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

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

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

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

◀ result
{"result":[{"cancer_study_identifier":"msk_met_2021","name":"MSK MetTropism (MSK, Cell 2021)","description":"MSK-MET (Memorial Sloan Kettering - Metastatic Events and Tropisms) is a pan-cancer cohort of tumor genomic and clinical outcome data from 25,000 patients. The dataset identifies associations between tumor genomic alterations and patterns of metastatic dissemination across 50 tumor types; showing that chromosomal instability is strongly correlated with metastatic burden in some tumor types, like prostate and lung adenocarcinomas and HR+/HER2+ breast ductal carcinoma, but not in others, such as colorectal MSS, pancreatic adenocarcinoma and high-grade serous ovarian cancer. The study also identifies somatic alterations associated with increased metastatic burden and routes of metastatic spread. Our data offers a resource for the investigation of the biologic basis for metastatic spread and highlights the role of chromosomal instability in cancer progression. This data is available under the <a href=\"https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en\">Creative Commons BY-NC-ND 4.0 license</a>.","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)","description":"Targeted and whole-exome sequencing of 2653 lung adenocarcinoma tumor/normal sample pairs.","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)","description":"Targeted sequencing of 860 patients with metastatic lung adenocarcinoma","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)","description":"Targeted sequencing of 604 lung adenocarcinoma tumor/normal pairs via MSK-IMPACT.","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)","description":"TCGA Lung Adenocarcinoma. Source data from <A HREF=\"http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/LUAD/20160128/\">GDAC Firehose</A>. Previously known as TCGA Provisional.","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)","description":"TCGA Lung Adenocarcinoma. Source data from <A HREF=\"https://gdc.cancer.gov\">NCI GDC</A> and generated in Aug 2025 using <A HREF=\"https://cda.readthedocs.io/en/latest/\" … (4811 more chars)

▶ clickhouse_run_select_query
{
 "query": "
SELECT 
  cancer_study_identifier,
  mutation_sample_count,
  cna_sample_count,
  sample_count
FROM cancer_study
WHERE cancer_study_identifier IN (
  'msk_met_2021',
  'luad_mskcc_2023_met_organotropism',
  'lung_msk_2017',
  'luad_mskcc_2020',
  'luad_tcga',
  'luad_tcga_gdc',
  'luad_tcga_pan_can_atlas_2018',
  'luad_msk_npjpo_2021',
  'luad_oncosg_2020',
  'lung_msk_mind_2020',
  'luad_cptac_gdc',
  'luad_tcga_pub',
  'luad_mskimpact_2021',
  'luad_broad',
  'luad_tsp',
  'luad_cptac_2020',
  'luad_cas_2020',
  'luad_mskcc_2015'
)
AND mutation_sample_count > 0
AND cna_sample_count > 0
ORDER BY sample_count DESC
",
 "max_rows": 100
}

◀ result
{"rows":[{"cancer_study_identifier":"msk_met_2021","mutation_sample_count":25775,"cna_sample_count":25775,"sample_count":25775},{"cancer_study_identifier":"luad_mskcc_2023_met_organotropism","mutation_sample_count":2653,"cna_sample_count":2422,"sample_count":2653},{"cancer_study_identifier":"lung_msk_2017","mutation_sample_count":915,"cna_sample_count":915,"sample_count":915},{"cancer_study_identifier":"luad_mskcc_2020","mutation_sample_count":604,"cna_sample_count":604,"sample_count":604},{"cancer_study_identifier":"luad_tcga","mutation_sample_count":230,"cna_sample_count":516,"sample_count":586},{"cancer_study_identifier":"luad_tcga_gdc","mutation_sample_count":559,"cna_sample_count":508,"sample_count":571},{"cancer_study_identifier":"luad_tcga_pan_can_atlas_2018","mutation_sample_count":566,"cna_sample_count":511,"sample_count":566},{"cancer_study_identifier":"luad_msk_npjpo_2021","mutation_sample_count":426,"cna_sample_count":426,"sample_count":426},{"cancer_study_identifier":"luad_oncosg_2020","mutation_sample_count":302,"cna_sample_count":302,"sample_count":305},{"cancer_study_identifier":"lung_msk_mind_2020","mutation_sample_count":247,"cna_sample_count":247,"sample_count":247},{"cancer_study_identifier":"luad_cptac_gdc","mutation_sample_count":236,"cna_sample_count":232,"sample_count":241},{"cancer_study_identifier":"luad_tcga_pub","mutation_sample_count":230,"cna_sample_count":230,"sample_count":230},{"cancer_study_identifier":"luad_mskimpact_2021","mutation_sample_count":186,"cna_sample_count":186,"sample_count":186},{"cancer_study_identifier":"luad_broad","mutation_sample_count":183,"cna_sample_count":183,"sample_count":183},{"cancer_study_identifier":"luad_cptac_2020","mutation_sample_count":110,"cna_sample_count":110,"sample_count":110}]}

═ answer (success)
## Lung Adenocarcinoma Studies with Mutation & Copy-Number Data

**15 studies** have lung adenocarcinoma samples with both mutation and copy-number alterations data:

| Study | Study ID | Samples | Mutations | Copy Number |
|-------|----------|---------|-----------|-------------|
| [MSK MetTropism (MSK, Cell 2021)](https://www.cbioportal.org/study/summary?id=msk_met_2021) | msk_met_2021 | 25,775 | 25,775 | 25,775 |
| [Lung Adenocarcinoma Met Organotropism (MSK, Cancer Cell 2023)](https://www.cbioportal.org/study/summary?id=luad_mskcc_2023_met_organotropism) | luad_mskcc_2023_met_organotropism | 2,653 | 2,653 | 2,422 |
| [Non-Small Cell Cancer (MSK, Cancer Discov 2017)](https://www.cbioportal.org/study/summary?id=lung_msk_2017) | lung_msk_2017 | 915 | 915 | 915 |
| [Lung Adenocarcinoma (MSK, J Thorac Oncol 2020)](https://www.cbioportal.org/study/summary?id=luad_mskcc_2020) | luad_mskcc_2020 | 604 | 604 | 604 |
| [Lung Adenocarcinoma (TCGA, PanCancer Atlas)](https://www.cbioportal.org/study/summary?id=luad_tcga_pan_can_atlas_2018) | luad_tcga_pan_can_atlas_2018 | 566 | 566 | 511 |
| [Lung Adenocarcinoma (TCGA GDC, 2025)](https://www.cbioportal.org/study/summary?id=luad_tcga_gdc) | luad_tcga_gdc | 571 | 559 | 508 |
| [Lung Adenocarcinoma (TCGA, Firehose Legacy)](https://www.cbioportal.org/study/summary?id=luad_tcga) | luad_tcga | 586 | 230 | 516 |
| [Lung Adenocarcinoma (MSK, NPJ Precision Oncology 2021)](https://www.cbioportal.org/study/summary?id=luad_msk_npjpo_2021) | luad_msk_npjpo_2021 | 426 | 426 | 426 |
| [Lung Adenocarcinoma (OncoSG, Nat Genet 2020)](https://www.cbioportal.org/study/summary?id=luad_oncosg_2020) | luad_oncosg_2020 | 305 | 302 | 302 |
| [Lung Adenocarcinoma (MSK Mind, Nature Cancer 2022)](https://www.cbioportal.org/study/summary?id=lung_msk_mind_2020) | lung_msk_mind_2020 | 247 | 247 | 247 |
| [Lung Adenocarcinoma (CPTAC GDC, 2025)](https://www.cbioportal.org/study/summary?id=luad_cptac_gdc) | luad_cptac_gdc | 241 | 236 | 232 |
| [Lung Adenocarcinoma (TCGA, Nature 2014)](https://www.cbioportal.org/study/summary?id=luad_tcga_pub) | luad_tcga_pub | 230 | 230 | 230 |
| [Lung Adenocarcinoma (MSK, 2021)](https://www.cbioportal.org/study/summary?id=luad_mskimpact_2021) | luad_mskimpact_2021 | 186 | 186 | 186 |
| [Lung Adenocarcinoma (Broad, Cell 2012)](https://www.cbioportal.org/study/summary?id=luad_broad) | luad_broad | 183 | 183 | 183 |
| [Lung Adenocarcinoma (CPTAC, Cell 2020)](https://www.cbioportal.org/study/summary?id=luad_cptac_2020) | luad_cptac_2020 | 110 | 110 | 110 |

**Key observations:**
- **Largest cohort:** MSK MetTropism (25,775 LUAD samples) — a pan-cancer study with comprehensive genomic data
- **Most focused LUAD cohorts:** TCGA PanCancer Atlas (566 samples) and TCGA GDC (571 samples) are the most comprehensive TCGA LUAD datasets
- **MSK-focused:** Several MSK-IMPACT studies offer targeted sequencing data with both mutation and CNA information