Q (sonnet-5.5): How many glioblastoma studies are in cBioPortal? ▶ list_studies { "search": "glioblastoma", "limit": 100 } ▶ read_guide { "uri": "cbioportal://faq-guide" } ◀ result {"result":[{"cancer_study_identifier":"gbm_tcga","name":"Glioblastoma Multiforme (TCGA, Firehose Legacy)","type_of_cancer_id":"difg","sample_count":619,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=gbm_tcga"},{"cancer_study_identifier":"gbm_tcga_gdc","name":"Glioblastoma Multiforme (TCGA GDC, 2025)","type_of_cancer_id":"difg","sample_count":611,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=gbm_tcga_gdc"},{"cancer_study_identifier":"gbm_tcga_pan_can_atlas_2018","name":"Glioblastoma Multiforme (TCGA, PanCancer Atlas)","type_of_cancer_id":"difg","sample_count":592,"has_guide":true,"url":"https://www.cbioportal.org/study/summary?id=gbm_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"gbm_tcga_pub2013","name":"Glioblastoma (TCGA, Cell 2013)","type_of_cancer_id":"difg","sample_count":577,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=gbm_tcga_pub2013"},{"cancer_study_identifier":"gbm_tcga_pub","name":"Glioblastoma (TCGA, Nature 2008)","type_of_cancer_id":"difg","sample_count":206,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=gbm_tcga_pub"},{"cancer_study_identifier":"gbm_cptac_2021","name":"Glioblastoma (CPTAC, Cell 2021)","type_of_cancer_id":"difg","sample_count":99,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=gbm_cptac_2021"},{"cancer_study_identifier":"gbm_columbia_2019","name":"Glioblastoma (Columbia, Nat Med. 2019)","type_of_cancer_id":"difg","sample_count":42,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=gbm_columbia_2019"},{"cancer_study_identifier":"gbm_iatlas_prins_2019","name":"Glioblastoma (Randomized Clinical Trial, Nat Med. 2019) - iAtlas Harmonized","type_of_cancer_id":"adifg","sample_count":30,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=gbm_iatlas_prins_2019"}]} ◀ result # cBioPortal FAQ Guide Curated answers to frequently asked general questions about cBioPortal. Source: [cBioPortal FAQ](https://docs.cbioportal.org/user-guide/faq/). ## What is cBioPortal? cBioPortal for Cancer Genomics is an open-access, open-source resource for interactive exploration of multidimensional cancer genomics data sets. It was originally developed at Memorial Sloan Kettering Cancer Center (MSK) and is now maintained by a multi-institutional team. ## History - **2008**: cBioPortal first became available online. - **2012**: First major publication — Cerami et al., *Cancer Discovery*. - **2013**: Second major publication — Gao et al., *Science Signaling*. - **2023**: Third major publication — de Bruijn et al., *Cancer Research*. ## How to Cite cBioPortal When using cBioPortal in publications, cite these three papers: 1. Cerami et al. "The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data." *Cancer Discovery* 2, 401–404 (2012). doi:10.1158/2159-8290.CD-12-0095 2. Gao et al. "Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal." *Science Signaling* 6, pl1 (2013). doi:10.1126/scisignal.2004088 3. de Bruijn et al. "Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal." *Cancer Research* 83, 3861–3867 (2023). doi:10.1158/0008-5472.CAN-23-0816 Also cite the specific study publication(s) whose data you used. ## What Data Types Does cBioPortal Contain? - **Mutations** (non-synonymous somatic mutations) - **DNA copy-number alterations** (CNA) from GISTIC or other methods - **mRNA expression** data (RNA-seq, microarray) - **Protein/phosphoprotein** levels (RPPA, mass spectrometry) - **DNA methylation** data - **Structural variants** (gene fusions, rearrangements) - **Clinical data** (demographics, diagnosis, treatment, outcomes) Note: Synonymous mutations are not included in cBioPortal. ## What Cancer Types Are in the Database? Answer from the studies actually loaded, not from the OncoTree ontology (OncoTree lists hundreds of codes, most with no study here). One query: ```sql SELECT tc.type_of_cancer_id, tc.name, tc.tissue, count() AS studies FROM cancer_study cs JOIN type_of_cancer tc ON cs.type_of_cancer_id = tc.type_of_cancer_id GROUP BY tc.type_of_cancer_id, tc.name, tc.tissue ORDER BY studies DESC; ``` Report how many distinct cancer types there are across how many studies, grouped by `tissue`. `mixed` ("Mixed Cancer Types") marks multi-cancer studies such as MSK-IMPACT and MSK-CHORD; their per-sample cancer types are in `clinical_data_derived` (`CANCER_TYPE`). ## Data Types Usually Not Stored Directly cBioPortal generally does not store: - raw CT, MRI, pathology-slide, or histology image files - raw sequencing files such as BAM, CRAM, or FASTQ - polygenic risk scores as a standard data type - full external clinical-trial databases However, this deployment … (7371 more chars) ▶ resolve_and_route { "studyIds": [ "gbm_tcga", "gbm_tcga_gdc", "gbm_tcga_pan_can_atlas_2018", "gbm_tcga_pub2013", "gbm_tcga_pub", "gbm_cptac_2021", "gbm_columbia_2019", "gbm_iatlas_prins_2019" ] } ◀ result {"success":true,"message":"Found 8 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":8,"studiesWithMetadata":[{"studyId":"gbm_tcga","name":"Glioblastoma Multiforme (TCGA, Firehose Legacy)","sampleCount":619,"studyViewUrl":"https://www.cbioportal.org/study?id=gbm_tcga","metadata":{"clinicalAttributeIds":["AGE","CANCER_TYPE","CANCER_TYPE_DETAILED","DAYS_TO_COLLECTION","DAYS_TO_INITIAL_PATHOLOGIC_DIAGNOSIS","DAYS_TO_SPECIMEN_COLLECTION","DFS_MONTHS","DFS_STATUS","DISEASE_CODE","ECOG_SCORE","ETHNICITY","FORM_COMPLETION_DATE","FRACTION_GENOME_ALTERED","HISTOLOGICAL_DIAGNOSIS","HISTORY_LGG_DX_OF_BRAIN_TISSUE","HISTORY_NEOADJUVANT_TRTYN","HISTORY_OTHER_MALIGNANCY","ICD_10","ICD_O_3_HISTOLOGY","ICD_O_3_SITE","INFORMED_CONSENT_VERIFIED","INITIAL_PATHOLOGIC_DX_YEAR","IS_FFPE","KARNOFSKY_PERFORMANCE_SCORE","LONGEST_DIMENSION","METHOD_OF_INITIAL_SAMPLE_PROCUREMENT","METHOD_OF_INITIAL_SAMPLE_PROCUREMENT_OTHER","METHOD_OF_SAMPLE_PROCUREMENT","MUTATION_COUNT","NEW_TUMOR_EVENT_AFTER_INITIAL_TREATMENT","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","PRIMARY_SITE_PATIENT","PROJECT_CODE","PROSPECTIVE_COLLECTION","RACE","RADIATION_TREATMENT_ADJUVANT","RETROSPECTIVE_COLLECTION","SAMPLE_COUNT","SAMPLE_INITIAL_WEIGHT","SAMPLE_TYPE","SAMPLE_TYPE_ID","SEX","SHORTEST_DIMENSION","SITE_OF_TUMOR_TISSUE","SOMATIC_STATUS","SPECIMEN_CURRENT_WEIGHT","SPECIMEN_FREEZING_METHOD","SPECIMEN_SECOND_LONGEST_DIMENSION","TIME_BETWEEN_CLAMPING_AND_FREEZING","TIME_BETWEEN_EXCISION_AND_FREEZING","TISSUE_SOURCE_SITE","TMB_NONSYNONYMOUS","TREATMENT_OUTCOME_FIRST_COURSE","TUMOR_STATUS","VIAL_NUMBER"],"molecularProfileIds":["gbm_tcga_gistic","gbm_tcga_linear_CNA","gbm_tcga_methylation_hm27","gbm_tcga_methylation_hm450","gbm_tcga_mrna","gbm_tcga_mrna_U133","gbm_tcga_mrna_U133_Zscores","gbm_tcga_mrna_U133_all_sample_Zscores","gbm_tcga_mrna_median_Zscores","gbm_tcga_mrna_median_all_sample_Zscores","gbm_tcga_mutations","gbm_tcga_rna_seq_v2_mrna","gbm_tcga_rna_seq_v2_mrna_median_Zscores","gbm_tcga_rna_seq_v2_mrna_median_all_sample_Zscores","gbm_tcga_rppa","gbm_tcga_rppa_Zscores"],"heatmapProfileIds":["gbm_tcga_methylation_hm27","gbm_tcga_methylation_hm450","gbm_tcga_mrna_U133_Zscores","gbm_tcga_mrna_U133_all_sample_Zscores","gbm_tcga_mrna_median_Zscores","gbm_tcga_mrna_median_all_sample_Zscores","gbm_tcga_rna_seq_v2_mrna_median_Zscores","gbm_tcga_rna_seq_v2_mrna_median_all_sample_Zscores","gbm_tcga_rppa_Zscores"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations","mrna","protein","dna_methylation"]}},{"studyId":"gbm_tcga_gdc","name":"Glioblastoma Multiforme (TCGA GDC, 2025)","sampleCount":611,"studyVi … (10785 more chars) ▶ navigate_to_study_view { "studyIds": [ "gbm_tcga", "gbm_tcga_gdc", "gbm_tcga_pan_can_atlas_2018", "gbm_tcga_pub2013", "gbm_tcga_pub", "gbm_cptac_2021", "gbm_columbia_2019", "gbm_iatlas_prins_2019" ] } ◀ result {"success":true,"message":"Navigating to https://www.cbioportal.org/study/summary?id=gbm_tcga%2Cgbm_tcga_gdc%2Cgbm_tcga_pan_can_atlas_2018%2Cgbm_tcga_pub2013%2Cgbm_tcga_pub%2Cgbm_cptac_2021%2Cgbm_columbia_2019%2Cgbm_iatlas_prins_2019","url":"https://www.cbioportal.org/study/summary?id=gbm_tcga%2Cgbm_tcga_gdc%2Cgbm_tcga_pan_can_atlas_2018%2Cgbm_tcga_pub2013%2Cgbm_tcga_pub%2Cgbm_cptac_2021%2Cgbm_columbia_2019%2Cgbm_iatlas_prins_2019","data":{"studyIds":["gbm_tcga","gbm_tcga_gdc","gbm_tcga_pan_can_atlas_2018","gbm_tcga_pub2013","gbm_tcga_pub","gbm_cptac_2021","gbm_columbia_2019","gbm_iatlas_prins_2019"],"studies":[{"studyId":"gbm_tcga","name":"Glioblastoma Multiforme (TCGA, Firehose Legacy)","sampleCount":619},{"studyId":"gbm_tcga_gdc","name":"Glioblastoma Multiforme (TCGA GDC, 2025)","sampleCount":611},{"studyId":"gbm_tcga_pan_can_atlas_2018","name":"Glioblastoma Multiforme (TCGA, PanCancer Atlas)","sampleCount":592},{"studyId":"gbm_tcga_pub2013","name":"Glioblastoma (TCGA, Cell 2013)","sampleCount":577},{"studyId":"gbm_tcga_pub","name":"Glioblastoma (TCGA, Nature 2008)","sampleCount":206},{"studyId":"gbm_cptac_2021","name":"Glioblastoma (CPTAC, Cell 2021)","sampleCount":99},{"studyId":"gbm_columbia_2019","name":"Glioblastoma (Columbia, Nat Med. 2019)","sampleCount":42},{"studyId":"gbm_iatlas_prins_2019","name":"Glioblastoma (Randomized Clinical Trial, Nat Med. 2019) - iAtlas Harmonized","sampleCount":30}],"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) cBioPortal has **8 studies** dedicated to glioblastoma: | Study | Samples | |---|---| | [Glioblastoma Multiforme (TCGA, Firehose Legacy)](https://www.cbioportal.org/study/summary?id=gbm_tcga) | 619 | | [Glioblastoma Multiforme (TCGA GDC, 2025)](https://www.cbioportal.org/study/summary?id=gbm_tcga_gdc) | 611 | | [Glioblastoma Multiforme (TCGA, PanCancer Atlas)](https://www.cbioportal.org/study/summary?id=gbm_tcga_pan_can_atlas_2018) | 592 | | [Glioblastoma (TCGA, Cell 2013)](https://www.cbioportal.org/study/summary?id=gbm_tcga_pub2013) | 577 | | [Glioblastoma (TCGA, Nature 2008)](https://www.cbioportal.org/study/summary?id=gbm_tcga_pub) | 206 | | [Glioblastoma (CPTAC, Cell 2021)](https://www.cbioportal.org/study/summary?id=gbm_cptac_2021) | 99 | | [Glioblastoma (Columbia, Nat Med. 2019)](https://www.cbioportal.org/study/summary?id=gbm_columbia_2019) | 42 | | [Glioblastoma (Randomized Clinical Trial, Nat Med. 2019), iAtlas Harmonized](https://www.cbioportal.org/study/summary?id=gbm_iatlas_prins_2019) | 30 | - **Overlap:** Five of the eight are TCGA cohorts, and they overlap substantially. Don't add their sample counts together, because that would double-count patients. - **Other studies:** This count covers studies with "glioblastoma" in the name or description. Broader glioma studies and pan-cancer studies such as MSK-IMPACT also contain GBM samples. They aren't counted here. [View all 8 glioblastoma studies together in cBioPortal](https://www.cbioportal.org/study/summary?id=gbm_tcga%2Cgbm_tcga_gdc%2Cgbm_tcga_pan_can_atlas_2018%2Cgbm_tcga_pub2013%2Cgbm_tcga_pub%2Cgbm_cptac_2021%2Cgbm_columbia_2019%2Cgbm_iatlas_prins_2019)