Q (sonnet): Give me an OncoPrint for RTK genes in lung cancer, limited to driver events. ▶ resolve_and_route { "studyKeywords": [ "lung", "adenocarcinoma", "TCGA" ] } ◀ result {"success":true,"message":"Found 4 matching studies. Pick the best match (prefer TCGA → prefer PanCancer Atlas), use its metadata to call the appropriate navigation tool(s) and generate URLs immediately. Present other studies as alternatives.","data":{"totalCount":4,"studiesWithMetadata":[{"studyId":"luad_tcga","name":"Lung Adenocarcinoma (TCGA, Firehose Legacy)","sampleCount":586,"studyViewUrl":"https://www.cbioportal.org/study?id=luad_tcga","metadata":{"clinicalAttributeIds":["AGE","AJCC_CLINICAL_TUMOR_STAGE","AJCC_METASTASIS_CLINICAL_CM","AJCC_METASTASIS_PATHOLOGIC_PM","AJCC_NODES_CLINICAL_CN","AJCC_NODES_CLINICAL_CT","AJCC_NODES_PATHOLOGIC_PN","AJCC_PATHOLOGIC_TUMOR_STAGE","AJCC_STAGING_EDITION","AJCC_TUMOR_PATHOLOGIC_PT","ALK_ANALYSIS_TYPE","ALK_TRANSLOCATION_STATUS","ALK_TRANSLOCATION_VARIANT","CANCER_TYPE","CANCER_TYPE_DETAILED","CARBON_MONOXIDE_DIFFUSION_DLCO","DAYS_TO_COLLECTION","DAYS_TO_INITIAL_PATHOLOGIC_DIAGNOSIS","DAYS_TO_PATIENT_PROGRESSION_FREE","DAYS_TO_SPECIMEN_COLLECTION","DAYS_TO_TUMOR_PROGRESSION","DFS_MONTHS","DFS_STATUS","DISEASE_CODE","ECOG_SCORE","ETHNICITY","EXTRANODAL_INVOLVEMENT","FEV1_FVC_RATIO_POSTBRONCHOLIATOR","FEV1_FVC_RATIO_PREBRONCHOLIATOR","FEV1_PERCENT_REF_POSTBRONCHOLIATOR","FEV1_PERCENT_REF_PREBRONCHOLIATOR","FORM_COMPLETION_DATE","FRACTION_GENOME_ALTERED","HISTOLOGICAL_DIAGNOSIS","HISTORY_IMMUNOLOGICAL_DISEASE","HISTORY_IMMUNOLOGICAL_DISEASE_OTHER","HISTORY_NEOADJUVANT_TRTYN","HISTORY_OTHER_MALIGNANCY","HISTORY_RELEVANT_INFECTIOUS_DX","HIV_STATUS","ICD_10","ICD_O_3_HISTOLOGY","ICD_O_3_SITE","INFORMED_CONSENT_VERIFIED","INITIAL_PATHOLOGIC_DX_YEAR","IS_FFPE","KARNOFSKY_PERFORMANCE_SCORE","KRAS_GENE_ANALYSIS_INDICATOR","KRAS_MUTATION","KRAS_MUTATION_IDENTIFIED_TYPE","LATERALITY","LOCATION_LUNG_PARENCHYMA","LONGEST_DIMENSION","METHOD_OF_INITIAL_SAMPLE_PROCUREMENT","METHOD_OF_INITIAL_SAMPLE_PROCUREMENT_OTHER","METHOD_OF_SAMPLE_PROCUREMENT","MUTATION_COUNT","MUTATION_STATUS","MUTATION_TYPE","NEW_TUMOR_EVENT_AFTER_INITIAL_TREATMENT","NUMBER_OF_LYMPHNODES_POSITIVE_BY_IHC","OCT_EMBEDDED","ONCOTREE_CODE","OS_MONTHS","OS_STATUS","OTHER_METHOD_OF_SAMPLE_PROCUREMENT","OTHER_PATIENT_ID","OTHER_SAMPLE_ID","PATHOLOGY_REPORT_FILE_NAME","PATHOLOGY_REPORT_UUID","PERFORMANCE_STATUS_TIMING","PHARMACEUTICAL_TX_ADJUVANT","POS_LYMPH_NODE_LOCATION","PRIMARY_SITE_OTHER","PRIMARY_SITE_PATIENT","PROJECT_CODE","PROSPECTIVE_COLLECTION","PULMONARY_FUNCTION_TEST_INDICATOR","RACE","RADIATION_TREATMENT_ADJUVANT","RESIDUAL_TUMOR","RETROSPECTIVE_COLLECTION","SAMPLE_COUNT","SAMPLE_INITIAL_WEIGHT","SAMPLE_TYPE","SAMPLE_TYPE_ID","SEX","SHORTEST_DIMENSION","SMOKING_PACK_YEARS","SMOKING_YEAR_STARTED","SMOKING_YEAR_STOPPED","SOMATIC_STATUS","SPECIMEN_CURRENT_WEIGHT","SPECIMEN_FREEZING_METHOD","SPECIMEN_SECOND_LONGEST_DIMENSION","STAGE_OTHER","TARGETED_MOLECULAR_THERAPY","TIME_BETWEEN_CLAMPING_AND_FREEZING","TIME_BETWEEN_EXCISION_AND_FREEZING","TISSUE_SOURCE_SITE","TMB_NONSYNONYMOUS","TOBACCO_SMOKING_HISTORY_INDICATOR","TREATMENT_OUTCOME_FIRST_COURS … (6466 more chars) ▶ navigate_to_results_view { "studyIds": [ "luad_tcga_pan_can_atlas_2018" ], "genes": [ "EGFR: MUT_DRIVER AMP_DRIVER", "ALK: MUT_DRIVER AMP_DRIVER", "MET: MUT_DRIVER AMP_DRIVER", "ERBB2: MUT_DRIVER AMP_DRIVER", "FGFR1: MUT_DRIVER AMP_DRIVER", "RET: MUT_DRIVER AMP_DRIVER", "ROS1: MUT_DRIVER AMP_DRIVER", "KIT: MUT_DRIVER AMP_DRIVER", "PDGFRA: MUT_DRIVER AMP_DRIVER", "NTRK1: MUT_DRIVER AMP_DRIVER" ], "tab": "oncoprint" } ◀ result {"success":true,"message":"Navigating to https://www.cbioportal.org/results/oncoprint?cancer_study_list=luad_tcga_pan_can_atlas_2018&gene_list=EGFR%3A+MUT_DRIVER+AMP_DRIVER%0AALK%3A+MUT_DRIVER+AMP_DRIVER%0AMET%3A+MUT_DRIVER+AMP_DRIVER%0AERBB2%3A+MUT_DRIVER+AMP_DRIVER%0AFGFR1%3A+MUT_DRIVER+AMP_DRIVER%0ARET%3A+MUT_DRIVER+AMP_DRIVER%0AROS1%3A+MUT_DRIVER+AMP_DRIVER%0AKIT%3A+MUT_DRIVER+AMP_DRIVER%0APDGFRA%3A+MUT_DRIVER+AMP_DRIVER%0ANTRK1%3A+MUT_DRIVER+AMP_DRIVER&case_set_id=luad_tcga_pan_can_atlas_2018_all","url":"https://www.cbioportal.org/results/oncoprint?cancer_study_list=luad_tcga_pan_can_atlas_2018&gene_list=EGFR%3A+MUT_DRIVER+AMP_DRIVER%0AALK%3A+MUT_DRIVER+AMP_DRIVER%0AMET%3A+MUT_DRIVER+AMP_DRIVER%0AERBB2%3A+MUT_DRIVER+AMP_DRIVER%0AFGFR1%3A+MUT_DRIVER+AMP_DRIVER%0ARET%3A+MUT_DRIVER+AMP_DRIVER%0AROS1%3A+MUT_DRIVER+AMP_DRIVER%0AKIT%3A+MUT_DRIVER+AMP_DRIVER%0APDGFRA%3A+MUT_DRIVER+AMP_DRIVER%0ANTRK1%3A+MUT_DRIVER+AMP_DRIVER&case_set_id=luad_tcga_pan_can_atlas_2018_all","data":{"studyIds":["luad_tcga_pan_can_atlas_2018"],"studies":[{"studyId":"luad_tcga_pan_can_atlas_2018","name":"Lung Adenocarcinoma (TCGA, PanCancer Atlas)","sampleCount":566}],"genes":["EGFR","ALK","MET","ERBB2","FGFR1","RET","ROS1","KIT","PDGFRA","NTRK1"],"caseSetId":"luad_tcga_pan_can_atlas_2018_all","pageDescription":"Visual summary of alterations in queried genes across samples."}} ═ answer (success) Here's the OncoPrint: **[RTK gene alterations, driver events only — Lung Adenocarcinoma (TCGA, PanCancer Atlas)](https://www.cbioportal.org/results/oncoprint?cancer_study_list=luad_tcga_pan_can_atlas_2018&gene_list=EGFR%3A+MUT_DRIVER+AMP_DRIVER%0AALK%3A+MUT_DRIVER+AMP_DRIVER%0AMET%3A+MUT_DRIVER+AMP_DRIVER%0AERBB2%3A+MUT_DRIVER+AMP_DRIVER%0AFGFR1%3A+MUT_DRIVER+AMP_DRIVER%0ARET%3A+MUT_DRIVER+AMP_DRIVER%0AROS1%3A+MUT_DRIVER+AMP_DRIVER%0AKIT%3A+MUT_DRIVER+AMP_DRIVER%0APDGFRA%3A+MUT_DRIVER+AMP_DRIVER%0ANTRK1%3A+MUT_DRIVER+AMP_DRIVER&case_set_id=luad_tcga_pan_can_atlas_2018_all) *Visual summary of alterations in queried genes across samples.* **Notes on setup:** - **Cohort:** Lung Adenocarcinoma (TCGA, PanCancer Atlas) — 566 samples. "Lung cancer" matches several cohorts (this LUAD PanCancer Atlas set, plus older LUAD releases and separate lung squamous cell carcinoma studies); I defaulted to the PanCancer Atlas LUAD cohort since it has the most complete driver annotations. Let me know if you'd like lung squamous cell carcinoma (LUSC) instead, or both combined. - **Genes:** Core receptor tyrosine kinase (RTK) panel relevant to lung adenocarcinoma — EGFR, ALK, MET, ERBB2 (HER2), FGFR1, RET, ROS1, KIT, PDGFRA, NTRK1. If you had a different/narrower RTK gene list in mind, tell me and I'll adjust. - **Driver restriction:** Query uses `MUT_DRIVER` and `AMP_DRIVER` OQL modifiers, so only mutations and amplifications flagged as drivers (OncoKB/CIViC-based annotation in cBioPortal) are shown — non-driver passenger mutations and non-driver amplifications are excluded from the oncoprint. Would you like me to also add a Study View link filtered to samples altered in any of these RTK genes, for cohort-level exploration?