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_list_table_columns
{
 "table": "generic_assay_meta_derived"
}

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

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT entity_type
FROM generic_assay_meta_derived
ORDER BY entity_type
LIMIT 100
"
}

◀ result
{"rows":[{"entity_type":"GENERIC_ASSAY"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT 
  entity_stable_id,
  properties
FROM generic_assay_meta_derived
WHERE entity_stable_id LIKE '%risk%' OR entity_stable_id LIKE '%PRS%' OR entity_stable_id LIKE '%polygenic%'
LIMIT 100
"
}

◀ result
{"rows":[{"entity_stable_id":"TMPRSS11B_K393k","properties":{"GENE_SYMBOL":"TMPRSS11B","DESCRIPTION":"1_1_393_393","ACETYLSITES":"K393k_1_1_393_393","NAME":"TMPRSS11B_K393k"}},{"entity_stable_id":"TMPRSS11B_acetylprotein","properties":{"GENE_SYMBOL":"TMPRSS11B","NAME":"S97s "}},{"entity_stable_id":"TMPRSS13_S135","properties":{"GENE_SYMBOL":"TMPRSS13"}},{"entity_stable_id":"TMPRSS13_S70","properties":{"GENE_SYMBOL":"TMPRSS13"}},{"entity_stable_id":"TMPRSS13_T29","properties":{"GENE_SYMBOL":"TMPRSS13"}},{"entity_stable_id":"TMPRSS13_T49","properties":{"GENE_SYMBOL":"TMPRSS13"}},{"entity_stable_id":"TMPRSS13_T64","properties":{"GENE_SYMBOL":"TMPRSS13"}},{"entity_stable_id":"TMPRSS13_acetylprotein","properties":{"GENE_SYMBOL":"TMPRSS13","NAME":"T29t-S70s-S135s "}},{"entity_stable_id":"TMPRSS13_pS134","properties":{"GENE_SYMBOL":"TMPRSS13","PHOSPHOSITE":"pS134"}},{"entity_stable_id":"TMPRSS13_pS135","properties":{"GENE_SYMBOL":"TMPRSS13","PHOSPHOSITE":"pS135"}},{"entity_stable_id":"TMPRSS13_pS25_T29","properties":{"GENE_SYMBOL":"TMPRSS13","PHOSPHOSITE":"pS25_T29"}},{"entity_stable_id":"TMPRSS13_pS45","properties":{"GENE_SYMBOL":"TMPRSS13","PHOSPHOSITE":"pS45"}},{"entity_stable_id":"TMPRSS13_pS70","properties":{"GENE_SYMBOL":"TMPRSS13","PHOSPHOSITE":"pS70"}},{"entity_stable_id":"TMPRSS13_pS90","properties":{"GENE_SYMBOL":"TMPRSS13","PHOSPHOSITE":"pS90"}},{"entity_stable_id":"TMPRSS13_pT29","properties":{"GENE_SYMBOL":"TMPRSS13","PHOSPHOSITE":"pT29"}},{"entity_stable_id":"TMPRSS13_pT49","properties":{"GENE_SYMBOL":"TMPRSS13","PHOSPHOSITE":"pT49"}},{"entity_stable_id":"TMPRSS13_pT64","properties":{"GENE_SYMBOL":"TMPRSS13","PHOSPHOSITE":"pT64"}},{"entity_stable_id":"TMPRSS13_pT64_S70","properties":{"GENE_SYMBOL":"TMPRSS13","PHOSPHOSITE":"pT64_S70"}},{"entity_stable_id":"TMPRSS9_Y333:NP_892018.1","properties":{"GENE_SYMBOL":"TMPRSS9"}},{"entity_stable_id":"1_220006106_220007338_EPRS","properties":{"GENE_SYMBOL":"EPRS"}},{"entity_stable_id":"ADPRS_K109k","properties":{"GENE_SYMBOL":"ADPRS","DESCRIPTION":"1_1_109_109","ACETYLSITES":"K109k_1_1_109_109","NAME":"ADPRS_K109k"}},{"entity_stable_id":"PRSS1_S124:NP_002760.1","properties":{"GENE_SYMBOL":"PRSS1"}},{"entity_stable_id":"PRSS1_S127:NP_002760.1","properties":{"GENE_SYMBOL":"PRSS1"}},{"entity_stable_id":"PRSS1_S149:NP_002760.1","properties":{"GENE_SYMBOL":"PRSS1"}},{"entity_stable_id":"PRSS1_S150:NP_002760.1","properties":{"GENE_SYMBOL":"PRSS1"}},{"entity_stable_id":"PRSS1_S167:NP_002760.1","properties":{"GENE_SYMBOL":"PRSS1"}},{"entity_stable_id":"PRSS1_S181:NP_002760.1","properties":{"GENE_SYMBOL":"PRSS1"}},{"entity_stable_id":"PRSS1_T125:NP_002760.1","properties":{"GENE_SYMBOL":"PRSS1"}},{"entity_stable_id":"PRSS1_T135:NP_002760.1","properties":{"GENE_SYMBOL":"PRSS1"}},{"entity_stable_id":"PRSS1_T137:NP_002760.1","properties":{"GENE_SYMBOL":"PRSS1"}},{"entity_stable_id":"PRSS1_T180:NP_002760.1","properties":{"GENE_SYMBOL":"PRSS1"}},{"entity_stable_id":"PRSS1_T230:NP_002760.1","properties":{"GENE_SYMBO … (7963 more chars)

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT attribute_id, data_type, count(*)
FROM clinical_attribute_meta
WHERE attribute_id LIKE '%risk%' OR attribute_id LIKE '%score%' OR attribute_id LIKE '%PRS%'
GROUP BY attribute_id, data_type
ORDER BY attribute_id
LIMIT 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 `attribute_id` in scope SELECT DISTINCT attribute_id, data_type, count(*) FROM clinical_attribute_meta WHERE (attribute_id LIKE '%risk%') OR (attribute_id LIKE '%score%') OR (attribute_id LIKE '%PRS%') GROUP BY attribute_id, data_type ORDER BY attribute_id ASC LIMIT 100. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_list_table_columns
{
 "table": "clinical_attribute_meta"
}

◀ 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 attr_id, display_name
FROM clinical_attribute_meta
WHERE attr_id LIKE '%risk%' OR attr_id LIKE '%score%' OR attr_id LIKE '%PRS%'
   OR display_name LIKE '%risk%' OR display_name LIKE '%score%' OR display_name LIKE '%polygenic%'
ORDER BY attr_id
LIMIT 100
"
}

◀ result
{"rows":[{"attr_id":"CLINICAL_PDL1_SCORE","display_name":"Clinically reported PD-L1 score"},{"attr_id":"ESTIMATE IMMUNESCORE","display_name":"ESTIMATE immune score"},{"attr_id":"ESTIMATE STROMALSCORE","display_name":"ESTIMATE stromal score"},{"attr_id":"ESTIMATESCORE","display_name":"Overall ESTIMATE score"},{"attr_id":"ESTIMATE_COMBINED_SCORE","display_name":"ESTIMATE combined score"},{"attr_id":"ESTIMATE_IMMUNESCORE","display_name":"ESTIMATE immune score"},{"attr_id":"ESTIMATE_IMMUNE_SCORE","display_name":"ESTIMATE immune score"},{"attr_id":"ESTIMATE_STROMALSCORE","display_name":"ESTIMATE stromal score"},{"attr_id":"ESTIMATE_STROMAL_SCORE","display_name":"ESTIMATE stromal score"},{"attr_id":"HALO_TUMOR_QUALITY","display_name":"Halo tumor quality score"},{"attr_id":"HER2_IHC_SCORE","display_name":"HER2 ihc score"},{"attr_id":"HIGHEST_CPS_SCORE_AT_BASELINE","display_name":"Highest CPS score at baseline"},{"attr_id":"HISTORY_HEPATO_CARCINOMA_RISK_FACTORS","display_name":"History hepato carcinoma risk factor"},{"attr_id":"ISHAK_FIBROSIS_SCORE","display_name":"Liver fibrosis ishak score category"},{"attr_id":"JS_PDL1_SCORE","display_name":"JS PD-L1 score"},{"attr_id":"NESTIN_STAINING_SCORE","display_name":"Nestin staining score"},{"attr_id":"NTE_ER_IHC_INTENSITY_SCORE","display_name":"Nte er ihc intensity score"},{"attr_id":"NTE_HER2_POSITIVITY_IHC_SCORE","display_name":"Nte HER2 positivity ihc score"},{"attr_id":"NTE_PR_IHC_INTENSITY_SCORE","display_name":"Nte pr ihc intensity score"},{"attr_id":"OTHER_HEPATO_CARCINOMA_RISK_FACTORS","display_name":"History hepato carcinoma risk factor other"},{"attr_id":"PERFORMANCE_STATUS_DAYS_TO","display_name":"Days to initial score performance status scale"},{"attr_id":"PR_POSITIVITY_IHC_INTENSITY_SCORE","display_name":"PR positivity ihc intensity score"},{"attr_id":"SAMPLE_CPS_SCORE","display_name":"Sample CPS score"},{"attr_id":"SBS3_SCORE","display_name":"SBS3 score"},{"attr_id":"SIGMA_SCORE","display_name":"SigMA score"},{"attr_id":"TMPRSS2_ERG_FUSION_STATUS","display_name":"TMPRSS2-ERG Fusion Status"},{"attr_id":"XCELL_STROMASCORE","display_name":"xCell Stromascore"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT cs.cancer_study_identifier, cam.attr_id, cam.display_name
FROM clinical_attribute_meta cam
JOIN cancer_study cs ON cam.cancer_study_id = cs.cancer_study_id
WHERE cam.attr_id IN ('CLINICAL_PDL1_SCORE', 'ESTIMATE IMMUNESCORE', 'ESTIMATE_IMMUNESCORE', 
                       'SIGMA_SCORE', 'SBS3_SCORE')
ORDER BY cs.cancer_study_identifier, cam.attr_id
LIMIT 200
"
}

◀ result
{"rows":[{"cancer_study_identifier":"luad_cptac_2020","attr_id":"ESTIMATE IMMUNESCORE","display_name":"ESTIMATE immune score"},{"cancer_study_identifier":"lung_msk_mind_2020","attr_id":"CLINICAL_PDL1_SCORE","display_name":"Clinically reported PD-L1 score"},{"cancer_study_identifier":"lusc_cptac_2021","attr_id":"ESTIMATE_IMMUNESCORE","display_name":"ESTIMATE immune score"},{"cancer_study_identifier":"prad_msk_2025","attr_id":"SBS3_SCORE","display_name":"SBS3 score"},{"cancer_study_identifier":"prad_msk_2025","attr_id":"SIGMA_SCORE","display_name":"SigMA score"},{"cancer_study_identifier":"ucec_cptac_2020","attr_id":"ESTIMATE_IMMUNESCORE","display_name":"ESTIMATE Immune Score"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT 
  gpm.molecular_profile_id,
  gpm.profile_name,
  gpm.genetic_profile_description
FROM genetic_profile gpm
WHERE gpm.genetic_profile_type = 'GENERIC_ASSAY'
  AND (gpm.profile_name LIKE '%risk%' OR gpm.profile_name LIKE '%polygenic%' OR gpm.profile_name LIKE '%PRS%'
       OR gpm.genetic_profile_description LIKE '%risk%' OR gpm.genetic_profile_description LIKE '%polygenic%')
LIMIT 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 'gpm.molecular_profile_id' cannot be resolved from table with name gpm. In scope SELECT DISTINCT gpm.molecular_profile_id, gpm.profile_name, gpm.genetic_profile_description FROM genetic_profile AS gpm WHERE (gpm.genetic_profile_type = 'GENERIC_ASSAY') AND ((gpm.profile_name LIKE '%risk%') OR (gpm.profile_name LIKE '%polygenic%') OR (gpm.profile_name LIKE '%PRS%') OR (gpm.genetic_profile_description LIKE '%risk%') OR (gpm.genetic_profile_description LIKE '%polygenic%')) LIMIT 100. Maybe you meant: ['gpm.genetic_profile_id']. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_list_table_columns
{
 "table": "genetic_profile"
}

◀ result
{"columns":[{"name":"genetic_profile_id","type":"Int64"},{"name":"stable_id","type":"String"},{"name":"cancer_study_id","type":"Int64"},{"name":"genetic_alteration_type","type":"String"},{"name":"generic_assay_type","type":"Nullable(String)"},{"name":"datatype","type":"String"},{"name":"name","type":"String"},{"name":"description","type":"Nullable(String)"},{"name":"show_profile_in_analysis_tab","type":"Int32"},{"name":"pivot_threshold","type":"Nullable(Float64)"},{"name":"sort_order","type":"Nullable(String)"},{"name":"patient_level","type":"Nullable(Int32)"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT 
  gp.stable_id,
  gp.name,
  gp.description,
  gp.genetic_alteration_type
FROM genetic_profile gp
WHERE gp.genetic_alteration_type = 'GENERIC_ASSAY'
  AND (gp.name LIKE '%risk%' OR gp.name LIKE '%polygenic%' OR gp.name LIKE '%PRS%'
       OR gp.description LIKE '%risk%' OR gp.description LIKE '%polygenic%')
ORDER BY gp.stable_id
LIMIT 100
"
}

◀ result
{"rows":[]}

═ answer (success)
Based on my comprehensive search of the cBioPortal database, **there are no studies with polygenic risk score (PRS) data currently available**.

I searched for:
- Polygenic risk scores or "PRS" in clinical attributes
- Risk score-related generic assay profiles
- All clinical attribute types containing "risk", "score", or "polygenic"

**What I found instead:**
The database contains some related score-based attributes in a few studies:
- **SigMA score** and **SBS3 score** in the prostate cancer MSK 2025 study (`prad_msk_2025`)
- **ESTIMATE immune/stromal scores** in CPTAC lung cancer studies (`luad_cptac_2020`, `lusc_cptac_2021`)
- **Clinical PD-L1 scores** in the MSK Mind lung cancer study (`lung_msk_mind_2020`)

These are distinct from polygenic risk scores—they are tumor-based or immunological scores, not germline genetic risk prediction models.

If you're interested in adding polygenic risk score data to cBioPortal, or if you're looking for a specific PRS-related attribute, I'd recommend checking the [official cBioPortal data submission guidelines](https://www.cbioportal.org).