Q (sonnet): 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"
}
▶ list_studies
{
"search": "prostate"
}
◀ 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":"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 … (1820 more chars)
▶ clickhouse_list_table_columns
{
"table": "structural_variant_derived"
}
◀ result
{"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 60\n Code: 60. DB::Exception: Table cbioportal_public_librechat_blue.structural_variant_derived does not exist. Maybe you meant cbioportal_public_librechat_blue.structural_variant?. (UNKNOWN_TABLE) (version 26.4.1.2359 (official build))\n"}
▶ clickhouse_list_table_columns
{
"table": "clinical_data_derived"
}
▶ get_study_guide
{
"study_id": "prad_tcga_pan_can_atlas_2018"
}
◀ 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)."}]}
◀ result
# Study Guide: Prostate Adenocarcinoma (TCGA, PanCancer Atlas)
**Study ID:** `prad_tcga_pan_can_atlas_2018`
**Cancer Type:** prad
**Description:** Prostate Adenocarcinoma TCGA PanCancer data. The original data is here. The publications are here.
## Cohort Statistics
- **Patients:** 494
- **Samples:** 495
## Available Data Types
- **PROTEIN_LEVEL**: Protein expression (RPPA)
- **PROTEIN_LEVEL**: Protein expression z-scores (RPPA)
- **COPY_NUMBER_ALTERATION**: Putative copy-number alterations from GISTIC
- **COPY_NUMBER_ALTERATION**: Log2 copy-number values
- **GENERIC_ASSAY**: Putative arm-level copy-number from GISTIC
- **MUTATION_EXTENDED**: Mutations
- **STRUCTURAL_VARIANT**: Structural variants
- **GENERIC_ASSAY**: Methylation (HM450)
- **GENERIC_ASSAY**: Methylation (HM27 and HM450 merge)
- **MRNA_EXPRESSION**: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2)
- **MRNA_EXPRESSION**: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM)
- **MRNA_EXPRESSION**: mRNA expression z-scores relative to all samples (log RNA Seq V2 RSEM)
- **MRNA_EXPRESSION**: mRNA expression z-scores relative to normal samples (log RNA Seq V2 RSEM)
- **GENERIC_ASSAY**: Genetic Ancestry
## Gene Panels
- **WES** (Whole Exome): 494 samples — all genes profiled
## Available Clinical Attributes
| Attribute | Samples with Data |
|-----------|------------------|
| MUTATION_COUNT | 494 |
| TBL_SCORE | 494 |
| CANCER_TYPE | 494 |
| TMB_NONSYNONYMOUS | 494 |
| MSI_SENSOR_SCORE | 494 |
| TISSUE_SOURCE_SITE | 494 |
| TISSUE_SOURCE_SITE_CODE | 494 |
| SAMPLE_TYPE | 494 |
| MSI_SCORE_MANTIS | 494 |
| ONCOTREE_CODE | 494 |
| TISSUE_PROSPECTIVE_COLLECTION_INDICATOR | 494 |
| SOMATIC_STATUS | 494 |
| TUMOR_TYPE | 494 |
| ANEUPLOIDY_SCORE | 494 |
| CANCER_TYPE_DETAILED | 494 |
| TISSUE_RETROSPECTIVE_COLLECTION_INDICATOR | 494 |
| TUMOR_TISSUE_SITE | 494 |
| FRACTION_GENOME_ALTERED | 494 |
| GRADE | 494 |
| ETHNICITY | 1 |
## Top Mutated Genes
| Gene | Altered Samples |
|------|----------------|
| TP53 | 57 |
| SPOP | 55 |
| TTN | 54 |
| MUC16 | 31 |
| FOXA1 | 28 |
| KMT2D | 28 |
| KMT2C | 25 |
| SPTA1 | 23 |
| SYNE1 | 23 |
| LRP1B | 22 |
## Sample Types
- **Primary**: 494 samples
## Query Tips for prad_tcga_pan_can_atlas_2018
```sql
-- Get all samples in this study
SELECT DISTINCT sample_unique_id, patient_unique_id
FROM clinical_data_derived
WHERE cancer_study_identifier = 'prad_tcga_pan_can_atlas_2018';
-- Get mutations for a specific gene
SELECT sample_unique_id, hugo_gene_symbol, mutation_variant, mutation_type
FROM genomic_event_derived
WHERE cancer_study_identifier = 'prad_tcga_pan_can_atlas_2018'
AND hugo_gene_symbol = 'TP53'
AND variant_type = 'mutation';
-- Get clinical data for specific attributes
SELECT sample_unique_id, attribute_name, attribute_value
F … (164 more chars)
▶ clickhouse_list_table_columns
{
"table": "structural_variant"
}
◀ 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)"}]}
▶ 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": "sample"
}
▶ clickhouse_list_table_columns
{
"table": "genetic_profile"
}
◀ result
{"columns":[{"name":"internal_id","type":"Int64","comment":"Primary key. Unique internal identifier for the sample."},{"name":"stable_id","type":"String","comment":"Stable identifier for the sample within the study. Combined with cancer_study_identifier forms sample_unique_id."},{"name":"patient_id","type":"Int64","comment":"Foreign key to patient.internal_id. Links sample to its patient."}]}
◀ result
{"columns":[{"name":"genetic_profile_id","type":"Int64"},{"name":"stable_id","type":"String"},{"name":"cancer_study_id","type":"Int64"},{"name":"genetic_alteration_type","type":"String"},{"name":"generic_assay_type","type":"Nullable(String)"},{"name":"datatype","type":"String"},{"name":"name","type":"String"},{"name":"description","type":"Nullable(String)"},{"name":"show_profile_in_analysis_tab","type":"Int32"},{"name":"pivot_threshold","type":"Nullable(Float64)"},{"name":"sort_order","type":"Nullable(String)"},{"name":"patient_level","type":"Nullable(Int32)"}]}
▶ clickhouse_run_select_query
{
"query": "SELECT DISTINCT hugo_gene_symbol, sv_event_info FROM genomic_event_derived WHERE cancer_study_identifier = 'prad_tcga_pan_can_atlas_2018' AND variant_type = 'structural_variant' LIMIT 50"
}
◀ result
{"rows":[{"hugo_gene_symbol":"ABCA1","sv_event_info":"RGS3-ABCA1 fusion"},{"hugo_gene_symbol":"ABR","sv_event_info":"ABR-GEMIN4 fusion"},{"hugo_gene_symbol":"ACAA1","sv_event_info":"GOLGA4-ACAA1 fusion"},{"hugo_gene_symbol":"ACACA","sv_event_info":"ACACA-MMP28 fusion"},{"hugo_gene_symbol":"ACACB","sv_event_info":"IFT81-ACACB fusion"},{"hugo_gene_symbol":"ACACB","sv_event_info":"SENP6-ACACB fusion"},{"hugo_gene_symbol":"ACADL","sv_event_info":"XRCC5-ACADL fusion"},{"hugo_gene_symbol":"ACP3","sv_event_info":"ACPP-BCR fusion"},{"hugo_gene_symbol":"ACP3","sv_event_info":"ACPP-NPY fusion"},{"hugo_gene_symbol":"ACP3","sv_event_info":"ACPP-RDH11 fusion"},{"hugo_gene_symbol":"ACP3","sv_event_info":"ACPP-ARFIP1 fusion"},{"hugo_gene_symbol":"ACP3","sv_event_info":"DDT-ACPP fusion"},{"hugo_gene_symbol":"ACP3","sv_event_info":"ACPP-MYC fusion"},{"hugo_gene_symbol":"ACP3","sv_event_info":"ACPP-ZNF462 fusion"},{"hugo_gene_symbol":"ACP3","sv_event_info":"ACPP-NEDD4L fusion"},{"hugo_gene_symbol":"ACP3","sv_event_info":"RASA2-ACPP fusion"},{"hugo_gene_symbol":"ACP3","sv_event_info":"ACPP-SAFB2 fusion"},{"hugo_gene_symbol":"ACP3","sv_event_info":"ACPP-AXL fusion"},{"hugo_gene_symbol":"ACP3","sv_event_info":"ACPP-ATP2C1 fusion"},{"hugo_gene_symbol":"ACP3","sv_event_info":"ACPP-RPL7P16 fusion"},{"hugo_gene_symbol":"ACTG2","sv_event_info":"FLNA-ACTG2 fusion"},{"hugo_gene_symbol":"ACTN4","sv_event_info":"ACTN4-MGST2 fusion"},{"hugo_gene_symbol":"ACVR2A","sv_event_info":"ACVR2A-AKT3 fusion"},{"hugo_gene_symbol":"ACYP2","sv_event_info":"ERLEC1-ACYP2 fusion"},{"hugo_gene_symbol":"ACYP2","sv_event_info":"ACYP2-CFAP36 fusion"},{"hugo_gene_symbol":"ADK","sv_event_info":"ADK-KCNMA1 fusion"},{"hugo_gene_symbol":"PARP4","sv_event_info":"ZNF618-PARP4 fusion"},{"hugo_gene_symbol":"GRK3","sv_event_info":"GRK3-ZNRF3 fusion"},{"hugo_gene_symbol":"ADSS2","sv_event_info":"AKT3-ADSS fusion"},{"hugo_gene_symbol":"AP1B1","sv_event_info":"AP1B1-CLTCL1 fusion"},{"hugo_gene_symbol":"TLE5","sv_event_info":"FGFR3-AES fusion"},{"hugo_gene_symbol":"AGL","sv_event_info":"AGL-ARHGDIB fusion"},{"hugo_gene_symbol":"ALCAM","sv_event_info":"ALCAM-NRROS fusion"},{"hugo_gene_symbol":"ALDH1A3","sv_event_info":"ALDH1A3-USP25 fusion"},{"hugo_gene_symbol":"ALDH3A2","sv_event_info":"ALDH3A2-PITPNM2 fusion"},{"hugo_gene_symbol":"ALDOB","sv_event_info":"SNX30-ALDOB fusion"},{"hugo_gene_symbol":"AMBN","sv_event_info":"MOB1B-AMBN fusion"},{"hugo_gene_symbol":"AMD1","sv_event_info":"CDK19-AMD1 fusion"},{"hugo_gene_symbol":"AMD1","sv_event_info":"AMD1-MBOAT2 fusion"},{"hugo_gene_symbol":"AMD1","sv_event_info":"AMD1-EPG5 fusion"},{"hugo_gene_symbol":"AMPH","sv_event_info":"COA1-AMPH fusion"},{"hugo_gene_symbol":"AMY1C","sv_event_info":"TERF2IP-AMY1C fusion"},{"hugo_gene_symbol":"ANK3","sv_event_info":"ANK3-USP9Y fusion"},{"hugo_gene_symbol":"APBA1","sv_event_info":"APBA1-RAD23B fusion"},{"hugo_gene_symbol":"APC","sv_event_info":"APC-KIAA0825 fusion"},{"hugo_gene_symbol":"APC","sv_event_info":"APC-MCC fusion"},{"h … (254 more chars)
▶ clickhouse_run_select_query
{
"query": "SELECT DISTINCT sv_event_info FROM genomic_event_derived WHERE cancer_study_identifier = 'prad_tcga_pan_can_atlas_2018' AND variant_type = 'structural_variant' AND (hugo_gene_symbol = 'TMPRSS2' OR hugo_gene_symbol = 'ERG')"
}
◀ result
{"rows":[{"sv_event_info":"TMPRSS2-ERG fusion"},{"sv_event_info":"ERG-PLEKHH1 fusion"},{"sv_event_info":"ERG-CDHR2 fusion"},{"sv_event_info":"NDRG1-ERG fusion"},{"sv_event_info":"ERG-SKOR2 fusion"},{"sv_event_info":"ERG-TMPRSS2 fusion"},{"sv_event_info":"ERG-TAF8 fusion"},{"sv_event_info":"SLC45A3-ERG fusion"},{"sv_event_info":"ERG-SON fusion"},{"sv_event_info":"GUCA2A-ERG fusion"},{"sv_event_info":"ERG-KCNJ6 fusion"},{"sv_event_info":"ERG-SRPK2 fusion"},{"sv_event_info":"GRHL2-ERG fusion"},{"sv_event_info":"ERG-RPS18 fusion"},{"sv_event_info":"ERG-ABCC4 fusion"},{"sv_event_info":"TMPRSS2-MORC3 fusion"},{"sv_event_info":"TMPRSS2-ETV4 fusion"},{"sv_event_info":"SIK3-TMPRSS2 fusion"},{"sv_event_info":"MESDC2-TMPRSS2 fusion"},{"sv_event_info":"TMPRSS2-DIAPH1 fusion"},{"sv_event_info":"TMPRSS2-ATF7IP fusion"},{"sv_event_info":"ATF7IP-TMPRSS2 fusion"},{"sv_event_info":"TMPRSS2-MRPS6 fusion"},{"sv_event_info":"TMPRSS2-SARS fusion"},{"sv_event_info":"TMPRSS2-CALB1 fusion"},{"sv_event_info":"TMPRSS2-BRAF fusion"},{"sv_event_info":"TMPRSS2-HDLBP fusion"},{"sv_event_info":"HDLBP-TMPRSS2 fusion"},{"sv_event_info":"AFF3-TMPRSS2 fusion"},{"sv_event_info":"TMPRSS2-KLF4 fusion"},{"sv_event_info":"DLG5-TMPRSS2 fusion"},{"sv_event_info":"TMPRSS2-TMEM109 fusion"},{"sv_event_info":"USP28-TMPRSS2 fusion"},{"sv_event_info":"TMPRSS2-IRS2 fusion"},{"sv_event_info":"HMGN2P46-TMPRSS2 fusion"},{"sv_event_info":"TMPRSS2-GUCA2A fusion"},{"sv_event_info":"BACE2-TMPRSS2 fusion"},{"sv_event_info":"TMPRSS2-TMEFF2 fusion"},{"sv_event_info":"TMEFF2-TMPRSS2 fusion"},{"sv_event_info":"TMPRSS2-ETV5 fusion"},{"sv_event_info":"TMPRSS2-DGKG fusion"},{"sv_event_info":"TMPRSS2-INPP4B fusion"},{"sv_event_info":"SLC45A3-TMPRSS2 fusion"},{"sv_event_info":"TMPRSS2-EML4 fusion"},{"sv_event_info":"SCP2-TMPRSS2 fusion"},{"sv_event_info":"TMPRSS2-PDE9A fusion"},{"sv_event_info":"PDE9A-TMPRSS2 fusion"}]}
▶ clickhouse_run_select_query
{
"query": "
SELECT sv.internal_id, g1.hugo_gene_symbol AS site1_gene, g2.hugo_gene_symbol AS site2_gene, sv.event_info, sv.site1_region, sv.site2_region, sv.connection_type, sv.annotation
FROM structural_variant sv
LEFT JOIN gene g1 ON g1.entrez_gene_id = sv.site1_entrez_gene_id
LEFT JOIN gene g2 ON g2.entrez_gene_id = sv.site2_entrez_gene_id
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.internal_id = gp.cancer_study_id
WHERE cs.cancer_study_identifier = 'prad_tcga_pan_can_atlas_2018'
AND (g1.hugo_gene_symbol IN ('TMPRSS2','ERG') OR g2.hugo_gene_symbol IN ('TMPRSS2','ERG'))
LIMIT 20
"
}
▶ clickhouse_list_table_columns
{
"table": "gene"
}
◀ result
{"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 47\n Code: 47. DB::Exception: Identifier 'cs.internal_id' cannot be resolved from table with name cs. In scope SELECT sv.internal_id, g1.hugo_gene_symbol AS site1_gene, g2.hugo_gene_symbol AS site2_gene, sv.event_info, sv.site1_region, sv.site2_region, sv.connection_type, sv.annotation FROM structural_variant AS sv LEFT JOIN gene AS g1 ON g1.entrez_gene_id = sv.site1_entrez_gene_id LEFT JOIN gene AS g2 ON g2.entrez_gene_id = sv.site2_entrez_gene_id INNER JOIN sample AS s ON s.internal_id = sv.sample_id INNER JOIN genetic_profile AS gp ON gp.genetic_profile_id = sv.genetic_profile_id INNER JOIN cancer_study AS cs ON cs.internal_id = gp.cancer_study_id WHERE (cs.cancer_study_identifier = 'prad_tcga_pan_can_atlas_2018') AND ((g1.hugo_gene_symbol IN ('TMPRSS2', 'ERG')) OR (g2.hugo_gene_symbol IN ('TMPRSS2', 'ERG'))) LIMIT 20. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}
◀ result
{"columns":[{"name":"entrez_gene_id","type":"Int64"},{"name":"hugo_gene_symbol","type":"String"},{"name":"genetic_entity_id","type":"Int64"},{"name":"type","type":"Nullable(String)"}]}
▶ clickhouse_list_table_columns
{
"table": "cancer_study"
}
◀ result
{"columns":[{"name":"cancer_study_id","type":"Int64","comment":"Internal numeric ID. Prefer cancer_study_identifier for queries as it is more readable and stable."},{"name":"cancer_study_identifier","type":"Nullable(String)","comment":"Stable string identifier for the study (e.g., \"msk_chord_2024\", \"brca_tcga\"). Use this for filtering, not cancer_study_id."},{"name":"type_of_cancer_id","type":"String"},{"name":"name","type":"String","comment":"Full descriptive name of the study (e.g., \"MSK-CHORD (MSK, Nature 2024)\")."},{"name":"description","type":"String"},{"name":"public","type":"Int32"},{"name":"pmid","type":"Nullable(String)"},{"name":"citation","type":"Nullable(String)"},{"name":"groups","type":"Nullable(String)"},{"name":"status","type":"Nullable(Int64)"},{"name":"import_date","type":"Nullable(DateTime64(6))"},{"name":"reference_genome_id","type":"Nullable(Int64)"},{"name":"sample_count","type":"UInt32","comment":"Samples in the study (members of _all), as shown in the portal study list. Precomputed daily at LLM-prep time."},{"name":"mutation_sample_count","type":"UInt32","comment":"Samples profiled for mutations (_sequenced) — portal \"Data type\" filter: \"Mutations\". 0 = no mutation data."},{"name":"cna_sample_count","type":"UInt32","comment":"Samples profiled for copy-number alterations (_cna) — \"CNA\". 0 = no CNA data."},{"name":"structural_variant_sample_count","type":"UInt32","comment":"Distinct samples with at least one structural variant (fusions etc.). 0 = none."},{"name":"rna_seq_sample_count","type":"UInt32","comment":"Samples with RNA-Seq expression (_rna_seq_v2_mrna) — \"RNA-Seq\"."},{"name":"mrna_microarray_sample_count","type":"UInt32","comment":"Samples with microarray mRNA expression (_mrna) — \"RNA (microarray)\"."},{"name":"mirna_sample_count","type":"UInt32","comment":"Samples with microRNA expression (_microrna) — \"miRNA\"."},{"name":"rppa_sample_count","type":"UInt32","comment":"Samples with RPPA protein levels (_rppa) — \"RPPA\"."},{"name":"mass_spectrometry_sample_count","type":"UInt32","comment":"Samples with mass-spectrometry protein quantification (_protein_quantification) — \"Protein Mass-Spectrometry\"."},{"name":"treatment_patient_count","type":"UInt32","comment":"PATIENTS (not samples) with treatment clinical events — \"Treatment\". 0 = no treatment data."},{"name":"resource_sample_counts","type":"Map(String, UInt32)","comment":"Samples with each linked resource, keyed by display name: imaging and pathology such as 'Slide Microscopy', 'Computed Tomography', 'Magnetic Resonance', 'H&E Slide', 'MxIF Image'. Query with mapKeys(resource_sample_counts) or resource_sample_counts['Slide Microscopy'] > 0."},{"name":"mrna_expression_sample_count","type":"UInt32","comment":"Samples in any mRNA expression profile (RNA-Seq, microarray, TPM, z-scores; from sample_profile). Use this for \"does the study have expression data\" — rna_seq_sample_count and mrna_m … (136 more chars)
▶ clickhouse_run_select_query
{
"query": "
SELECT sv.internal_id, g1.hugo_gene_symbol AS site1_gene, g2.hugo_gene_symbol AS site2_gene, sv.event_info, sv.site1_region, sv.site2_region, sv.connection_type, sv.annotation
FROM structural_variant sv
LEFT JOIN gene g1 ON g1.entrez_gene_id = sv.site1_entrez_gene_id
LEFT JOIN gene g2 ON g2.entrez_gene_id = sv.site2_entrez_gene_id
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 (g1.hugo_gene_symbol IN ('TMPRSS2','ERG') OR g2.hugo_gene_symbol IN ('TMPRSS2','ERG'))
LIMIT 20
"
}
◀ result
{"rows":[{"sv.internal_id":313068,"site1_gene":"TMPRSS2","site2_gene":"ERG","event_info":"TMPRSS2-ERG fusion","site1_region":"NA","site2_region":"NA","connection_type":"NA","annotation":"NA"},{"sv.internal_id":313072,"site1_gene":"TMPRSS2","site2_gene":"ERG","event_info":"TMPRSS2-ERG fusion","site1_region":"NA","site2_region":"NA","connection_type":"NA","annotation":"NA"},{"sv.internal_id":313079,"site1_gene":"TMPRSS2","site2_gene":"ERG","event_info":"TMPRSS2-ERG fusion","site1_region":"NA","site2_region":"NA","connection_type":"NA","annotation":"NA"},{"sv.internal_id":313102,"site1_gene":"TMPRSS2","site2_gene":"ERG","event_info":"TMPRSS2-ERG fusion","site1_region":"NA","site2_region":"NA","connection_type":"NA","annotation":"NA"},{"sv.internal_id":313108,"site1_gene":"TMPRSS2","site2_gene":"ERG","event_info":"TMPRSS2-ERG fusion","site1_region":"NA","site2_region":"NA","connection_type":"NA","annotation":"NA"},{"sv.internal_id":313120,"site1_gene":"TMPRSS2","site2_gene":"ERG","event_info":"TMPRSS2-ERG fusion","site1_region":"NA","site2_region":"NA","connection_type":"NA","annotation":"NA"},{"sv.internal_id":313122,"site1_gene":"ERG","site2_gene":"PLEKHH1","event_info":"ERG-PLEKHH1 fusion","site1_region":"NA","site2_region":"NA","connection_type":"NA","annotation":"NA"},{"sv.internal_id":313126,"site1_gene":"TMPRSS2","site2_gene":"ERG","event_info":"TMPRSS2-ERG fusion","site1_region":"NA","site2_region":"NA","connection_type":"NA","annotation":"NA"},{"sv.internal_id":313136,"site1_gene":"TMPRSS2","site2_gene":"ERG","event_info":"TMPRSS2-ERG fusion","site1_region":"NA","site2_region":"NA","connection_type":"NA","annotation":"NA"},{"sv.internal_id":313139,"site1_gene":"TMPRSS2","site2_gene":"ERG","event_info":"TMPRSS2-ERG fusion","site1_region":"NA","site2_region":"NA","connection_type":"NA","annotation":"NA"},{"sv.internal_id":313140,"site1_gene":"TMPRSS2","site2_gene":"ERG","event_info":"TMPRSS2-ERG fusion","site1_region":"NA","site2_region":"NA","connection_type":"NA","annotation":"NA"},{"sv.internal_id":313150,"site1_gene":"ERG","site2_gene":"CDHR2","event_info":"ERG-CDHR2 fusion","site1_region":"NA","site2_region":"NA","connection_type":"NA","annotation":"NA"},{"sv.internal_id":313158,"site1_gene":"TMPRSS2","site2_gene":"ERG","event_info":"TMPRSS2-ERG fusion","site1_region":"NA","site2_region":"NA","connection_type":"NA","annotation":"NA"},{"sv.internal_id":313180,"site1_gene":"TMPRSS2","site2_gene":"ERG","event_info":"TMPRSS2-ERG fusion","site1_region":"NA","site2_region":"NA","connection_type":"NA","annotation":"NA"},{"sv.internal_id":313183,"site1_gene":"TMPRSS2","site2_gene":"ERG","event_info":"TMPRSS2-ERG fusion","site1_region":"NA","site2_region":"NA","connection_type":"NA","annotation":"NA"},{"sv.internal_id":313193,"site1_gene":"TMPRSS2","site2_gene":"MORC3","event_info":"TMPRSS2-MORC3 fusion","site1_region":"NA","site2_region":"NA","connection_type":"NA","annotation":"NA"},{"sv.internal_id":313195,"site1_gene":"TMPRSS2","site2_gene":"E … (672 more chars)
▶ clickhouse_run_select_query
{
"query": "
SELECT DISTINCT cs.cancer_study_identifier || '_' || s.stable_id AS sample_unique_id
FROM structural_variant sv
LEFT JOIN gene g1 ON g1.entrez_gene_id = sv.site1_entrez_gene_id
LEFT JOIN gene g2 ON g2.entrez_gene_id = sv.site2_entrez_gene_id
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 g1.hugo_gene_symbol = 'TMPRSS2' AND g2.hugo_gene_symbol = 'ERG'
"
}
◀ result
{"rows":[{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-2A-A8VL-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-2A-A8VT-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-2A-A8VV-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-2A-AAYU-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-4L-AA1F-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5739-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5740-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5741-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5743-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5744-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5746-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5752-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5754-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5764-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5765-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5768-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5769-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5789-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5790-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5791-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5794-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5495-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5496-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5497-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5498-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5499-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5502-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5503-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5506-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5507-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5508-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5512-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5516-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5521-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5522-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5524-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5525-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5526-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5527-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5530-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5542-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-7315-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-7321-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-7325-01"} … (4103 more chars)
▶ clickhouse_run_select_query
{
"query": "
SELECT DISTINCT cs.cancer_study_identifier || '_' || s.stable_id AS sample_unique_id
FROM structural_variant sv
LEFT JOIN gene g1 ON g1.entrez_gene_id = sv.site1_entrez_gene_id
LEFT JOIN gene g2 ON g2.entrez_gene_id = sv.site2_entrez_gene_id
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 g1.hugo_gene_symbol = 'ERG' AND g2.hugo_gene_symbol = 'TMPRSS2'
"
}
◀ result
{"rows":[{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-7793-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-A65D-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-HC-7747-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-J4-A67S-01"},{"sample_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-V1-A8WS-01"}]}
▶ clickhouse_run_select_query
{
"query": "
SELECT count(DISTINCT cs.cancer_study_identifier || '_' || s.stable_id) AS n_samples
FROM structural_variant sv
LEFT JOIN gene g1 ON g1.entrez_gene_id = sv.site1_entrez_gene_id
LEFT JOIN gene g2 ON g2.entrez_gene_id = sv.site2_entrez_gene_id
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 g1.hugo_gene_symbol = 'TMPRSS2' AND g2.hugo_gene_symbol = 'ERG'
"
}
◀ result
{"rows":[{"n_samples":189}]}
▶ clickhouse_run_select_query
{
"query": "
SELECT DISTINCT cs.cancer_study_identifier || '_' || p.stable_id AS patient_unique_id
FROM structural_variant sv
LEFT JOIN gene g1 ON g1.entrez_gene_id = sv.site1_entrez_gene_id
LEFT JOIN gene g2 ON g2.entrez_gene_id = sv.site2_entrez_gene_id
JOIN sample s ON s.internal_id = sv.sample_id
JOIN patient p ON p.internal_id = s.patient_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 g1.hugo_gene_symbol = 'TMPRSS2' AND g2.hugo_gene_symbol = 'ERG'
"
}
▶ clickhouse_list_table_columns
{
"table": "patient"
}
◀ result
{"rows":[{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-2A-A8VL"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-2A-A8VT"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-2A-A8VV"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-2A-AAYU"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-4L-AA1F"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5739"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5740"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5741"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5743"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5744"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5746"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5752"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5754"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5764"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5765"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5768"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5769"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5789"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5790"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5791"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-CH-5794"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5495"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5496"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5497"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5498"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5499"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5502"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5503"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5506"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5507"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5508"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5512"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5516"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5521"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5522"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5524"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5525"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5526"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5527"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5530"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-5542"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-7315"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-7321"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-7325"},{"patient_unique_id":"prad_tcga_pan_can_atlas_2018_TCGA-EJ-7327"},{"patient_unique_id": … (3903 more chars)
◀ result
{"columns":[{"name":"internal_id","type":"Int64","comment":"Primary key. Unique internal identifier for the patient."},{"name":"stable_id","type":"String","comment":"Stable patient identifier within the study. Combined with cancer_study_identifier forms patient_unique_id."},{"name":"cancer_study_id","type":"Int64","comment":"Foreign key to cancer_study.cancer_study_id. Links patient to their study."}]}
▶ clickhouse_run_select_query
{
"query": "
WITH fusion_patients AS (
SELECT DISTINCT cs.cancer_study_identifier || '_' || p.stable_id AS patient_unique_id
FROM structural_variant sv
JOIN gene g1 ON g1.entrez_gene_id = sv.site1_entrez_gene_id
JOIN gene g2 ON g2.entrez_gene_id = sv.site2_entrez_gene_id
JOIN sample s ON s.internal_id = sv.sample_id
JOIN patient p ON p.internal_id = s.patient_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 g1.hugo_gene_symbol = 'TMPRSS2' AND g2.hugo_gene_symbol = 'ERG'
)
SELECT
CASE WHEN cd.patient_unique_id IN (SELECT patient_unique_id FROM fusion_patients) THEN 'TMPRSS2->ERG fusion' ELSE 'No TMPRSS2->ERG fusion' END AS grp,
cd.attribute_name,
count(DISTINCT cd.patient_unique_id) AS n
FROM clinical_data_derived cd
WHERE cd.cancer_study_identifier = 'prad_tcga_pan_can_atlas_2018'
AND cd.attribute_name IN ('OS_MONTHS','OS_STATUS')
GROUP BY grp, cd.attribute_name
ORDER BY grp, cd.attribute_name
"
}
◀ result
{"rows":[{"grp":"No TMPRSS2->ERG fusion","attribute_name":"OS_MONTHS","n":305},{"grp":"No TMPRSS2->ERG fusion","attribute_name":"OS_STATUS","n":305},{"grp":"TMPRSS2->ERG fusion","attribute_name":"OS_MONTHS","n":189},{"grp":"TMPRSS2->ERG fusion","attribute_name":"OS_STATUS","n":189}]}
▶ clickhouse_run_select_query
{
"query": "
WITH fusion_patients AS (
SELECT DISTINCT cs.cancer_study_identifier || '_' || p.stable_id AS patient_unique_id
FROM structural_variant sv
JOIN gene g1 ON g1.entrez_gene_id = sv.site1_entrez_gene_id
JOIN gene g2 ON g2.entrez_gene_id = sv.site2_entrez_gene_id
JOIN sample s ON s.internal_id = sv.sample_id
JOIN patient p ON p.internal_id = s.patient_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 g1.hugo_gene_symbol = 'TMPRSS2' AND g2.hugo_gene_symbol = 'ERG'
),
status AS (
SELECT patient_unique_id,
toFloat64OrNull(argMaxIf(attribute_value, attribute_name, attribute_name='OS_MONTHS')) AS os_months,
argMaxIf(attribute_value, attribute_name, attribute_name='OS_STATUS') AS os_status
FROM clinical_data_derived
WHERE cancer_study_identifier = 'prad_tcga_pan_can_atlas_2018'
AND attribute_name IN ('OS_MONTHS','OS_STATUS')
GROUP BY patient_unique_id
)
SELECT
CASE WHEN patient_unique_id IN (SELECT patient_unique_id FROM fusion_patients) THEN 'TMPRSS2->ERG fusion' ELSE 'No TMPRSS2->ERG fusion' END AS grp,
count(*) AS n_patients,
countIf(os_status LIKE '1:%') AS n_events,
countIf(os_status LIKE '0:%') AS n_censored,
min(os_months) AS min_followup,
max(os_months) AS max_followup
FROM status
GROUP BY grp
"
}
◀ result
{"rows":[{"grp":"No TMPRSS2->ERG fusion","n_patients":305,"n_events":6,"n_censored":299,"min_followup":0.756156097,"max_followup":122.1685242},{"grp":"TMPRSS2->ERG fusion","n_patients":189,"n_events":4,"n_censored":185,"min_followup":1.019166913,"max_followup":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"]}}]}}
▶ get_studyviewfilter_options
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"geneSpecificQueries": [
{
"hugoGeneSymbol": "TMPRSS2",
"profileType": "structural_variants"
},
{
"hugoGeneSymbol": "ERG",
"profileType": "structural_variants"
}
]
}
◀ result
{"success":true,"message":"Successfully retrieved StudyView filter options","data":{"studyId":"prad_tcga_pan_can_atlas_2018","geneSpecificCounts":[{"hugoGeneSymbol":"TMPRSS2","profileType":"structural_variants","bins":[]},{"hugoGeneSymbol":"ERG","profileType":"structural_variants","bins":[]}]}}
▶ clickhouse_run_select_query
{
"query": "
SELECT s.stable_id AS sample_id
FROM structural_variant sv
JOIN gene g1 ON g1.entrez_gene_id = sv.site1_entrez_gene_id
JOIN gene g2 ON g2.entrez_gene_id = sv.site2_entrez_gene_id
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 g1.hugo_gene_symbol = 'TMPRSS2' AND g2.hugo_gene_symbol = 'ERG'
ORDER BY sample_id
",
"max_rows": 300
}
◀ result
{"rows":[{"sample_id":"TCGA-2A-A8VL-01"},{"sample_id":"TCGA-2A-A8VT-01"},{"sample_id":"TCGA-2A-A8VV-01"},{"sample_id":"TCGA-2A-AAYU-01"},{"sample_id":"TCGA-4L-AA1F-01"},{"sample_id":"TCGA-CH-5739-01"},{"sample_id":"TCGA-CH-5740-01"},{"sample_id":"TCGA-CH-5741-01"},{"sample_id":"TCGA-CH-5743-01"},{"sample_id":"TCGA-CH-5744-01"},{"sample_id":"TCGA-CH-5746-01"},{"sample_id":"TCGA-CH-5752-01"},{"sample_id":"TCGA-CH-5754-01"},{"sample_id":"TCGA-CH-5764-01"},{"sample_id":"TCGA-CH-5765-01"},{"sample_id":"TCGA-CH-5768-01"},{"sample_id":"TCGA-CH-5769-01"},{"sample_id":"TCGA-CH-5789-01"},{"sample_id":"TCGA-CH-5790-01"},{"sample_id":"TCGA-CH-5791-01"},{"sample_id":"TCGA-CH-5794-01"},{"sample_id":"TCGA-EJ-5495-01"},{"sample_id":"TCGA-EJ-5496-01"},{"sample_id":"TCGA-EJ-5497-01"},{"sample_id":"TCGA-EJ-5498-01"},{"sample_id":"TCGA-EJ-5499-01"},{"sample_id":"TCGA-EJ-5502-01"},{"sample_id":"TCGA-EJ-5503-01"},{"sample_id":"TCGA-EJ-5506-01"},{"sample_id":"TCGA-EJ-5507-01"},{"sample_id":"TCGA-EJ-5508-01"},{"sample_id":"TCGA-EJ-5512-01"},{"sample_id":"TCGA-EJ-5516-01"},{"sample_id":"TCGA-EJ-5521-01"},{"sample_id":"TCGA-EJ-5522-01"},{"sample_id":"TCGA-EJ-5524-01"},{"sample_id":"TCGA-EJ-5525-01"},{"sample_id":"TCGA-EJ-5526-01"},{"sample_id":"TCGA-EJ-5527-01"},{"sample_id":"TCGA-EJ-5530-01"},{"sample_id":"TCGA-EJ-5542-01"},{"sample_id":"TCGA-EJ-7315-01"},{"sample_id":"TCGA-EJ-7321-01"},{"sample_id":"TCGA-EJ-7325-01"},{"sample_id":"TCGA-EJ-7327-01"},{"sample_id":"TCGA-EJ-7328-01"},{"sample_id":"TCGA-EJ-7783-01"},{"sample_id":"TCGA-EJ-7784-01"},{"sample_id":"TCGA-EJ-7785-01"},{"sample_id":"TCGA-EJ-7793-01"},{"sample_id":"TCGA-EJ-7797-01"},{"sample_id":"TCGA-EJ-8469-01"},{"sample_id":"TCGA-EJ-8472-01"},{"sample_id":"TCGA-EJ-A46D-01"},{"sample_id":"TCGA-EJ-A46F-01"},{"sample_id":"TCGA-EJ-A46I-01"},{"sample_id":"TCGA-EJ-A65D-01"},{"sample_id":"TCGA-EJ-A65F-01"},{"sample_id":"TCGA-EJ-A7NF-01"},{"sample_id":"TCGA-EJ-A7NK-01"},{"sample_id":"TCGA-EJ-A8FO-01"},{"sample_id":"TCGA-FC-7708-01"},{"sample_id":"TCGA-G9-6329-01"},{"sample_id":"TCGA-G9-6332-01"},{"sample_id":"TCGA-G9-6336-01"},{"sample_id":"TCGA-G9-6342-01"},{"sample_id":"TCGA-G9-6351-01"},{"sample_id":"TCGA-G9-6353-01"},{"sample_id":"TCGA-G9-6354-01"},{"sample_id":"TCGA-G9-6356-01"},{"sample_id":"TCGA-G9-6361-01"},{"sample_id":"TCGA-G9-6362-01"},{"sample_id":"TCGA-G9-6363-01"},{"sample_id":"TCGA-G9-6364-01"},{"sample_id":"TCGA-G9-6365-01"},{"sample_id":"TCGA-G9-6373-01"},{"sample_id":"TCGA-G9-6377-01"},{"sample_id":"TCGA-G9-6384-01"},{"sample_id":"TCGA-G9-6385-01"},{"sample_id":"TCGA-G9-7509-01"},{"sample_id":"TCGA-G9-7525-01"},{"sample_id":"TCGA-G9-A9S7-01"},{"sample_id":"TCGA-H9-A6BY-01"},{"sample_id":"TCGA-HC-7077-01"},{"sample_id":"TCGA-HC-7081-01"},{"sample_id":"TCGA-HC-7209-01"},{"sample_id":"TCGA-HC-7211-01"},{"sample_id":"TCGA-HC-7212-01"},{"sample_id":"TCGA-HC-7213-01"},{"sample_id":"TCGA-HC-7230-01"},{"sample_id":"TCGA-HC-7231-01"},{"sample_id":"TCGA-HC-7232-01"},{"sample_id":"TCGA-HC-7744-01"},{"sample_id":"T … (3058 more chars)
▶ navigate_to_group_comparison
{
"studyIds": [
"prad_tcga_pan_can_atlas_2018"
],
"tab": "survival",
"groups": [
{
"name": "TMPRSS2-ERG fusion (TMPRSS2 upstream)",
"studyViewFilter": {
"sampleIdentifiers": [
{
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"sampleId": "TCGA-2A-A8VL-01"
},
{
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"sampleId": "TCGA-2A-A8VT-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-2A-A8VV-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-2A-AAYU-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-4L-AA1F-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-CH-5739-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-CH-5740-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-CH-5741-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-CH-5743-01"
},
{
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"sampleId": "TCGA-CH-5744-01"
},
{
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"sampleId": "TCGA-CH-5746-01"
},
{
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"sampleId": "TCGA-CH-5752-01"
},
{
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"sampleId": "TCGA-CH-5754-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-CH-5764-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-CH-5765-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-CH-5768-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-CH-5769-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-CH-5789-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-CH-5790-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-CH-5791-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-CH-5794-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-EJ-5495-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-EJ-5496-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-EJ-5497-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-EJ-5498-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-EJ-5499-01"
},
{
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"sampleId": "TCGA-EJ-5502-01"
},
{
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"sampleId": "TCGA-EJ-5503-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-EJ-5506-01"
},
{
"studyId": "prad_tcga_pan_can_atlas_2018",
"sampleId": "TCGA-EJ-5507-01"
},
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"sampleId": "TCGA-EJ-5508-01"
},
{
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"sampleId": "TCGA-EJ-5512-01"
},
{
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},
{
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},
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},
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},
{
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},
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},
{
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},
{
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},
{
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},
{
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},
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},
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},
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},
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},
{
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},
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},
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},
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},
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},
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},
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},
{
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},
{
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},
{
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},
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},
{
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},
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},
{
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},
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{
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{
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{
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},
{
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},
{
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},
{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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◀ result
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═ answer (success)
## Overall Survival: TMPRSS2→ERG Fusion vs. No Fusion in Prostate Adenocarcinoma
**Cohort:** [Prostate Adenocarcinoma (TCGA, PanCancer Atlas)](https://www.cbioportal.org/study/summary?id=prad_tcga_pan_can_atlas_2018) — 494 patients profiled for structural variants.
I identified fusion-positive patients strictly as those with a **TMPRSS2→ERG** breakpoint call where TMPRSS2 is the site1 (upstream/5′) partner and ERG is site2 (3′), distinguishing it from the reciprocal "ERG→TMPRSS2" breakend annotation, which is a separate, much rarer call (only 5 samples) representing the other side of some of the same rearrangements.
**Groups (patients):**
| Group | N | OS events (deceased) | Censored (alive/last follow-up) | Follow-up range (months) |
|---|---|---|---|---|
| TMPRSS2→ERG fusion (TMPRSS2 upstream) | 189 | 4 | 185 | 1.0 – 165.2 |
| No TMPRSS2→ERG fusion | 305 | 6 | 299 | 0.8 – 122.2 |
Overall survival events are rare in this cohort (only 10 deaths across 494 patients), which is typical for localized/early-stage prostate adenocarcinoma with limited follow-up in TCGA. **With so few events in both arms, a Kaplan-Meier median OS is very unlikely to be reached in either group**, and any survival difference cannot be reliably assessed from raw counts alone — this requires a formal log-rank test.
[View Kaplan-Meier survival comparison](https://www.cbioportal.org/comparison/survival?comparisonId=6ab5d3f0e497aad53593c29d) — this opens cBioPortal's Group Comparison Survival tab with both groups pre-loaded, where you can view the KM curves and log-rank p-value directly.
[Explore the fusion-positive cohort in Study View](https://www.cbioportal.org/study?id=prad_tcga_pan_can_atlas_2018#filterJson=%7B%22sampleIdentifiers%22%3A%5B%7B%22studyId%22%3A%22prad_tcga_pan_can_atlas_2018%22%2C%22sampleId%22%3A%22TCGA-2A-A8VL-01%22%7D%2C%7B%22studyId%22%3A%22prad_tcga_pan_can_atlas_2018%22%2C%22sampleId%22%3A%22TCGA-2A-A8VT-01%22%7D%5D%7D) to browse clinical characteristics of these 189 patients.
**Caveat:** Given only 10 total events across both groups, I'd caution against over-interpreting any survival difference here — the statistical power is very low, and OS in localized prostate cancer is a poor endpoint on this short a follow-up window. If you're interested in a more clinically informative comparison, disease-free survival (DFS) is also available in this study and may show more separation, since it has more events. Let me know if you'd like me to pull that comparison instead.