Q (sonnet-5.5): How does overall survival compare between prostate cancer patients where TMPRSS2 is acting as the upstream donor to an ERG fusion event and patients without this fusion? ▶ read_guide { "uri": "cbioportal://statistical-tests-guide" } ◀ 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) ▶ list_studies { "search": "prostate", "limit": 50 } ◀ result {"result":[{"cancer_study_identifier":"msk_met_2021","name":"MSK MetTropism (MSK, Cell 2021)","type_of_cancer_id":"mixed","sample_count":25775,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=msk_met_2021"},{"cancer_study_identifier":"prostate_msk_2024","name":"Prostate Cancer (MSK, Clin Cancer Res 2024)","type_of_cancer_id":"prostate","sample_count":2260,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=prostate_msk_2024"},{"cancer_study_identifier":"prad_msk_stopsack_2021","name":"Race Differences in Prostate Cancer (MSK, 2021)","type_of_cancer_id":"prad","sample_count":2069,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=prad_msk_stopsack_2021"},{"cancer_study_identifier":"prad_cdk12_mskcc_2020","name":"Prostate Adenocarcinoma (MSK, Eur Urol 2020)","type_of_cancer_id":"prad","sample_count":1465,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=prad_cdk12_mskcc_2020"},{"cancer_study_identifier":"prad_pik3r1_msk_2021","name":"Prostate Adenocarcinoma (MSK, Clin Cancer Res. 2022)","type_of_cancer_id":"prad","sample_count":1417,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=prad_pik3r1_msk_2021"},{"cancer_study_identifier":"prad_p1000","name":"Prostate Adenocarcinoma (MSK/DFCI, Nature Genetics 2018)","type_of_cancer_id":"prad","sample_count":1013,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=prad_p1000"},{"cancer_study_identifier":"prad_mskcc_2017","name":"Prostate Cancer (MSK, JCO Precis Oncol 2017)","type_of_cancer_id":"prad","sample_count":504,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=prad_mskcc_2017"},{"cancer_study_identifier":"prad_tcga","name":"Prostate Adenocarcinoma (TCGA, Firehose Legacy)","type_of_cancer_id":"prad","sample_count":501,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=prad_tcga"},{"cancer_study_identifier":"prad_tcga_gdc","name":"Prostate Adenocarcinoma (TCGA GDC, 2025)","type_of_cancer_id":"prad","sample_count":501,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=prad_tcga_gdc"},{"cancer_study_identifier":"prad_tcga_pan_can_atlas_2018","name":"Prostate Adenocarcinoma (TCGA, PanCancer Atlas)","type_of_cancer_id":"prad","sample_count":494,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=prad_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"prad_cpcg_2017","name":"Prostate Adenocarcinoma (CPC-GENE, Nature 2017)","type_of_cancer_id":"prad","sample_count":477,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=prad_cpcg_2017"},{"cancer_study_identifier":"prad_su2c_2019","name":"Metastatic Prostate Adenocarcinoma (SU2C/PCF Dream Team, PNAS 2019)","type_of_cancer_id":"prad","sample_count":444,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=prad_su2c_2019"},{"cancer_study_identifier":"prad_mcspc_mskcc_2020","name":"Metastatic castration-sensitive prostate cancer (MSK, Clin Cancer R … (4738 more chars) ▶ clickhouse_list_tables {} ◀ 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_list_table_columns { "table": "structural_variant" } ▶ clickhouse_list_table_columns { "table": "clinical_data_derived" } ◀ result {"columns":[{"name":"internal_id","type":"Int64"},{"name":"genetic_profile_id","type":"Int64"},{"name":"sample_id","type":"Int64"},{"name":"site1_entrez_gene_id","type":"Nullable(Int64)"},{"name":"site1_ensembl_transcript_id","type":"Nullable(String)"},{"name":"site1_chromosome","type":"Nullable(String)"},{"name":"site1_region","type":"Nullable(String)"},{"name":"site1_region_number","type":"Nullable(Int64)"},{"name":"site1_contig","type":"Nullable(String)"},{"name":"site1_position","type":"Nullable(Int64)"},{"name":"site1_description","type":"Nullable(String)"},{"name":"site2_entrez_gene_id","type":"Nullable(Int64)"},{"name":"site2_ensembl_transcript_id","type":"Nullable(String)"},{"name":"site2_chromosome","type":"Nullable(String)"},{"name":"site2_region","type":"Nullable(String)"},{"name":"site2_region_number","type":"Nullable(Int64)"},{"name":"site2_contig","type":"Nullable(String)"},{"name":"site2_position","type":"Nullable(Int64)"},{"name":"site2_description","type":"Nullable(String)"},{"name":"site2_effect_on_frame","type":"Nullable(String)"},{"name":"ncbi_build","type":"Nullable(String)"},{"name":"dna_support","type":"Nullable(String)"},{"name":"rna_support","type":"Nullable(String)"},{"name":"normal_read_count","type":"Nullable(Int64)"},{"name":"tumor_read_count","type":"Nullable(Int64)"},{"name":"normal_variant_count","type":"Nullable(Int64)"},{"name":"tumor_variant_count","type":"Nullable(Int64)"},{"name":"normal_paired_end_read_count","type":"Nullable(Int64)"},{"name":"tumor_paired_end_read_count","type":"Nullable(Int64)"},{"name":"normal_split_read_count","type":"Nullable(Int64)"},{"name":"tumor_split_read_count","type":"Nullable(Int64)"},{"name":"annotation","type":"Nullable(String)"},{"name":"breakpoint_type","type":"Nullable(String)"},{"name":"connection_type","type":"Nullable(String)"},{"name":"event_info","type":"Nullable(String)"},{"name":"class","type":"Nullable(String)"},{"name":"length","type":"Nullable(Int64)"},{"name":"comments","type":"Nullable(String)"},{"name":"sv_status","type":"String"},{"name":"annotation_json","type":"Nullable(String)"}]} ◀ 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)."}]} ▶ 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 cs.cancer_study_identifier study, countDistinct(sv.sample_id) n_samples, countIf(sv.site1_entrez_gene_id=7113 AND sv.site2_entrez_gene_id=2078) fwd, countIf(sv.site1_entrez_gene_id=2078 AND sv.site2_entrez_gene_id=7113) rev FROM structural_variant sv JOIN genetic_profile gp ON gp.genetic_profile_id=sv.genetic_profile_id JOIN cancer_study cs ON cs.cancer_study_id=gp.cancer_study_id WHERE (sv.site1_entrez_gene_id IN (7113,2078) AND sv.site2_entrez_gene_id IN (7113,2078)) GROUP BY study ORDER BY n_samples DESC" } ◀ result {"rows":[{"study":"msk_impact_50k_2026","n_samples":981,"fwd":336,"rev":489},{"study":"msk_chord_2024","n_samples":782,"fwd":399,"rev":310},{"study":"msk_met_2021","n_samples":612,"fwd":153,"rev":426},{"study":"prad_msk_stopsack_2021","n_samples":562,"fwd":129,"rev":403},{"study":"prostate_msk_2024","n_samples":436,"fwd":279,"rev":106},{"study":"prad_pik3r1_msk_2021","n_samples":409,"fwd":241,"rev":130},{"study":"prad_cdk12_mskcc_2020","n_samples":377,"fwd":16,"rev":345},{"study":"prad_p1000","n_samples":305,"fwd":0,"rev":305},{"study":"prad_tcga_pan_can_atlas_2018","n_samples":189,"fwd":189,"rev":5},{"study":"msk_impact_2017","n_samples":182,"fwd":6,"rev":169},{"study":"prad_tcga_pub","n_samples":152,"fwd":0,"rev":0},{"study":"prad_mskcc_2017","n_samples":128,"fwd":6,"rev":121},{"study":"prad_su2c_2019","n_samples":128,"fwd":0,"rev":128},{"study":"prad_mcspc_mskcc_2020","n_samples":108,"fwd":6,"rev":99},{"study":"prad_su2c_2015","n_samples":59,"fwd":59,"rev":0},{"study":"mycf_msk_2026","n_samples":47,"fwd":26,"rev":22},{"study":"metastatic_solid_tumors_mich_2017","n_samples":43,"fwd":43,"rev":0},{"study":"prad_mich","n_samples":29,"fwd":0,"rev":0},{"study":"prad_broad_2013","n_samples":26,"fwd":0,"rev":0},{"study":"prad_msk_2025","n_samples":26,"fwd":20,"rev":7},{"study":"msk_access_2021","n_samples":15,"fwd":5,"rev":9},{"study":"prad_msk_mdanderson_2023","n_samples":13,"fwd":13,"rev":0},{"study":"pancan_mimsi_msk_2024","n_samples":12,"fwd":2,"rev":7},{"study":"mixed_cfdna_msk_2020","n_samples":11,"fwd":4,"rev":7},{"study":"prad_idhmut_msk_2025","n_samples":8,"fwd":6,"rev":2},{"study":"prad_organoids_msk_2022","n_samples":6,"fwd":5,"rev":1},{"study":"prad_msk_2019","n_samples":4,"fwd":0,"rev":4},{"study":"prad_eururol_2017","n_samples":4,"fwd":0,"rev":4},{"study":"sarcoma_msk_2022","n_samples":3,"fwd":2,"rev":1},{"study":"paired_bladder_2022","n_samples":2,"fwd":0,"rev":0},{"study":"nsclc_ctdx_msk_2022","n_samples":2,"fwd":1,"rev":0},{"study":"pog570_bcgsc_2020","n_samples":2,"fwd":0,"rev":0},{"study":"ccle_broad_2019","n_samples":2,"fwd":9,"rev":0},{"study":"luad_mskcc_2023_met_organotropism","n_samples":2,"fwd":0,"rev":0},{"study":"breast_ink4_msk_2021","n_samples":1,"fwd":0,"rev":0},{"study":"luad_mskimpact_2021","n_samples":1,"fwd":0,"rev":0},{"study":"pancan_hcmi_2025","n_samples":1,"fwd":0,"rev":0},{"study":"breast_msk_2018","n_samples":1,"fwd":0,"rev":0},{"study":"sarcoma_dfci_genie_2026","n_samples":1,"fwd":0,"rev":0},{"study":"pan_origimed_2020","n_samples":1,"fwd":1,"rev":0},{"study":"lung_msk_2017","n_samples":1,"fwd":0,"rev":0},{"study":"tmb_mskcc_2018","n_samples":1,"fwd":0,"rev":1},{"study":"pcpg_tcga_pan_can_atlas_2018","n_samples":1,"fwd":1,"rev":0}]} ▶ clickhouse_run_select_query { "query": "WITH fus AS ( SELECT DISTINCT s.patient_id pid FROM structural_variant sv JOIN sample s ON s.internal_id=sv.sample_id JOIN genetic_profile gp ON gp.genetic_profile_id=sv.genetic_profile_id JOIN cancer_study cs ON cs.cancer_study_id=gp.cancer_study_id WHERE cs.cancer_study_identifier='prad_tcga_pan_can_atlas_2018' AND sv.site1_entrez_gene_id=7113 AND sv.site2_entrez_gene_id=2078), fpat AS (SELECT p.stable_id sid FROM patient p WHERE p.internal_id IN (SELECT pid FROM fus)), os AS ( SELECT replace(patient_unique_id,'prad_tcga_pan_can_atlas_2018_','') sid, maxIf(attribute_value, attribute_name='OS_STATUS') st, maxIf(toFloat64OrNull(attribute_value), attribute_name='OS_MONTHS') mo FROM clinical_data_derived WHERE cancer_study_identifier='prad_tcga_pan_can_atlas_2018' AND attribute_name IN ('OS_STATUS','OS_MONTHS') GROUP BY sid), prof AS (SELECT DISTINCT replace(patient_unique_id,'prad_tcga_pan_can_atlas_2018_','') sid FROM sample_derived WHERE cancer_study_identifier='prad_tcga_pan_can_atlas_2018') SELECT sid IN (SELECT sid FROM fpat) AS fusion, count() n, countIf(st LIKE '1:%') events, countIf(st LIKE '0:%') censored, min(mo) mn, max(mo) mx FROM os WHERE mo IS NOT NULL AND st!='' GROUP BY fusion" } ◀ result {"rows":[{"fusion":0,"n":305,"events":6,"censored":299,"mn":0.756156097,"mx":122.1685242},{"fusion":1,"n":189,"events":4,"censored":185,"mn":1.019166913,"mx":165.1707927}]} ▶ resolve_and_route { "studyIds": [ "prad_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":"prad_tcga_pan_can_atlas_2018","name":"Prostate Adenocarcinoma (TCGA, PanCancer Atlas)","sampleCount":494,"studyViewUrl":"https://www.cbioportal.org/study?id=prad_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":["prad_tcga_pan_can_atlas_2018_gistic","prad_tcga_pan_can_atlas_2018_log2CNA","prad_tcga_pan_can_atlas_2018_mutations","prad_tcga_pan_can_atlas_2018_rna_seq_v2_mrna","prad_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","prad_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","prad_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_ref_normal_Zscores","prad_tcga_pan_can_atlas_2018_rppa","prad_tcga_pan_can_atlas_2018_rppa_Zscores","prad_tcga_pan_can_atlas_2018_structural_variants"],"genericAssayProfiles":["prad_tcga_pan_can_atlas_2018_armlevel_cna","prad_tcga_pan_can_atlas_2018_genetic_ancestry","prad_tcga_pan_can_atlas_2018_methylation_hm27_hm450_merge","prad_tcga_pan_can_atlas_2018_methylation_hm450"],"heatmapProfileIds":["prad_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","prad_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","prad_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_ref_normal_Zscores","prad_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_group_comparison { "studyIds": [ "prad_tcga_pan_can_atlas_2018" ], "tab": "survival", "groups": [ { "name": "TMPRSS2::ERG fusion", "studyViewFilter": { "geneFilters": [ { "molecularProfileIds": [ "prad_tcga_pan_can_atlas_2018_structural_variants" ], "geneQueries": [ [ { "hugoGeneSymbol": "TMPRSS2" } ], [ { "hugoGeneSymbol": "ERG" } ] ] } ] } }, { "name": "No fusion (rest)", "isUnselected": true } ] } ◀ result {"success":true,"message":"Navigating to https://www.cbioportal.org/comparison/survival?comparisonId=6abb42c0c2115c492d8855cc","url":"https://www.cbioportal.org/comparison/survival?comparisonId=6abb42c0c2115c492d8855cc","data":{"description":"Group comparison (2 custom groups)","studies":["prad_tcga_pan_can_atlas_2018"],"totalGroups":2,"groups":[{"name":"TMPRSS2::ERG fusion","sampleCount":189},{"name":"No fusion (rest)","sampleCount":305}],"studyViewUrl":"https://www.cbioportal.org/study?id=prad_tcga_pan_can_atlas_2018","groupUrls":[{"groupName":"TMPRSS2::ERG fusion","url":"https://www.cbioportal.org/study?id=prad_tcga_pan_can_atlas_2018#filterJson=%7B%22geneFilters%22%3A%5B%7B%22molecularProfileIds%22%3A%5B%22prad_tcga_pan_can_atlas_2018_structural_variants%22%5D%2C%22geneQueries%22%3A%5B%5B%7B%22hugoGeneSymbol%22%3A%22TMPRSS2%22%7D%5D%2C%5B%7B%22hugoGeneSymbol%22%3A%22ERG%22%7D%5D%5D%7D%5D%7D"}],"pageDescription":"Kaplan-Meier survival analysis comparing TMPRSS2::ERG fusion (189) vs No fusion (rest) (305)."}} ═ answer (success) I can't give you a survival result, because the Kaplan-Meier and log-rank comparison has to be run in cBioPortal. I've set it up for you below. The counts show very few deaths in either group. **Cohort:** Prostate Adenocarcinoma (TCGA, PanCancer Atlas). I picked this study because it records TMPRSS2 as the 5′ donor partner of ERG. Several other prostate studies in cBioPortal also have this fusion, but they list the gene order less consistently, so I didn't pool them. Tell me if you want a different study. Counts are by patient. | Group | Patients | Deaths | Censored (alive at last follow-up) | Follow-up range (months) | |---|---|---|---|---| | TMPRSS2 (donor)::ERG fusion | 189 | 4 | 185 | 1.0 – 165.2 | | No such fusion | 305 | 6 | 299 | 0.8 – 122.2 | - **Median OS:** Fewer than half of either group died, so the Kaplan-Meier median is likely not reached in either group. Raw medians of follow-up time would be misleading because of censoring, so I haven't reported any. - **Statistical comparison:** I haven't computed a p-value or hazard ratio, and the counts alone don't support a claim about which group does better. With only 10 deaths in total, any comparison will have very little power. The appropriate test is a Kaplan-Meier curve with a log-rank test, and the link below runs it with those defaults. - **Fusion-negative group:** It includes every patient without a TMPRSS2-donor ERG fusion, including patients with other alterations. [View the Kaplan-Meier survival comparison (fusion vs. no fusion)](https://www.cbioportal.org/comparison/survival?comparisonId=6abb42c0c2115c492d8855cc) The fusion group is defined as tumors with structural variants involving both TMPRSS2 and ERG. In this study, all 189 such patients have TMPRSS2 as the 5′ partner, and 5 of them also have a reverse-ordered call. Group sizes on the page match the table above (189 vs. 305). You can also open the [study overview](https://www.cbioportal.org/study?id=prad_tcga_pan_can_atlas_2018).