cBioPortal MCP Server

# serializer version: 1 # name: test_get_cancer_studies_snapshot dict({ 'pagination': dict({ 'has_more': True, 'page': 0, 'page_size': 2, 'total_found': 2, }), 'studies': list([ dict({ 'allSampleCount': 92, 'cancerTypeId': 'acc', 'citation': 'Cancer Genome Atlas Research Network. (2018). The Immune Landscape of Cancer. Immunity, 48(4).', 'cnaSampleCount': 90, 'description': 'TCGA PanCanAtlas ACC', 'groups': 'PANCANCER;PANCAN', 'importDate': '2018-04-10 00:00:00', 'massSpectrometrySampleCount': 0, 'methylationHm27SampleCount': 0, 'miRnaSampleCount': 0, 'mrnaMicroarraySampleCount': 0, 'mrnaRnaSeqSampleCount': 79, 'mrnaRnaSeqV2SampleCount': 0, 'name': 'Adrenocortical Carcinoma (TCGA, PanCancer Atlas)', 'pmid': '29622464', 'publicStudy': True, 'referenceGenome': 'hg19', 'rppaSampleCount': 0, 'sequencedSampleCount': 90, 'status': 0, 'studyId': 'acc_tcga', 'svSampleCount': 0, }), dict({ 'allSampleCount': 131, 'cancerTypeId': 'blca', 'citation': 'Rosenberg et al. Nat Genet 2014', 'cnaSampleCount': 130, 'description': 'Comprehensive molecular characterization of urothelial bladder carcinoma. Nat Genet 2014.', 'groups': 'PANCAN', 'importDate': '2014-05-15 00:00:00', 'massSpectrometrySampleCount': 0, 'methylationHm27SampleCount': 0, 'miRnaSampleCount': 131, 'mrnaMicroarraySampleCount': 131, 'mrnaRnaSeqSampleCount': 0, 'mrnaRnaSeqV2SampleCount': 0, 'name': 'Bladder Urothelial Carcinoma (TCGA, Nature 2014)', 'pmid': '24658044', 'publicStudy': True, 'referenceGenome': 'hg19', 'rppaSampleCount': 0, 'sequencedSampleCount': 131, 'status': 0, 'studyId': 'blca_tcga_pub', 'svSampleCount': 0, }), ]), }) # --- # name: test_get_cancer_types_snapshot dict({ 'cancer_types': list([ dict({ 'cancerTypeId': 'acc', 'dedicatedColor': 'LightGreen', 'name': 'Adrenocortical Carcinoma', 'parentCancerTypeId': 'adrenal_gland', 'shortName': 'ACC', }), dict({ 'cancerTypeId': 'blca', 'dedicatedColor': 'Blue', 'name': 'Bladder Urothelial Carcinoma', 'parentCancerTypeId': 'bladder', 'shortName': 'BLCA', }), ]), 'pagination': dict({ 'has_more': True, 'page': 0, 'page_size': 2, 'total_found': 2, }), }) # --- # name: test_get_clinical_data_snapshot dict({ 'clinical_data_by_patient': dict({ 'TCGA-OR-A5J1': dict({ 'AGE': '50', 'SEX': 'Female', }), 'TCGA-OR-A5J2': dict({ 'AGE': '65', 'SEX': 'Male', }), 'TCGA-OR-A5J3': dict({ 'AJCC_PATHOLOGIC_TUMOR_STAGE': 'STAGE I', }), }), 'pagination': dict({ 'has_more': False, 'page': 0, 'page_size': 50, 'total_found': 3, }), }) # --- # name: test_get_clinical_data_specific_attributes_snapshot dict({ 'clinical_data_by_patient': dict({ 'TCGA-OR-A5J1': dict({ 'AGE': '50', 'SEX': 'Female', }), 'TCGA-OR-A5J2': dict({ 'AGE': '65', 'SEX': 'Male', }), }), 'pagination': dict({ 'has_more': False, 'page': 0, 'page_size': 50, 'total_found': 2, }), }) # --- # name: test_get_gene_panel_details_snapshot dict({ 'description': '468 key cancer genes', 'genePanelId': 'IMPACT468', 'genes': list([ dict({ 'entrezGeneId': 7157, 'hugoGeneSymbol': 'TP53', }), dict({ 'entrezGeneId': 207, 'hugoGeneSymbol': 'AKT1', }), dict({ 'entrezGeneId': 595, 'hugoGeneSymbol': 'CCND1', }), ]), 'name': 'MSK-IMPACT Clinical Sequencing Cohort (MSK, Cancer Cell 2015)', }) # --- # name: test_get_gene_panels_for_study_snapshot list([ dict({ 'description': '341 cancer-associated genes', 'genePanelId': 'IMPACT341', 'genes': list([ dict({ 'entrezGeneId': 1, 'hugoGeneSymbol': 'GENE1', }), dict({ 'entrezGeneId': 2, 'hugoGeneSymbol': 'GENE2', }), ]), 'name': 'MSK-IMPACT Clinical Sequencing Cohort (MSK, Nat Med 2017)', }), dict({ 'description': 'Pediatric panel of genes', 'genePanelId': 'PEDS-IMPACT', 'genes': list([ dict({ 'entrezGeneId': 3, 'hugoGeneSymbol': 'GENE3', }), dict({ 'entrezGeneId': 4, 'hugoGeneSymbol': 'P53_MUTANT', }), ]), 'name': 'MSK-IMPACT Pediatric Panel', }), ]) # --- # name: test_get_molecular_profiles_snapshot dict({ 'molecular_profiles': list([ dict({ 'datatype': 'CONTINUOUS', 'description': 'mRNA expression from RNA Sequencing (version 2, RSEM normalized)', 'genericAssayType': 'MRNA_EXPRESSION', 'molecularAlterationType': 'MRNA_EXPRESSION', 'molecularProfileId': 'acc_tcga_rna_seq_v2_mrna', 'name': 'mRNA expression (RNA Seq V2 RSEM)', 'patientLevel': False, 'showProfileInAnalysisTab': True, 'sortOrder': 0, 'studyId': 'acc_tcga', }), dict({ 'datatype': 'MAF', 'description': 'Somatic non-silent mutations from whole exome sequencing.', 'genericAssayType': 'MUTATION', 'molecularAlterationType': 'MUTATION_EXTENDED', 'molecularProfileId': 'acc_tcga_mutations', 'name': 'Mutations', 'patientLevel': False, 'showProfileInAnalysisTab': True, 'sortOrder': 10, 'studyId': 'acc_tcga', }), ]), 'pagination': dict({ 'has_more': False, 'page': 0, 'page_size': 2, 'total_found': 2, }), }) # --- # name: test_get_mutations_in_gene_snapshot dict({ 'mutations': list([ dict({ 'aminoAcidChange': 'R248W', 'chromosome': '17', 'endPosition': 7577538, 'entrezGeneId': 7157, 'hugoGeneSymbol': 'TP53', 'keyword': 'TP53 Missense_Mutation R248W', 'molecularProfileId': 'acc_tcga_mutations', 'mutationStatus': 'SOMATIC', 'mutationType': 'Missense_Mutation', 'patientId': 'TCGA-OR-A5J1', 'proteinPosEnd': 248, 'proteinPosStart': 248, 'referenceAllele': 'C', 'sampleId': 'TCGA-OR-A5J1-01', 'startPosition': 7577538, 'uniquePatientKey': 'TCGA-OR-A5J1:acc_tcga_mutations', 'uniqueSampleKey': 'TCGA-OR-A5J1-01:acc_tcga_mutations', 'variantAllele': 'T', }), dict({ 'aminoAcidChange': 'Q136*', 'chromosome': '17', 'endPosition': 7578459, 'entrezGeneId': 7157, 'hugoGeneSymbol': 'TP53', 'keyword': 'TP53 Nonsense_Mutation Q136*', 'molecularProfileId': 'acc_tcga_mutations', 'mutationStatus': 'SOMATIC', 'mutationType': 'Nonsense_Mutation', 'patientId': 'TCGA-OR-A5J2', 'proteinPosEnd': 136, 'proteinPosStart': 136, 'referenceAllele': 'C', 'sampleId': 'TCGA-OR-A5J2-01', 'startPosition': 7578459, 'uniquePatientKey': 'TCGA-OR-A5J2:acc_tcga_mutations', 'uniqueSampleKey': 'TCGA-OR-A5J2-01:acc_tcga_mutations', 'variantAllele': 'T', }), ]), 'pagination': dict({ 'has_more': False, 'page': 0, 'page_size': 50, 'total_found': 2, }), }) # --- # name: test_get_samples_in_study_snapshot dict({ 'pagination': dict({ 'has_more': True, 'page': 0, 'page_size': 2, 'total_found': 2, }), 'samples': list([ dict({ 'cancerType': 'Adrenocortical Carcinoma', 'patientId': 'TCGA-OR-A5J1', 'sampleId': 'TCGA-OR-A5J1-01', 'sampleType': 'PRIMARY', 'studyId': 'acc_tcga', }), dict({ 'cancerType': 'Adrenocortical Carcinoma', 'patientId': 'TCGA-OR-A5J2', 'sampleId': 'TCGA-OR-A5J2-01', 'sampleType': 'PRIMARY', 'studyId': 'acc_tcga', }), ]), }) # --- # name: test_get_study_details_snapshot dict({ 'study': dict({ 'allSampleCount': 92, 'cancerType': dict({ 'cancerTypeId': 'acc', 'dedicatedColor': 'LightGreen', 'name': 'Adrenocortical Carcinoma', 'parentCancerTypeId': 'adrenal_gland', 'shortName': 'ACC', }), 'cancerTypeId': 'acc', 'citation': 'Cancer Genome Atlas Research Network. (2018). The Immune Landscape of Cancer. Immunity, 48(4).', 'cnaSampleCount': 90, 'description': 'TCGA PanCanAtlas ACC', 'groups': 'PANCANCER;PANCAN', 'importDate': '2018-04-10 00:00:00', 'massSpectrometrySampleCount': 0, 'methylationHm27SampleCount': 0, 'miRnaSampleCount': 0, 'mrnaMicroarraySampleCount': 0, 'mrnaRnaSeqSampleCount': 79, 'mrnaRnaSeqV2SampleCount': 0, 'name': 'Adrenocortical Carcinoma (TCGA, PanCancer Atlas)', 'numberOfSamplesWithCompleteSampleData': 90, 'pmid': '29622464', 'publicStudy': True, 'readPermission': True, 'referenceGenome': 'hg19', 'rppaSampleCount': 0, 'sequencedSampleCount': 90, 'status': 0, 'studyId': 'acc_tcga', 'svSampleCount': 0, }), }) # --- # name: test_search_genes_snapshot dict({ 'genes': list([ dict({ 'entrezGeneId': 672, 'hugoGeneSymbol': 'BRCA1', 'oncogene': False, 'tumorSuppressor': True, 'type': 'protein-coding', }), dict({ 'entrezGeneId': 675, 'hugoGeneSymbol': 'BRCA2', 'oncogene': False, 'tumorSuppressor': True, 'type': 'protein-coding', }), ]), 'pagination': dict({ 'has_more': True, 'page': 0, 'page_size': 2, 'total_found': 2, }), }) # --- # name: test_search_studies_snapshot dict({ 'pagination': dict({ 'has_more': False, 'page': 0, 'page_size': 2, 'total_found': 0, }), 'studies': list([ ]), }) # ---