan_can_atlas_2018&gene_list=CIC%3A+MUT&case_set_id=lgg_tcga_pan_can_atlas_2018_all&profileFilter=mutations) — this opens Altered (CIC-mutant) vs. Unaltered group comparison; select the **Generic Assay: Arm-level CNA** tab and choose the 19q entity to see the true arm-level relationship, or the **Alterations** tab for co-occurrence statistics computed by the portal itself (including its own Fisher's exact p-value).