Q (haiku): Is there any study with a polygenic risk score?

▶ clickhouse_list_tables
{}

◀ result
{"tables":[{"name":"allele_specific_copy_number"},{"name":"alteration_driver_annotation"},{"name":"cancer_study"},{"name":"cancer_study_query_preferences"},{"name":"cancer_study_tags"},{"name":"cbioportal_sequence_state"},{"name":"clinical_attribute_counts"},{"name":"clinical_attribute_meta"},{"name":"clinical_data_derived"},{"name":"clinical_event"},{"name":"clinical_event_data"},{"name":"clinical_event_data_derived"},{"name":"clinical_event_derived"},{"name":"clinical_patient"},{"name":"clinical_sample"},{"name":"cna_event"},{"name":"cna_panel_gene_coverage"},{"name":"cna_wes_coverage"},{"name":"co_altered_genes_in_study"},{"name":"copy_number_seg"},{"name":"copy_number_seg_file"},{"name":"gene"},{"name":"gene_alias"},{"name":"gene_alteration_frequency_by_cancer_type"},{"name":"gene_cna_distribution_in_study"},{"name":"gene_mutation_frequency_by_cancer_type"},{"name":"gene_mutation_frequency_in_studies"},{"name":"gene_mutation_frequency_in_study"},{"name":"gene_mutation_variants_in_study"},{"name":"gene_pair_coexpression"},{"name":"gene_panel"},{"name":"gene_panel_list"},{"name":"gene_panel_to_gene_derived"},{"name":"generic_assay_data_derived"},{"name":"generic_assay_meta_derived"},{"name":"generic_assay_profile_entity_derived"},{"name":"generic_entity_properties"},{"name":"geneset"},{"name":"geneset_gene"},{"name":"geneset_hierarchy_leaf"},{"name":"geneset_hierarchy_node"},{"name":"genetic_alteration"},{"name":"genetic_alteration_derived"},{"name":"genetic_entity"},{"name":"genetic_profile"},{"name":"genetic_profile_link"},{"name":"genetic_profile_samples"},{"name":"genomic_event_derived"},{"name":"gistic"},{"name":"gistic_to_gene"},{"name":"info"},{"name":"mut_sig"},{"name":"mutation"},{"name":"mutation_count_by_keyword"},{"name":"mutation_derived"},{"name":"mutation_event"},{"name":"mutation_panel_gene_coverage"},{"name":"mutation_wes_coverage"},{"name":"patient"},{"name":"reference_genome"},{"name":"reference_genome_gene"},{"name":"resource_definition"},{"name":"resource_patient"},{"name":"resource_sample"},{"name":"resource_study"},{"name":"sample"},{"name":"sample_cna_event"},{"name":"sample_derived"},{"name":"sample_list"},{"name":"sample_list_list"},{"name":"sample_profile"},{"name":"sample_to_gene_panel_derived"},{"name":"structural_variant"},{"name":"sv_panel_gene_coverage"},{"name":"sv_wes_coverage"},{"name":"top_cna_genes_in_study"},{"name":"top_mutated_genes_in_cohort"},{"name":"top_mutated_genes_in_study"},{"name":"top_sv_genes_in_study"},{"name":"treatment_counts_in_study"},{"name":"treatment_regimens_in_study"},{"name":"type_of_cancer"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT cancer_study_identifier, display_name
FROM cancer_study
WHERE LOWER(display_name) LIKE '%polygenic%' 
   OR LOWER(display_name) LIKE '%prs%'
   OR LOWER(display_name) LIKE '%risk score%'
ORDER BY 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: Unknown expression identifier `display_name` in scope SELECT DISTINCT cancer_study_identifier, display_name FROM cancer_study WHERE (LOWER(display_name) LIKE '%polygenic%') OR (LOWER(display_name) LIKE '%prs%') OR (LOWER(display_name) LIKE '%risk score%') ORDER BY cancer_study_identifier ASC. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT cs.cancer_study_identifier, cs.display_name, gam.NAME
FROM cancer_study cs
INNER JOIN genetic_profile gp ON cs.CANCER_STUDY_ID = gp.CANCER_STUDY_ID
INNER JOIN generic_assay_meta_derived gam ON gp.GENETIC_PROFILE_ID = gam.GENETIC_PROFILE_ID
WHERE LOWER(gam.NAME) LIKE '%polygenic%'
   OR LOWER(gam.NAME) LIKE '%prs%'
   OR LOWER(gam.STABLE_ID) LIKE '%polygenic%'
   OR LOWER(gam.STABLE_ID) LIKE '%prs%'
ORDER BY cs.cancer_study_identifier
LIMIT 100
",
 "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 'cs.CANCER_STUDY_ID' cannot be resolved from table with name cs. In scope SELECT DISTINCT cs.cancer_study_identifier, cs.display_name, gam.NAME FROM cancer_study AS cs INNER JOIN genetic_profile AS gp ON cs.CANCER_STUDY_ID = gp.CANCER_STUDY_ID INNER JOIN generic_assay_meta_derived AS gam ON gp.GENETIC_PROFILE_ID = gam.GENETIC_PROFILE_ID WHERE (LOWER(gam.NAME) LIKE '%polygenic%') OR (LOWER(gam.NAME) LIKE '%prs%') OR (LOWER(gam.STABLE_ID) LIKE '%polygenic%') OR (LOWER(gam.STABLE_ID) LIKE '%prs%') ORDER BY cs.cancer_study_identifier ASC LIMIT 100. Maybe you meant: ['cs.cancer_study_id']. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT cs.cancer_study_identifier, cs.display_name, cam.DISPLAY_NAME as attribute_name
FROM cancer_study cs
INNER JOIN clinical_attribute_meta cam ON cs.CANCER_STUDY_ID = cam.CANCER_STUDY_ID
WHERE LOWER(cam.DISPLAY_NAME) LIKE '%polygenic%'
   OR LOWER(cam.DISPLAY_NAME) LIKE '%prs%'
   OR LOWER(cam.ATTR_ID) LIKE '%polygenic%'
   OR LOWER(cam.ATTR_ID) LIKE '%prs%'
ORDER BY cs.cancer_study_identifier
LIMIT 100
",
 "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 'cs.CANCER_STUDY_ID' cannot be resolved from table with name cs. In scope SELECT DISTINCT cs.cancer_study_identifier, cs.display_name, cam.DISPLAY_NAME AS attribute_name FROM cancer_study AS cs INNER JOIN clinical_attribute_meta AS cam ON cs.CANCER_STUDY_ID = cam.CANCER_STUDY_ID WHERE (LOWER(cam.DISPLAY_NAME) LIKE '%polygenic%') OR (LOWER(cam.DISPLAY_NAME) LIKE '%prs%') OR (LOWER(cam.ATTR_ID) LIKE '%polygenic%') OR (LOWER(cam.ATTR_ID) LIKE '%prs%') ORDER BY cs.cancer_study_identifier ASC LIMIT 100. Maybe you meant: ['cs.cancer_study_id']. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_list_table_columns
{
 "table": "cancer_study"
}

▶ clickhouse_list_table_columns
{
 "table": "generic_assay_meta_derived"
}

◀ result
{"columns":[{"name":"cancer_study_id","type":"Int64","comment":"Internal numeric ID. Prefer cancer_study_identifier for queries as it is more readable and stable."},{"name":"cancer_study_identifier","type":"Nullable(String)","comment":"Stable string identifier for the study (e.g., \"msk_chord_2024\", \"brca_tcga\"). Use this for filtering, not cancer_study_id."},{"name":"type_of_cancer_id","type":"String"},{"name":"name","type":"String","comment":"Full descriptive name of the study (e.g., \"MSK-CHORD (MSK, Nature 2024)\")."},{"name":"description","type":"String"},{"name":"public","type":"Int32"},{"name":"pmid","type":"Nullable(String)"},{"name":"citation","type":"Nullable(String)"},{"name":"groups","type":"Nullable(String)"},{"name":"status","type":"Nullable(Int64)"},{"name":"import_date","type":"Nullable(DateTime64(6))"},{"name":"reference_genome_id","type":"Nullable(Int64)"},{"name":"sample_count","type":"UInt32","comment":"Samples in the study (members of <study>_all), as shown in the portal study list. Precomputed daily at LLM-prep time."},{"name":"mutation_sample_count","type":"UInt32","comment":"Samples profiled for mutations (<study>_sequenced) — portal \"Data type\" filter: \"Mutations\". 0 = no mutation data."},{"name":"cna_sample_count","type":"UInt32","comment":"Samples profiled for copy-number alterations (<study>_cna) — \"CNA\". 0 = no CNA data."},{"name":"structural_variant_sample_count","type":"UInt32","comment":"Distinct samples with at least one structural variant (fusions etc.). 0 = none."},{"name":"rna_seq_sample_count","type":"UInt32","comment":"Samples with RNA-Seq expression (<study>_rna_seq_v2_mrna) — \"RNA-Seq\"."},{"name":"mrna_microarray_sample_count","type":"UInt32","comment":"Samples with microarray mRNA expression (<study>_mrna) — \"RNA (microarray)\"."},{"name":"mirna_sample_count","type":"UInt32","comment":"Samples with microRNA expression (<study>_microrna) — \"miRNA\"."},{"name":"rppa_sample_count","type":"UInt32","comment":"Samples with RPPA protein levels (<study>_rppa) — \"RPPA\"."},{"name":"mass_spectrometry_sample_count","type":"UInt32","comment":"Samples with mass-spectrometry protein quantification (<study>_protein_quantification) — \"Protein Mass-Spectrometry\"."},{"name":"treatment_patient_count","type":"UInt32","comment":"PATIENTS (not samples) with treatment clinical events — \"Treatment\". 0 = no treatment data."},{"name":"resource_sample_counts","type":"Map(String, UInt32)","comment":"Samples with each linked resource, keyed by display name: imaging and pathology such as 'Slide Microscopy', 'Computed Tomography', 'Magnetic Resonance', 'H&E Slide', 'MxIF Image'. Query with mapKeys(resource_sample_counts) or resource_sample_counts['Slide Microscopy'] > 0."},{"name":"mrna_expression_sample_count","type":"UInt32","comment":"Samples in any mRNA expression profile (RNA-Seq, microarray, TPM, z-scores; from sample_profile). Use this for \"does the study have expression data\" — rna_seq_sample_count and mrna_m … (136 more chars)

▶ clickhouse_list_table_columns
{
 "table": "clinical_attribute_meta"
}

◀ result
{"columns":[{"name":"entity_stable_id","type":"String"},{"name":"entity_type","type":"LowCardinality(String)"},{"name":"properties","type":"Map(String, String)"}]}

◀ result
{"columns":[{"name":"attr_id","type":"String"},{"name":"display_name","type":"String"},{"name":"description","type":"String"},{"name":"datatype","type":"String"},{"name":"patient_attribute","type":"Int32"},{"name":"priority","type":"String"},{"name":"cancer_study_id","type":"Int64"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT cs.cancer_study_identifier, cs.name
FROM cancer_study cs
WHERE LOWER(cs.name) LIKE '%polygenic%' 
   OR LOWER(cs.name) LIKE '%prs%'
   OR LOWER(cs.name) LIKE '%risk score%'
ORDER BY cs.cancer_study_identifier
",
 "max_rows": 100
}

◀ result
{"rows":[]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT cs.cancer_study_identifier, cs.name, cam.display_name as attribute_name
FROM cancer_study cs
INNER JOIN clinical_attribute_meta cam ON cs.cancer_study_id = cam.cancer_study_id
WHERE LOWER(cam.display_name) LIKE '%polygenic%'
   OR LOWER(cam.display_name) LIKE '%prs%'
   OR LOWER(cam.attr_id) LIKE '%polygenic%'
   OR LOWER(cam.attr_id) LIKE '%prs%'
ORDER BY cs.cancer_study_identifier
",
 "max_rows": 100
}

◀ result
{"rows":[{"cancer_study_identifier":"prad_broad","name":"Prostate Adenocarcinoma (Broad/Cornell, Nat Genet 2012)","attribute_name":"TMPRSS2-ERG Fusion Status"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT cs.cancer_study_identifier, cs.name
FROM cancer_study cs
INNER JOIN genetic_profile gp ON cs.cancer_study_id = gp.cancer_study_id
INNER JOIN genetic_entity ge ON gp.genetic_profile_id = ge.genetic_profile_id
WHERE LOWER(ge.stable_id) LIKE '%polygenic%'
   OR LOWER(ge.name) LIKE '%polygenic%'
   OR LOWER(ge.stable_id) LIKE '%_prs_%'
   OR LOWER(ge.name) LIKE '%prs%'
ORDER BY cs.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 'ge.genetic_profile_id' cannot be resolved from table with name ge. In scope SELECT DISTINCT cs.cancer_study_identifier, cs.name FROM cancer_study AS cs INNER JOIN genetic_profile AS gp ON cs.cancer_study_id = gp.cancer_study_id INNER JOIN genetic_entity AS ge ON gp.genetic_profile_id = ge.genetic_profile_id WHERE (LOWER(ge.stable_id) LIKE '%polygenic%') OR (LOWER(ge.name) LIKE '%polygenic%') OR (LOWER(ge.stable_id) LIKE '%_prs_%') OR (LOWER(ge.name) LIKE '%prs%') ORDER BY cs.cancer_study_identifier ASC. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_list_table_columns
{
 "table": "genetic_entity"
}

◀ result
{"columns":[{"name":"id","type":"Int64"},{"name":"entity_type","type":"String"},{"name":"stable_id","type":"Nullable(String)"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT cs.cancer_study_identifier, cs.name, gp.stable_id, gp.genetic_alteration_type
FROM cancer_study cs
INNER JOIN genetic_profile gp ON cs.cancer_study_id = gp.cancer_study_id
WHERE LOWER(gp.stable_id) LIKE '%polygenic%'
   OR LOWER(gp.stable_id) LIKE '%prs%'
   OR LOWER(gp.genetic_alteration_type) LIKE '%polygenic%'
   OR LOWER(gp.genetic_alteration_type) LIKE '%prs%'
ORDER BY cs.cancer_study_identifier
",
 "max_rows": 100
}

◀ result
{"rows":[]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT cs.cancer_study_identifier, cs.name
FROM cancer_study cs
INNER JOIN genetic_profile gp ON cs.cancer_study_id = gp.cancer_study_id
WHERE LOWER(gp.genetic_alteration_type) IN ('generic_assay')
  AND (
    LOWER(gp.stable_id) LIKE '%risk%'
    OR LOWER(gp.stable_id) LIKE '%genetic_ancestry%'
    OR LOWER(gp.stable_id) LIKE '%ancestry%'
    OR LOWER(gp.stable_id) LIKE '%prs%'
  )
ORDER BY cs.cancer_study_identifier
",
 "max_rows": 100
}

◀ result
{"rows":[{"cancer_study_identifier":"acc_tcga_pan_can_atlas_2018","name":"Adrenocortical Carcinoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"blca_tcga_pan_can_atlas_2018","name":"Bladder Urothelial Carcinoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"cesc_tcga_pan_can_atlas_2018","name":"Cervical Squamous Cell Carcinoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"chol_tcga_pan_can_atlas_2018","name":"Cholangiocarcinoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"coadread_tcga_pan_can_atlas_2018","name":"Colorectal Adenocarcinoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"dlbc_tcga_pan_can_atlas_2018","name":"Diffuse Large B-Cell Lymphoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"esca_tcga_pan_can_atlas_2018","name":"Esophageal Adenocarcinoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"gbm_tcga_pan_can_atlas_2018","name":"Glioblastoma Multiforme (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"hnsc_tcga_pan_can_atlas_2018","name":"Head and Neck Squamous Cell Carcinoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"kich_tcga_pan_can_atlas_2018","name":"Kidney Chromophobe (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"kirc_tcga_pan_can_atlas_2018","name":"Kidney Renal Clear Cell Carcinoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"kirp_tcga_pan_can_atlas_2018","name":"Kidney Renal Papillary Cell Carcinoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018","name":"Brain Lower Grade Glioma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"lihc_tcga_pan_can_atlas_2018","name":"Liver Hepatocellular Carcinoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"luad_tcga_pan_can_atlas_2018","name":"Lung Adenocarcinoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"lusc_tcga_pan_can_atlas_2018","name":"Lung Squamous Cell Carcinoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"meso_tcga_pan_can_atlas_2018","name":"Mesothelioma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"ov_tcga_pan_can_atlas_2018","name":"Ovarian Serous Cystadenocarcinoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"paad_tcga_pan_can_atlas_2018","name":"Pancreatic Adenocarcinoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"pcpg_tcga_pan_can_atlas_2018","name":"Pheochromocytoma and Paraganglioma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"prad_tcga_pan_can_atlas_2018","name":"Prostate Adenocarcinoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"sarc_tcga_pan_can_atlas_2018","name":"Sarcoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"skcm_tcga_pan_can_atlas_2018","name":"Skin Cutaneous Melanoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"stad_tcga_pan_can_atlas_2018","name":"Stomach Adenocarcinoma (TCGA, PanCancer Atlas)"},{"cancer_study_identifier":"tgct_ … (647 more chars)

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT gp.stable_id, gp.genetic_alteration_type
FROM cancer_study cs
INNER JOIN genetic_profile gp ON cs.cancer_study_id = gp.cancer_study_id
WHERE cs.cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018'
  AND gp.genetic_alteration_type = 'generic_assay'
ORDER BY gp.stable_id
",
 "max_rows": 100
}

◀ result
{"rows":[]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT cs.cancer_study_identifier, cs.name, gp.stable_id
FROM cancer_study cs
INNER JOIN genetic_profile gp ON cs.cancer_study_id = gp.cancer_study_id
WHERE cs.cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018'
ORDER BY gp.stable_id
",
 "max_rows": 100
}

◀ result
{"rows":[{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","stable_id":"brca_tcga_pan_can_atlas_2018_armlevel_cna"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","stable_id":"brca_tcga_pan_can_atlas_2018_genetic_ancestry"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","stable_id":"brca_tcga_pan_can_atlas_2018_gistic"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","stable_id":"brca_tcga_pan_can_atlas_2018_log2CNA"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","stable_id":"brca_tcga_pan_can_atlas_2018_methylation_hm27_hm450_merge"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","stable_id":"brca_tcga_pan_can_atlas_2018_methylation_hm450"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","stable_id":"brca_tcga_pan_can_atlas_2018_mutations"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","stable_id":"brca_tcga_pan_can_atlas_2018_phosphoprotein_quantification"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","stable_id":"brca_tcga_pan_can_atlas_2018_protein_quantification"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","stable_id":"brca_tcga_pan_can_atlas_2018_protein_quantification_zscores"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","stable_id":"brca_tcga_pan_can_atlas_2018_rna_seq_v2_mrna"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","stable_id":"brca_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","stable_id":"brca_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","stable_id":"brca_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_ref_normal_Zscores"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","stable_id":"brca_tcga_pan_can_atlas_2018_rppa"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","stable_id":"brca_tcga_pan_can_atlas_2018_rppa_Zscores"},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Bre … (113 more chars)

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT ge.stable_id, COUNT(*) as count
FROM cancer_study cs
INNER JOIN genetic_profile gp ON cs.cancer_study_id = gp.cancer_study_id
INNER JOIN genetic_entity ge ON gp.genetic_profile_id = ge.genetic_profile_id
WHERE cs.cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018'
  AND gp.stable_id = 'brca_tcga_pan_can_atlas_2018_genetic_ancestry'
GROUP BY ge.stable_id
ORDER BY ge.stable_id
",
 "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 'ge.genetic_profile_id' cannot be resolved from table with name ge. In scope SELECT DISTINCT ge.stable_id, COUNT(*) AS count FROM cancer_study AS cs INNER JOIN genetic_profile AS gp ON cs.cancer_study_id = gp.cancer_study_id INNER JOIN genetic_entity AS ge ON gp.genetic_profile_id = ge.genetic_profile_id WHERE (cs.cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018') AND (gp.stable_id = 'brca_tcga_pan_can_atlas_2018_genetic_ancestry') GROUP BY ge.stable_id ORDER BY ge.stable_id ASC. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_list_table_columns
{
 "table": "genetic_alteration"
}

◀ result
{"columns":[{"name":"genetic_profile_id","type":"Int64"},{"name":"genetic_entity_id","type":"Int64"},{"name":"values","type":"String"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT ge.stable_id, COUNT(*) as count
FROM cancer_study cs
INNER JOIN genetic_profile gp ON cs.cancer_study_id = gp.cancer_study_id
INNER JOIN genetic_alteration ga ON gp.genetic_profile_id = ga.genetic_profile_id
INNER JOIN genetic_entity ge ON ga.genetic_entity_id = ge.id
WHERE cs.cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018'
  AND gp.stable_id = 'brca_tcga_pan_can_atlas_2018_genetic_ancestry'
GROUP BY ge.stable_id
ORDER BY ge.stable_id
",
 "max_rows": 100
}

◀ result
{"rows":[{"ge.stable_id":"AFR","count":1},{"ge.stable_id":"AMR","count":1},{"ge.stable_id":"EAS","count":1},{"ge.stable_id":"EUR","count":1},{"ge.stable_id":"SAS","count":1}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT cs.cancer_study_identifier, cs.name, gp.stable_id, gp.genetic_alteration_type
FROM cancer_study cs
INNER JOIN genetic_profile gp ON cs.cancer_study_id = gp.cancer_study_id
WHERE LOWER(gp.stable_id) LIKE '%prs%'
   OR LOWER(gp.stable_id) LIKE '%polygenic%'
   OR LOWER(gp.stable_id) LIKE '%risk_score%'
   OR LOWER(gp.genetic_alteration_type) LIKE '%prs%'
   OR LOWER(gp.genetic_alteration_type) LIKE '%polygenic%'
ORDER BY cs.cancer_study_identifier
LIMIT 100
",
 "max_rows": 100
}

◀ result
{"rows":[]}

═ answer (success)
Based on my comprehensive search of the cBioPortal database, **I found no studies with polygenic risk score (PRS) data** stored in cBioPortal.

Here's what I found instead:

**Related data available:**
- **Genetic ancestry** — All 32 TCGA PanCancer Atlas studies (BRCA, LUAD, GBM, etc.) contain genetic ancestry classifications (AFR, AMR, EAS, EUR, SAS), which are population ancestry categories. These are different from polygenic risk scores.
- Polygenic risk scores are computed from the combined effects of many genetic variants and are not currently part of the cBioPortal data model.

**If you're looking for polygenic risk score data:**
1. Check external databases like the **PGS Catalog** (https://www.pgscatalog.org/) for pre-computed PRS scores across cohorts
2. Reach out to the individual study consortiums (e.g., TCGA Data Portal, GDC) to see if PRS data exists as supplementary files
3. Contact the cBioPortal team if you have access to PRS data you'd like to deposit

Would you like help finding other genomic or clinical data in cBioPortal instead?