Q (sonnet-5.5): What treatment did most patients receive in the MSK-CHORD Study? ▶ read_guide { "uri": "cbioportal://treatment-guide" } ▶ list_studies { "search": "MSK-CHORD" } ◀ result # Treatment Data Query Guide ## Overview Treatment data in cBioPortal is stored in **clinical event tables**, separate from clinical attributes. This allows for timeline-based treatment records with start/stop dates. ## Start Here: Treatment Views For "most common treatments / agents / regimens in study X", use the parameterized views (documented in `cbioportal://clinical-data-guide`, Study-View Chart Counts): ```sql -- Patients per agent (the portal's Treatment chart), with type/subtype arrays SELECT * FROM treatment_counts_in_study(study='msk_chord_2024') ORDER BY patients DESC LIMIT 20; -- Same-day agent combinations (investigational, prior-medication and radiation events excluded) SELECT * FROM treatment_regimens_in_study(study='msk_chord_2024') ORDER BY patients DESC LIMIT 20; ``` Write raw event queries (below) only for subgroups, timelines or keys the views do not expose. ## Key Tables | Table | Description | |-------|-------------| | `clinical_event` | Event records with patient_id, event_type, start_date, stop_date | | `clinical_event_data` | Key-value pairs linked to each clinical_event_id | ## Schema ``` clinical_event ├── clinical_event_id (PK) ├── patient_id (FK → patient.internal_id) ├── event_type (Treatment, TREATMENT, Diagnosis, SURGERY, etc.) ├── start_date (days from diagnosis) └── stop_date (days from diagnosis) clinical_event_data ├── clinical_event_id (FK) ├── key (AGENT, SUBTYPE, etc.) └── value ``` ## Event Types Not all studies have all event types. Common ones include: | Event Type | Description | |------------|-------------| | `Treatment` / `TREATMENT` | Drug/therapy administration | | `SURGERY` | Surgical procedures | | `Diagnosis` | Diagnosis events | | `LAB_TEST` | Laboratory results | | `Sequencing` | Sequencing events | | `Sample acquisition` | Sample collection | | `PATHOLOGY` / `Pathology` | Pathology reports | ## Basic *** Queries ### List Available Event Types in a Study ```sql SELECT DISTINCT ce.event_type, COUNT(*) as event_count FROM clinical_event ce JOIN patient p ON ce.patient_id = p.internal_id JOIN cancer_study cs ON p.cancer_study_id = cs.cancer_study_id WHERE cs.cancer_study_identifier = 'your_study_id' GROUP BY ce.event_type ORDER BY event_count DESC; ``` ### List Treatment Data Keys in a Study ```sql SELECT DISTINCT ced.key, COUNT(*) as cnt FROM clinical_event ce JOIN clinical_event_data ced ON ce.clinical_event_id = ced.clinical_event_id JOIN patient p ON ce.patient_id = p.internal_id JOIN cancer_study cs ON p.cancer_study_id = cs.cancer_study_id WHERE cs.cancer_study_identifier = 'your_study_id' AND ce.event_type IN ('Treatment', 'TREATMENT') GROUP BY ced.key ORDER BY cnt DESC; ``` ### Get Most Common Treatment Agents ```sql SELECT ced.value as agent, COUNT(DISTINCT ce.patient_id) as patient_count FROM clinical_event ce JOIN clinical_event_data ced ON ce.clinical_event_id = ced.clinical_event_id JOIN patient p ON ce.patient_id = p.internal_id JOIN cancer_stud … (6220 more chars) ◀ result {"result":[{"cancer_study_identifier":"msk_chord_2024","name":"MSK-CHORD (MSK, Nature 2024)","type_of_cancer_id":"mixed","sample_count":25040,"has_guide":true,"url":"https://www.cbioportal.org/study/summary?id=msk_chord_2024"}]} ▶ run_select_query { "query": "SELECT * FROM treatment_counts_in_study(study='msk_chord_2024') ORDER BY patients DESC LIMIT 15" } ✗ error Error: No such tool available: mcp__claude_ai_cBioPortal_MCP__run_select_query ▶ run_select_query { "query": "SELECT * FROM treatment_regimens_in_study(study='msk_chord_2024') ORDER BY patients DESC LIMIT 10" } ✗ error Error: No such tool available: mcp__claude_ai_cBioPortal_MCP__run_select_query ▶ clickhouse_run_select_query { "query": "SELECT * FROM treatment_counts_in_study(study='msk_chord_2024') ORDER BY patients DESC LIMIT 15" } ▶ clickhouse_run_select_query { "query": "SELECT * FROM treatment_regimens_in_study(study='msk_chord_2024') ORDER BY patients DESC LIMIT 10" } ◀ result {"rows":[{"agent":"FLUOROURACIL","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":6319,"treated_patients":21473,"pct_of_treated_patients":29.4},{"agent":"LEUCOVORIN","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":5573,"treated_patients":21473,"pct_of_treated_patients":26},{"agent":"OXALIPLATIN","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":5489,"treated_patients":21473,"pct_of_treated_patients":25.6},{"agent":"CAPECITABINE","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":4808,"treated_patients":21473,"pct_of_treated_patients":22.4},{"agent":"CARBOPLATIN","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":4604,"treated_patients":21473,"pct_of_treated_patients":21.4},{"agent":"IRINOTECAN","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":4329,"treated_patients":21473,"pct_of_treated_patients":20.2},{"agent":"INVESTIGATIONAL","treatment_types":[],"treatment_subtypes":["Investigational"],"patients":4114,"treated_patients":21473,"pct_of_treated_patients":19.2},{"agent":"GEMCITABINE","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":4038,"treated_patients":21473,"pct_of_treated_patients":18.8},{"agent":"LEUPROLIDE","treatment_types":[],"treatment_subtypes":["Hormone"],"patients":3708,"treated_patients":21473,"pct_of_treated_patients":17.3},{"agent":"PACLITAXEL","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":3679,"treated_patients":21473,"pct_of_treated_patients":17.1},{"agent":"PEMETREXED","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":3357,"treated_patients":21473,"pct_of_treated_patients":15.6},{"agent":"BEVACIZUMAB","treatment_types":[],"treatment_subtypes":["Biologic"],"patients":2629,"treated_patients":21473,"pct_of_treated_patients":12.2},{"agent":"CYCLOPHOSPHAMIDE","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":2494,"treated_patients":21473,"pct_of_treated_patients":11.6},{"agent":"PACLITAXEL PROTEIN-BOUND","treatment_types":[],"treatment_subtypes":["Chemo"],"patients":2357,"treated_patients":21473,"pct_of_treated_patients":11},{"agent":"LETROZOLE","treatment_types":[],"treatment_subtypes":["Hormone"],"patients":2260,"treated_patients":21473,"pct_of_treated_patients":10.5}]} ◀ result {"rows":[{"regimen":"CAPECITABINE","n_agents":1,"patients":4434,"treated_patients":21224,"pct_of_treated_patients":20.9},{"regimen":"FLUOROURACIL + LEUCOVORIN + OXALIPLATIN","n_agents":3,"patients":2974,"treated_patients":21224,"pct_of_treated_patients":14},{"regimen":"LEUPROLIDE","n_agents":1,"patients":2846,"treated_patients":21224,"pct_of_treated_patients":13.4},{"regimen":"PACLITAXEL","n_agents":1,"patients":2279,"treated_patients":21224,"pct_of_treated_patients":10.7},{"regimen":"GEMCITABINE","n_agents":1,"patients":2038,"treated_patients":21224,"pct_of_treated_patients":9.6},{"regimen":"ZOLEDRONIC ACID","n_agents":1,"patients":1902,"treated_patients":21224,"pct_of_treated_patients":9},{"regimen":"LETROZOLE","n_agents":1,"patients":1700,"treated_patients":21224,"pct_of_treated_patients":8},{"regimen":"IRINOTECAN","n_agents":1,"patients":1624,"treated_patients":21224,"pct_of_treated_patients":7.7},{"regimen":"CYCLOPHOSPHAMIDE + DOXORUBICIN","n_agents":2,"patients":1612,"treated_patients":21224,"pct_of_treated_patients":7.6},{"regimen":"ANASTROZOLE","n_agents":1,"patients":1519,"treated_patients":21224,"pct_of_treated_patients":7.2}]} ▶ resolve_and_route { "studyIds": [ "msk_chord_2024" ] } ◀ result {"success":true,"message":"Found 1 study. Use the metadata to call the appropriate navigation tool(s).","data":{"totalCount":1,"studiesWithMetadata":[{"studyId":"msk_chord_2024","name":"MSK-CHORD (MSK, Nature 2024)","sampleCount":25040,"studyViewUrl":"https://www.cbioportal.org/study?id=msk_chord_2024","metadata":{"clinicalAttributeIds":["ADRENAL_GLANDS","BONE","CANCER_TYPE","CANCER_TYPE_DETAILED","CLINICAL_GROUP","CLINICAL_SUMMARY","CNS_BRAIN","CURRENT_AGE_DEID","DIAGNOSIS_DESCRIPTION","ETHNICITY","FRACTION_GENOME_ALTERED","GENDER","GENE_PANEL","GLEASON_FIRST_REPORTED","GLEASON_HIGHEST_REPORTED","GLEASON_SAMPLE_LEVEL","HER2","HISTORY_OF_PDL1","HR","ICD_O_HISTOLOGY_DESCRIPTION","INTRA_ABDOMINAL","LIVER","LUNG","LYMPH_NODES","METASTATIC_SITE","MSI_COMMENT","MSI_SCORE","MSI_TYPE","MUTATION_COUNT","NUM_ICDO_DX","ONCOTREE_CODE","OS_MONTHS","OS_STATUS","OTHER","PATHOLOGICAL_GROUP","PDL1_POSITIVE","PLEURA","PRIMARY_SITE","PRIOR_MED_TO_MSK","RACE","REPRODUCTIVE_ORGANS","SAMPLE_CLASS","SAMPLE_COUNT","SAMPLE_COVERAGE","SAMPLE_TYPE","SMOKING_PREDICTIONS_3_CLASSES","SOMATIC_STATUS","STAGE_HIGHEST_RECORDED","TMB_NONSYNONYMOUS","TUMOR_PURITY"],"molecularProfileIds":["msk_chord_2024_cna","msk_chord_2024_mutations","msk_chord_2024_structural_variants"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations"]}}]}} ▶ navigate_to_study_view { "studyIds": [ "msk_chord_2024" ] } ◀ result {"success":true,"message":"Navigating to https://www.cbioportal.org/study/summary?id=msk_chord_2024","url":"https://www.cbioportal.org/study/summary?id=msk_chord_2024","data":{"studyIds":["msk_chord_2024"],"studies":[{"studyId":"msk_chord_2024","name":"MSK-CHORD (MSK, Nature 2024)","sampleCount":25040}],"tab":"summary","hasFilters":false,"hasPlotsConfig":false,"pageDescription":"Overview of all study data displayed as interactive charts summarizing available clinical and genomic data. Click within a chart to filter. Additional charts may be available in the Charts menu."}} ═ answer (success) In the MSK-CHORD study (MSK, Nature 2024), the treatment given to the most patients was **fluorouracil (5-FU)**, a chemotherapy, with **6,319 patients**. **Most common single agents** (number of patients who received each): | Rank | Agent | Category | Patients | |---|---|---|---| | 1 | Fluorouracil | Chemo | 6,319 | | 2 | Leucovorin | Chemo | 5,573 | | 3 | Oxaliplatin | Chemo | 5,489 | | 4 | Capecitabine | Chemo | 4,808 | | 5 | Carboplatin | Chemo | 4,604 | | 6 | Irinotecan | Chemo | 4,329 | | 7 | Investigational agents | Investigational | 4,114 | | 8 | Gemcitabine | Chemo | 4,038 | | 9 | Leuprolide | Hormone | 3,708 | | 10 | Paclitaxel | Chemo | 3,679 | Chemotherapy makes up most of the top agents. Leuprolide and letrozole (hormone therapies) and bevacizumab (a biologic) also appear in the top 15. **Most common regimens**, meaning agents given on the same day: - Capecitabine alone was the most common, with 4,434 patients. - Fluorouracil + leucovorin + oxaliplatin (the FOLFOX combination) was next, with 2,974 patients. - Leuprolide alone followed, with 2,846 patients. I've reported raw patient counts only. The data can't separate patients who received no treatment from patients whose treatment wasn't recorded, so percentages of the whole cohort would be unreliable. Each patient can also appear under several agents. [Open the MSK-CHORD study in cBioPortal](https://www.cbioportal.org/study/summary?id=msk_chord_2024)