Q (haiku): Which cBioPortal studies include lung adenocarcinoma samples with mutation and copy-number data?

▶ list_studies
{
 "search": "lung adenocarcinoma",
 "limit": "100"
}

✗ error
<tool_use_error>Error: No such tool available: mcp__navigator__list_studies</tool_use_error>

▶ list_studies
{
 "search": "lung adenocarcinoma",
 "limit": 100
}

◀ result
{"result":[{"cancer_study_identifier":"msk_met_2021","name":"MSK MetTropism (MSK, Cell 2021)","type_of_cancer_id":"mixed","sample_count":25775,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=msk_met_2021"},{"cancer_study_identifier":"luad_mskcc_2023_met_organotropism","name":"Lung Adenocarcinoma Met Organotropism (MSK, Cancer Cell 2023)","type_of_cancer_id":"luad","sample_count":2653,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=luad_mskcc_2023_met_organotropism"},{"cancer_study_identifier":"lung_msk_2017","name":"Non-Small Cell Cancer (MSK, Cancer Discov 2017)","type_of_cancer_id":"luad","sample_count":915,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=lung_msk_2017"},{"cancer_study_identifier":"luad_mskcc_2020","name":"Lung Adenocarcinoma (MSK, J Thorac Oncol 2020)","type_of_cancer_id":"luad","sample_count":604,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=luad_mskcc_2020"},{"cancer_study_identifier":"luad_tcga","name":"Lung Adenocarcinoma (TCGA, Firehose Legacy)","type_of_cancer_id":"luad","sample_count":586,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=luad_tcga"},{"cancer_study_identifier":"luad_tcga_gdc","name":"Lung Adenocarcinoma (TCGA GDC, 2025)","type_of_cancer_id":"luad","sample_count":571,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=luad_tcga_gdc"},{"cancer_study_identifier":"luad_tcga_pan_can_atlas_2018","name":"Lung Adenocarcinoma (TCGA, PanCancer Atlas)","type_of_cancer_id":"luad","sample_count":566,"has_guide":true,"url":"https://www.cbioportal.org/study/summary?id=luad_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"luad_msk_npjpo_2021","name":"Lung Adenocarcinoma (MSK, NPJ Precision Oncology 2021)","type_of_cancer_id":"luad","sample_count":426,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=luad_msk_npjpo_2021"},{"cancer_study_identifier":"luad_oncosg_2020","name":"Lung Adenocarcinoma (OncoSG, Nat Genet 2020)","type_of_cancer_id":"luad","sample_count":305,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=luad_oncosg_2020"},{"cancer_study_identifier":"lung_msk_mind_2020","name":"Lung Adenocarcinoma (MSK Mind,Nature Cancer 2022)","type_of_cancer_id":"lung","sample_count":247,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=lung_msk_mind_2020"},{"cancer_study_identifier":"luad_cptac_gdc","name":"Lung Adenocarcinoma (CPTAC GDC, 2025)","type_of_cancer_id":"luad","sample_count":241,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=luad_cptac_gdc"},{"cancer_study_identifier":"luad_tcga_pub","name":"Lung Adenocarcinoma (TCGA, Nature 2014)","type_of_cancer_id":"luad","sample_count":230,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=luad_tcga_pub"},{"cancer_study_identifier":"luad_mskimpact_2021","name":"Lung Adenocarcinoma (MSK, 2021)","type_of_cancer_id":"luad","sample_count":186,"has_guide":false, … (1174 more chars)

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT
    cs.cancer_study_identifier,
    cs.name,
    cs.description,
    COUNT(DISTINCT CASE WHEN mp.genetic_alteration_type = 'MUTATION_EXTENDED' THEN mp.molecular_profile_id END) as has_mutations,
    COUNT(DISTINCT CASE WHEN mp.genetic_alteration_type = 'COPY_NUMBER_ALTERATION' THEN mp.molecular_profile_id END) as has_cna,
    COUNT(DISTINCT CASE WHEN mp.genetic_alteration_type IN ('MUTATION_EXTENDED', 'COPY_NUMBER_ALTERATION') THEN mp.molecular_profile_id END) as total_relevant_profiles,
    COUNT(DISTINCT s.sample_id) as sample_count
FROM cancer_study cs
JOIN study_sample ss ON cs.cancer_study_identifier = ss.cancer_study_identifier
JOIN sample s ON ss.sample_id = s.sample_id
LEFT JOIN molecular_profile mp ON cs.cancer_study_identifier = mp.cancer_study_identifier
WHERE cs.type_of_cancer_id = 'luad'
GROUP BY cs.cancer_study_identifier, cs.name, cs.description
HAVING has_mutations > 0 AND has_cna > 0
ORDER BY sample_count DESC
",
 "max_rows": 100
}

◀ result
{"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 60\n Code: 60. DB::Exception: Unknown table expression identifier 'molecular_profile' in scope SELECT DISTINCT cs.cancer_study_identifier, cs.name, cs.description, COUNTDistinct(multiIf(mp.genetic_alteration_type = 'MUTATION_EXTENDED', mp.molecular_profile_id, NULL)) AS has_mutations, COUNTDistinct(multiIf(mp.genetic_alteration_type = 'COPY_NUMBER_ALTERATION', mp.molecular_profile_id, NULL)) AS has_cna, COUNTDistinct(multiIf((mp.genetic_alteration_type IN ('MUTATION_EXTENDED', 'COPY_NUMBER_ALTERATION')), mp.molecular_profile_id, NULL)) AS total_relevant_profiles, COUNTDistinct(s.sample_id) AS sample_count FROM cancer_study AS cs INNER JOIN study_sample AS ss ON cs.cancer_study_identifier = ss.cancer_study_identifier INNER JOIN sample AS s ON ss.sample_id = s.sample_id LEFT JOIN molecular_profile AS mp ON cs.cancer_study_identifier = mp.cancer_study_identifier WHERE cs.type_of_cancer_id = 'luad' GROUP BY cs.cancer_study_identifier, cs.name, cs.description HAVING (has_mutations > 0) AND (has_cna > 0) ORDER BY sample_count DESC. (UNKNOWN_TABLE) (version 26.4.1.2359 (official build))\n"}

▶ 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": "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
    cs.cancer_study_identifier,
    cs.name,
    COUNT(DISTINCT CASE WHEN gp.genetic_alteration_type = 'MUTATION_EXTENDED' THEN gp.genetic_profile_id END) as has_mutations,
    COUNT(DISTINCT CASE WHEN gp.genetic_alteration_type = 'COPY_NUMBER_ALTERATION' THEN gp.genetic_profile_id END) as has_cna,
    COUNT(DISTINCT s.sample_id) as sample_count
FROM cancer_study cs
LEFT JOIN genetic_profile gp ON cs.cancer_study_id = gp.cancer_study_id
LEFT JOIN genetic_alteration ga ON gp.genetic_profile_id = ga.genetic_profile_id
LEFT JOIN sample_derived s ON cs.cancer_study_identifier = s.cancer_study_identifier
WHERE cs.type_of_cancer_id = 'luad'
GROUP BY cs.cancer_study_identifier, cs.name
HAVING has_mutations > 0 AND has_cna > 0
ORDER BY sample_count DESC
",
 "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 's.sample_id' cannot be resolved from table with name s. In scope SELECT DISTINCT cs.cancer_study_identifier, cs.name, COUNTDistinct(multiIf(gp.genetic_alteration_type = 'MUTATION_EXTENDED', gp.genetic_profile_id, NULL)) AS has_mutations, COUNTDistinct(multiIf(gp.genetic_alteration_type = 'COPY_NUMBER_ALTERATION', gp.genetic_profile_id, NULL)) AS has_cna, COUNTDistinct(s.sample_id) AS sample_count FROM cancer_study AS cs LEFT JOIN genetic_profile AS gp ON cs.cancer_study_id = gp.cancer_study_id LEFT JOIN genetic_alteration AS ga ON gp.genetic_profile_id = ga.genetic_profile_id LEFT JOIN sample_derived AS s ON cs.cancer_study_identifier = s.cancer_study_identifier WHERE cs.type_of_cancer_id = 'luad' GROUP BY cs.cancer_study_identifier, cs.name HAVING (has_mutations > 0) AND (has_cna > 0) ORDER BY sample_count DESC. Maybe you meant: ['s.sample_type']. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_list_table_columns
{
 "table": "sample_derived"
}

◀ result
{"columns":[{"name":"sample_unique_id","type":"String"},{"name":"sample_unique_id_base64","type":"String"},{"name":"sample_stable_id","type":"String"},{"name":"patient_unique_id","type":"String"},{"name":"patient_unique_id_base64","type":"String"},{"name":"patient_stable_id","type":"String"},{"name":"cancer_study_identifier","type":"LowCardinality(String)"},{"name":"internal_id","type":"Int32"},{"name":"patient_internal_id","type":"Int32"},{"name":"sample_type","type":"String"},{"name":"sequenced","type":"Int32"},{"name":"copy_number_segment_present","type":"Int32"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT
    cs.cancer_study_identifier,
    cs.name,
    COUNT(DISTINCT CASE WHEN gp.genetic_alteration_type = 'MUTATION_EXTENDED' THEN gp.genetic_profile_id END) as has_mutations,
    COUNT(DISTINCT CASE WHEN gp.genetic_alteration_type = 'COPY_NUMBER_ALTERATION' THEN gp.genetic_profile_id END) as has_cna,
    COUNT(DISTINCT s.sample_unique_id) as sample_count
FROM cancer_study cs
LEFT JOIN genetic_profile gp ON cs.cancer_study_id = gp.cancer_study_id
LEFT JOIN sample_derived s ON cs.cancer_study_identifier = s.cancer_study_identifier
WHERE cs.type_of_cancer_id = 'luad'
GROUP BY cs.cancer_study_identifier, cs.name
HAVING has_mutations > 0 AND has_cna > 0
ORDER BY sample_count DESC
",
 "max_rows": 100
}

◀ result
{"rows":[{"cs.cancer_study_identifier":"luad_mskcc_2023_met_organotropism","cs.name":"Lung Adenocarcinoma Met Organotropism (MSK, Cancer Cell 2023)","has_mutations":1,"has_cna":1,"sample_count":2653},{"cs.cancer_study_identifier":"lung_msk_2017","cs.name":"Non-Small Cell Cancer (MSK, Cancer Discov 2017)","has_mutations":1,"has_cna":1,"sample_count":915},{"cs.cancer_study_identifier":"luad_mskcc_2020","cs.name":"Lung Adenocarcinoma (MSK, J Thorac Oncol 2020)","has_mutations":1,"has_cna":1,"sample_count":604},{"cs.cancer_study_identifier":"luad_tcga","cs.name":"Lung Adenocarcinoma (TCGA, Firehose Legacy)","has_mutations":1,"has_cna":2,"sample_count":586},{"cs.cancer_study_identifier":"luad_tcga_gdc","cs.name":"Lung Adenocarcinoma (TCGA GDC, 2025)","has_mutations":1,"has_cna":1,"sample_count":571},{"cs.cancer_study_identifier":"luad_tcga_pan_can_atlas_2018","cs.name":"Lung Adenocarcinoma (TCGA, PanCancer Atlas)","has_mutations":1,"has_cna":2,"sample_count":566},{"cs.cancer_study_identifier":"luad_msk_npjpo_2021","cs.name":"Lung Adenocarcinoma (MSK, NPJ Precision Oncology 2021)","has_mutations":1,"has_cna":1,"sample_count":426},{"cs.cancer_study_identifier":"luad_oncosg_2020","cs.name":"Lung Adenocarcinoma (OncoSG, Nat Genet 2020)","has_mutations":1,"has_cna":1,"sample_count":305},{"cs.cancer_study_identifier":"luad_cptac_gdc","cs.name":"Lung Adenocarcinoma (CPTAC GDC, 2025)","has_mutations":1,"has_cna":1,"sample_count":241},{"cs.cancer_study_identifier":"luad_tcga_pub","cs.name":"Lung Adenocarcinoma (TCGA, Nature 2014)","has_mutations":1,"has_cna":2,"sample_count":230},{"cs.cancer_study_identifier":"luad_mskimpact_2021","cs.name":"Lung Adenocarcinoma (MSK, 2021)","has_mutations":1,"has_cna":1,"sample_count":186},{"cs.cancer_study_identifier":"luad_broad","cs.name":"Lung Adenocarcinoma (Broad, Cell 2012)","has_mutations":1,"has_cna":1,"sample_count":183},{"cs.cancer_study_identifier":"luad_cptac_2020","cs.name":"Lung Adenocarcinoma (CPTAC, Cell 2020)","has_mutations":1,"has_cna":1,"sample_count":110}]}

═ answer (success)
Perfect! Here are the **13 lung adenocarcinoma (LUAD) studies** in cBioPortal that include both mutation and copy-number alteration data:

| Study ID | Study Name | Samples | Data Types |
|-----------|-----------|---------|-----------|
| **luad_mskcc_2023_met_organotropism** | Lung Adenocarcinoma Met Organotropism (MSK, Cancer Cell 2023) | 2,653 | Mutations, CNA |
| **lung_msk_2017** | Non-Small Cell Cancer (MSK, Cancer Discov 2017) | 915 | Mutations, CNA |
| **luad_mskcc_2020** | Lung Adenocarcinoma (MSK, J Thorac Oncol 2020) | 604 | Mutations, CNA |
| **luad_tcga** | Lung Adenocarcinoma (TCGA, Firehose Legacy) | 586 | Mutations, CNA (×2) |
| **luad_tcga_gdc** | Lung Adenocarcinoma (TCGA GDC, 2025) | 571 | Mutations, CNA |
| **luad_tcga_pan_can_atlas_2018** | Lung Adenocarcinoma (TCGA, PanCancer Atlas) | 566 | Mutations, CNA (×2) |
| **luad_msk_npjpo_2021** | Lung Adenocarcinoma (MSK, NPJ Precision Oncology 2021) | 426 | Mutations, CNA |
| **luad_oncosg_2020** | Lung Adenocarcinoma (OncoSG, Nat Genet 2020) | 305 | Mutations, CNA |
| **luad_cptac_gdc** | Lung Adenocarcinoma (CPTAC GDC, 2025) | 241 | Mutations, CNA |
| **luad_tcga_pub** | Lung Adenocarcinoma (TCGA, Nature 2014) | 230 | Mutations, CNA (×2) |
| **luad_mskimpact_2021** | Lung Adenocarcinoma (MSK, 2021) | 186 | Mutations, CNA |
| **luad_broad** | Lung Adenocarcinoma (Broad, Cell 2012) | 183 | Mutations, CNA |
| **luad_cptac_2020** | Lung Adenocarcinoma (CPTAC, Cell 2020) | 110 | Mutations, CNA |

**Highlighted recommendations:**
- **Largest cohort:** MSK Met Organotropism (2,653 samples)
- **Most comprehensive (TCGA):** PanCancer Atlas or Firehose Legacy (both have dual CNA profiles; ~566–586 samples)
- **Most clinically relevant:** MSK studies (luad_mskcc_2023_met_organotropism, luad_mskcc_2020) for precision oncology data

Would you like to explore any of these studies further, or query specific genes/mutations?