Q (haiku): Is there a lower grade glioma study with race data? ▶ list_studies { "search": "glioma low grade", "limit": "20", "verbose": "true" } ✗ error Error: No such tool available: mcp__navigator__list_studies ▶ list_studies { "search": "glioma low grade", "limit": 20, "verbose": true } ◀ result {"result":[{"cancer_study_identifier":"lgg_tcga","name":"Brain Lower Grade Glioma (TCGA, Firehose Legacy)","description":"TCGA Brain Lower Grade Glioma. Source data from GDAC Firehose. Previously known as TCGA Provisional.","type_of_cancer_id":"difg","sample_count":530,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=lgg_tcga"},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018","name":"Brain Lower Grade Glioma (TCGA, PanCancer Atlas)","description":"Brain Lower Grade Glioma TCGA PanCancer data. The original data is here. The publications are here.","type_of_cancer_id":"difg","sample_count":514,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=lgg_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"brain_cptac_2020","name":"Pediatric Brain Cancer (CPTAC/CHOP, Cell 2020)","description":"Integrated proteogenomic characterization across major histological types of pediatric brain cancer . We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 histological types of childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade glioma (25), medulloblastoma (22), ganglio-glioma (18), craniopharyngioma (16), and atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span histological boundaries, suggesting that treatments used for one histological type may be applied effectively to other tumors sharing similar proteomics features. Immune landscape characterization reveals diverse tumor microenvironments across and within diagnoses. Proteomics data further reveal functional effects of somatic mutations and copy number variations (CNVs) not evident in transcriptomics data.","type_of_cancer_id":"brain","sample_count":218,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=brain_cptac_2020"},{"cancer_study_identifier":"difg_msk_2023","name":"IDH-mutated Diffuse Glioma (MSK, Clin Cancer Res 2024)","description":"Targeted sequencing of 73 IDH-mutated low-grade gliomas and their matched normal pairs via MSK-IMPACT. The data is available on Synapse.","type_of_cancer_id":"difg","sample_count":73,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=difg_msk_2023"},{"cancer_study_identifier":"lgg_ucsf_2014","name":"Low-Grade Gliomas (UCSF, Science 2014)","description":"Whole exome sequencing of 23 grade II glioma tumor/normal pairs.","type_of_cancer_id":"difg","sample_count":61,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=lgg_ucsf_2014"},{"cancer_study_identifier":"l … (521 more chars) ▶ clickhouse_run_select_query { "query": " SELECT DISTINCT csp.cancer_study_identifier, csp.cancer_study_name, ccd.attribute_name FROM clinical_data_derived ccd JOIN cancer_study_query_preferences csp ON ccd.cancer_study_id = csp.internal_id WHERE csp.cancer_study_identifier IN ('lgg_tcga', 'lgg_tcga_pan_can_atlas_2018', 'brain_cptac_2020', 'difg_msk_2023', 'lgg_ucsf_2014', 'lgg_ctf_synodos_2025') AND lower(ccd.attribute_name) LIKE '%race%' ORDER BY csp.cancer_study_identifier ", "max_rows": 100 } ◀ result {"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 47\n Code: 47. DB::Exception: Identifier 'ccd.cancer_study_id' cannot be resolved from table with name ccd. In scope SELECT DISTINCT csp.cancer_study_identifier, csp.cancer_study_name, ccd.attribute_name FROM clinical_data_derived AS ccd INNER JOIN cancer_study_query_preferences AS csp ON ccd.cancer_study_id = csp.internal_id WHERE (csp.cancer_study_identifier IN ('lgg_tcga', 'lgg_tcga_pan_can_atlas_2018', 'brain_cptac_2020', 'difg_msk_2023', 'lgg_ucsf_2014', 'lgg_ctf_synodos_2025')) AND (lower(ccd.attribute_name) LIKE '%race%') ORDER BY csp.cancer_study_identifier ASC. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"} ▶ clickhouse_list_table_columns { "table": "clinical_data_derived" } ▶ clickhouse_list_table_columns { "table": "cancer_study_query_preferences" } ◀ result {"columns":[{"name":"internal_id","type":"Int32"},{"name":"sample_unique_id","type":"String","comment":"Globally unique sample ID: cancer_study_identifier + \"_\" + sample.stable_id. Empty for patient-level attributes. Use this for sample filtering and joins."},{"name":"patient_unique_id","type":"String","comment":"Globally unique patient ID: cancer_study_identifier + \"_\" + patient.stable_id. Present for both sample and patient-level attributes."},{"name":"attribute_name","type":"LowCardinality(String)","comment":"Clinical attribute name (e.g., SAMPLE_TYPE, CANCER_TYPE, AGE, OS_MONTHS). Use with attribute_value for filtering. AGE may be floored or capped for de-identification (e.g. all children recorded as 18, or everyone 89+ recorded as 89 or 90): before age statistics check for a pile-up at the min/max, and if present compute age from DAYS_TO_BIRTH (-days / 365.25)."},{"name":"attribute_value","type":"String","comment":"Value of the clinical attribute (String). For SAMPLE_TYPE: Primary, Metastasis, Local Recurrence, Unknown. Missing values are empty strings, so use toFloat64OrNull(attribute_value) for numeric comparisons — CAST fails on them."},{"name":"cancer_study_identifier","type":"LowCardinality(String)"},{"name":"type","type":"LowCardinality(String)","comment":"Data level: \"sample\" for sample-level attributes (e.g., SAMPLE_TYPE), \"patient\" for patient-level attributes (e.g., AGE, OS_MONTHS)."}]} ◀ result {"columns":[{"name":"preference_name","type":"LowCardinality(String)","comment":"Named purpose. See SELECT DISTINCT preference_name FROM cancer_study_query_preferences for what this deployment loaded."},{"name":"cancer_study_identifier","type":"String","comment":"cancer_study.cancer_study_identifier — join key"},{"name":"notes","type":"String","comment":"Why this study is recommended for this preference"}]} ▶ clickhouse_run_select_query { "query": " SELECT DISTINCT cancer_study_identifier, attribute_name FROM clinical_data_derived WHERE cancer_study_identifier IN ('lgg_tcga', 'lgg_tcga_pan_can_atlas_2018', 'brain_cptac_2020', 'difg_msk_2023', 'lgg_ucsf_2014', 'lgg_ctf_synodos_2025') AND lower(attribute_name) LIKE '%race%' ORDER BY cancer_study_identifier ", "max_rows": 100 } ◀ result {"rows":[{"cancer_study_identifier":"brain_cptac_2020","attribute_name":"RACE"},{"cancer_study_identifier":"difg_msk_2023","attribute_name":"RACE"},{"cancer_study_identifier":"lgg_ctf_synodos_2025","attribute_name":"RACE"},{"cancer_study_identifier":"lgg_tcga","attribute_name":"RACE"},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018","attribute_name":"RACE"}]} ▶ clickhouse_run_select_query { "query": " SELECT cancer_study_identifier, attribute_value as RACE, COUNT(*) as patient_count FROM clinical_data_derived WHERE cancer_study_identifier IN ('lgg_tcga', 'lgg_tcga_pan_can_atlas_2018', 'brain_cptac_2020', 'difg_msk_2023', 'lgg_ucsf_2014', 'lgg_ctf_synodos_2025') AND attribute_name = 'RACE' AND attribute_value != '' GROUP BY cancer_study_identifier, attribute_value ORDER BY cancer_study_identifier, patient_count DESC ", "max_rows": 100 } ◀ result {"rows":[{"cancer_study_identifier":"brain_cptac_2020","RACE":"White","patient_count":146},{"cancer_study_identifier":"brain_cptac_2020","RACE":"Other/Unavailable/Not Reported","patient_count":27},{"cancer_study_identifier":"brain_cptac_2020","RACE":"Black or African American","patient_count":18},{"cancer_study_identifier":"brain_cptac_2020","RACE":"Asian","patient_count":4},{"cancer_study_identifier":"brain_cptac_2020","RACE":"American Indian or Alaska Native","patient_count":3},{"cancer_study_identifier":"brain_cptac_2020","RACE":"Native Hawaiian or Other Pacific Islander","patient_count":1},{"cancer_study_identifier":"difg_msk_2023","RACE":"WHITE","patient_count":49},{"cancer_study_identifier":"difg_msk_2023","RACE":"ASIAN-FAR EAST/INDIAN SUBCONT","patient_count":8},{"cancer_study_identifier":"difg_msk_2023","RACE":"OTHER","patient_count":4},{"cancer_study_identifier":"difg_msk_2023","RACE":"PT REFUSED TO ANSWER","patient_count":3},{"cancer_study_identifier":"difg_msk_2023","RACE":"BLACK OR AFRICAN AMERICAN","patient_count":1},{"cancer_study_identifier":"lgg_ctf_synodos_2025","RACE":"White/Non-Hispanic or Latino","patient_count":21},{"cancer_study_identifier":"lgg_ctf_synodos_2025","RACE":"White/Hispanic or Latino","patient_count":3},{"cancer_study_identifier":"lgg_ctf_synodos_2025","RACE":"Other/Non-Hispanic or Latino","patient_count":1},{"cancer_study_identifier":"lgg_tcga","RACE":"WHITE","patient_count":475},{"cancer_study_identifier":"lgg_tcga","RACE":"BLACK OR AFRICAN AMERICAN","patient_count":21},{"cancer_study_identifier":"lgg_tcga","RACE":"ASIAN","patient_count":8},{"cancer_study_identifier":"lgg_tcga","RACE":"AMERICAN INDIAN OR ALASKA NATIVE","patient_count":1},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018","RACE":"White","patient_count":474},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018","RACE":"Black or African American","patient_count":21},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018","RACE":"Asian","patient_count":7},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018","RACE":"American Indian or Alaska Native","patient_count":1}]} ═ answer (success) Perfect! **Yes, there are several lower grade glioma studies with race data.** Here are the main options: ## Studies with Race Data | Study | Identifier | Samples | Race Data Coverage | |---|---|---|---| | **Brain Lower Grade Glioma (TCGA, PanCancer Atlas)** | `lgg_tcga_pan_can_atlas_2018` | 514 | 503 patients with race: White (474), Black/African American (21), Asian (7), Native American (1) | | **Brain Lower Grade Glioma (TCGA, Firehose Legacy)** | `lgg_tcga` | 530 | 505 patients with race: White (475), Black/African American (21), Asian (8), Native American (1) | | **Pediatric Brain Cancer (CPTAC/CHOP, Cell 2020)** | `brain_cptac_2020` | 218 | 199 patients with race data (includes 93 low-grade gliomas): White (146), Black/African American (18), Asian (4), Native American (3), Pacific Islander (1) | | **IDH-mutated Diffuse Glioma (MSK, 2024)** | `difg_msk_2023` | 73 | 65 patients with race: White (49), Asian (8), Black/African American (1), Other (4), Refused (3) | | **Pediatric Low-Grade Glioma (CTF, 2021)** | `lgg_ctf_synodos_2025` | 31 | 25 patients with race data (largely White, some Hispanic) | ### Recommendation **`lgg_tcga_pan_can_atlas_2018`** or **`lgg_tcga`** are the largest and best-characterized, with the most complete race data (~500 patients each). The **CPTAC study** offers the most detailed racial diversity if you're interested in pediatric cases specifically. Would you like me to navigate you to one of these studies for analysis, or do you need more details about specific attributes?