Q (sonnet): <conversation_so_far>
<user>
Show me an OncoPrint of KRAS, TP53 and CDKN2A in TCGA pancreatic cancer.
</user>

<assistant>
Here is the OncoPrint for KRAS, TP53 and CDKN2A in Pancreatic Adenocarcinoma (TCGA, PanCancer Atlas):
[Open OncoPrint](https://www.cbioportal.org/results/oncoprint?cancer_study_list=paad_tcga_pan_can_atlas_2018&gene_list=KRAS%20TP53%20CDKN2A)
</assistant>
</conversation_so_far>

Continue this conversation: reply to the user's new message.

<user>
can you do the same for lung adenocarcinoma?
</user>

▶ resolve_and_route
{
 "studyKeywords": [
  "TCGA",
  "lung",
  "adenocarcinoma"
 ]
}

◀ 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": [
  "KRAS",
  "TP53",
  "CDKN2A"
 ],
 "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=KRAS%0ATP53%0ACDKN2A&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=KRAS%0ATP53%0ACDKN2A&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":["KRAS","TP53","CDKN2A"],"caseSetId":"luad_tcga_pan_can_atlas_2018_all","pageDescription":"Visual summary of alterations in queried genes across samples."}}

═ answer (success)
Here is the OncoPrint for KRAS, TP53, and CDKN2A in Lung Adenocarcinoma (TCGA, PanCancer Atlas), 566 samples:

[Open OncoPrint](https://www.cbioportal.org/results/oncoprint?cancer_study_list=luad_tcga_pan_can_atlas_2018&gene_list=KRAS%0ATP53%0ACDKN2A&case_set_id=luad_tcga_pan_can_atlas_2018_all)

Visual summary of alterations in the three queried genes across samples. Note other Lung Adenocarcinoma TCGA cohorts exist (Firehose Legacy, GDC 2025, Nature 2014) if you'd prefer a different version.