Q (sonnet): are lung carcinosarcomas associated with BRIP1 mutations?

▶ list_guides
{}

▶ search_oncotree
{
 "search_term": "carcinosarcoma lung"
}

◀ result
{"result":[{"uri":"cbioportal://mutation-frequency-guide","description":"Comprehensive guide for calculating gene mutation frequencies with gene-specific profiling denominators"},{"uri":"cbioportal://clinical-data-guide","description":"Guide for querying clinical data including patient vs sample level considerations"},{"uri":"cbioportal://sample-filtering-guide","description":"Guide for filtering samples and studies in cBioPortal queries"},{"uri":"cbioportal://common-pitfalls","description":"Guide to avoid common mistakes when querying cBioPortal data. If you already know which numbered pitfall applies, fetch just that section via read_guide(\"cbioportal://common-pitfalls#<number>\") (e.g. #16) instead of the full guide"},{"uri":"cbioportal://treatment-guide","description":"Guide for querying treatment/clinical event data including drug agents, timelines, and linking to genomic data"},{"uri":"cbioportal://faq-guide","description":"General cBioPortal FAQ: history, how to cite, data types, reference genome, abbreviations, GISTIC thresholds, API access"},{"uri":"cbioportal://statistical-tests-guide","description":"Statistical test selection guide — decision matrix for choosing Fisher's exact, Wilcoxon, chi-squared, t-test, ANOVA, etc. based on data type and group count"},{"uri":"cbioportal://gene-expression-guide","description":"Gene expression / copy-number / methylation analysis. Covers genetic_alteration_derived, profile_type discovery, and the gene_pair_coexpression view for Spearman correlation between two genes"},{"uri":"cbioportal://external-resources-guide","description":"Guide for finding external linked resources such as imaging, pathology, Minerva, HTAN, or other resource_* table links before declaring data unavailable"},{"uri":"cbioportal://gene-resolution-guide","description":"Guide for resolving ambiguous gene symbols, aliases, gene families, and shorthand such as CD3 before querying expression or alteration data"},{"uri":"cbioportal://study-resolution-guide","description":"Guide for resolving requested studies, avoiding silent substitute cohorts, and redirecting to known external cBioPortal instances when data is not in this deployment"},{"uri":"cbioportal://germline-guide","description":"Guide for querying germline variant data — storage columns, study discovery, query patterns, and somatic vs germline considerations"},{"uri":"cbioportal://study-guide/{study_id}","description":"Dynamic study-specific guide - use get_study_guide(study_id) tool to generate"}]}

◀ result
{"result":[]}

▶ search_oncotree
{
 "search_term": "carcinosarcoma"
}

▶ read_guide
{
 "uri": "cbioportal://mutation-frequency-guide"
}

◀ result
{"result":[{"code":"CSNOS","name":"Breast Invasive Carcinosarcoma, NOS","score":50,"mainType":"Breast Cancer","tissue":"Breast","hierarchy":"BREAST > BRCA > CSNOS"},{"code":"MCS","name":"Metaplastic Carcinosarcoma","score":50,"mainType":"Breast Cancer","tissue":"Breast","hierarchy":"BREAST > MBC > MMBC > MCS"},{"code":"OCS","name":"Ovarian Carcinosarcoma/Malignant Mixed Mesodermal Tumor","score":50,"mainType":"Ovarian Cancer","tissue":"Ovary/Fallopian Tube","hierarchy":"OVARY > OVT > OCS"},{"code":"UCS","name":"Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor","score":50,"mainType":"Endometrial Cancer","tissue":"Uterus","hierarchy":"UTERUS > UCEC > UCS"}]}

◀ result
# Mutation Frequency Analysis Guide

## IMPORTANT: Reporting Mutation Frequencies
- **ALWAYS report frequencies as percentages**, not raw counts: `frequency = (altered_samples / total_profiled_samples) × 100`
- For quick frequency lookups, **prefer the TCGA Pan-Cancer Atlas study first**, then offer to expand to other studies
- When reporting across multiple studies, show **ranges** (e.g., "TP53 is mutated in 30–60% of samples") rather than a single average
- **NEVER** sum mutation events across studies to compute an aggregate frequency — this can exceed 100% due to double-counting
- Warn users that samples may overlap across cohorts (e.g., MSK studies may share patients)
- **Choose and state the counting unit**: use patient-level frequencies for prevalence/rate questions unless the user explicitly asks for samples; use sample-level frequencies when the user asks about samples.
- **For "across cancer types" questions**, jump to the [Cross-Cancer-Type Mutation Frequency](#cross-cancer-type-mutation-frequency) section below — there is one correct recipe and several common wrong ones.

## Counting Unit: Samples vs Patients

Before answering any mutation count or frequency question, decide whether the unit is samples or patients and state that choice in the answer.

| User wording | Counting unit |
|--------------|---------------|
| "prevalence", "rate", "fraction of patients", "patients with", "how common is" | Patient-level: `COUNT(DISTINCT patient_unique_id)` |
| "samples", "specimens", "biopsies", sample-level cohort composition | Sample-level: `COUNT(DISTINCT sample_unique_id)` |
| Ambiguous | Ask, or default to patient-level for prevalence/rate language and say so |

### Cross-study sample-count caveat

When an answer touches more than one study and reports a sample count, prepend a one-line caveat:

> Sample IDs are unique within cBioPortal study prefixes, not guaranteed biological-sample identifiers across studies; overlapping cohorts can count the same patient/sample more than once.

Prefer one of these safer approaches:

- Use a shipped `cancer_study_query_preferences` cohort such as `pan_cancer_tcga` or `all_studies_non_redundant`.
- Restrict to one named study.
- Aggregate by `patient_unique_id` when the biological question is patient prevalence.

## STOP rule: a frequency above 100% means your query is wrong

If your query returns a frequency over 100%, **do not try to debug or explain the data inconsistency to the user**. The cause is always one of these query bugs:

- Summing mutation events instead of `COUNT(DISTINCT sample_unique_id)` for the numerator
- Using a study-wide sample count as the denominator instead of the gene-specific profiled count
- Cross-study aggregation where the same biological sample appears under multiple `sample_unique_id` values (e.g., MSK-IMPACT and MSK-CHORD share patients)
- **Joining the profiled CTE through `gene_panel` / `gene_panel_list` without a WES branch.** `gene_panel_id = 'WES'` is *not* a row in … (35166 more chars)

▶ clickhouse_run_select_query
{
 "query": "
SELECT cancer_study_identifier, attribute_name, attribute_value, COUNT(DISTINCT sample_unique_id) AS n
FROM clinical_data_derived
WHERE lower(attribute_value) LIKE '%carcinosarcoma%'
GROUP BY cancer_study_identifier, attribute_name, attribute_value
ORDER BY n DESC
",
 "max_rows": 100
}

◀ result
{"rows":[{"cancer_study_identifier":"msk_impact_50k_2026","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor","n":293},{"cancer_study_identifier":"ucec_ancestry_cds_msk_2023","attribute_name":"HISTOLOGY","attribute_value":"Carcinosarcoma","n":225},{"cancer_study_identifier":"ucec_ancestry_cds_msk_2023","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor","n":225},{"cancer_study_identifier":"msk_met_2021","attribute_name":"SUBTYPE","attribute_value":"Uterine Carcinosarcoma","n":192},{"cancer_study_identifier":"msk_met_2021","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor","n":192},{"cancer_study_identifier":"pancan_mimsi_msk_2024","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor","n":136},{"cancer_study_identifier":"pancan_pdmr_2025","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor","n":105},{"cancer_study_identifier":"msk_impact_50k_2026","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Ovarian Carcinosarcoma/Malignant Mixed Mesodermal Tumor","n":81},{"cancer_study_identifier":"ucs_tcga","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor","n":57},{"cancer_study_identifier":"ucs_tcga_gdc","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor","n":57},{"cancer_study_identifier":"ucs_tcga_pan_can_atlas_2018","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor","n":57},{"cancer_study_identifier":"ucs_tcga_gdc","attribute_name":"CANCER_TYPE","attribute_value":"Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor","n":57},{"cancer_study_identifier":"cellline_ccle_broad","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Ovarian Carcinosarcoma/Malignant Mixed Mesodermal Tumor","n":47},{"cancer_study_identifier":"mycf_msk_2026","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor","n":40},{"cancer_study_identifier":"msk_impact_2017","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor","n":38},{"cancer_study_identifier":"ucec_msk_2018","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor","n":37},{"cancer_study_identifier":"ucs_tcga_pan_can_atlas_2018","attribute_name":"TUMOR_TYPE","attribute_value":"Uterine Carcinosarcoma","n":30},{"cancer_study_identifier":"ucs_jhu_2014","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Uterine Carcinosarcoma/Uterine Mal … (7821 more chars)

▶ clickhouse_run_select_query
{
 "query": "
SELECT sample_unique_id, patient_unique_id, hugo_gene_symbol, mutation_variant, mutation_type
FROM genomic_event_derived
WHERE cancer_study_identifier = 'nsclc_tracerx_2017'
  AND sample_unique_id IN (
    SELECT sample_unique_id FROM clinical_data_derived
    WHERE cancer_study_identifier = 'nsclc_tracerx_2017' AND attribute_name = 'HISTOLOGY' AND attribute_value = 'Carcinosarcoma'
  )
  AND hugo_gene_symbol = 'BRIP1'
"
}

◀ result
{"rows":[]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT cancer_study_identifier, attribute_name, attribute_value, COUNT(DISTINCT sample_unique_id) AS n
FROM clinical_data_derived
WHERE (lower(attribute_value) LIKE '%sarcomatoid%' OR lower(attribute_value) LIKE '%pleomorphic%')
  AND attribute_name IN ('HISTOLOGY','CANCER_TYPE_DETAILED','HISTOLOGIC_SUBTYPE','HISTOLOGICAL_DIAGNOSIS','SUBTYPE')
GROUP BY cancer_study_identifier, attribute_name, attribute_value
ORDER BY n DESC
LIMIT 30
"
}

◀ result
{"rows":[{"cancer_study_identifier":"sarcoma_msk_2022","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Undifferentiated Pleomorphic Sarcoma","n":329},{"cancer_study_identifier":"msk_impact_50k_2026","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Undifferentiated Pleomorphic Sarcoma/Malignant Fibrous Histiocytoma/High-Grade Spindle Cell Sarcoma","n":230},{"cancer_study_identifier":"pancan_pdmr_2025","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Undifferentiated Pleomorphic Sarcoma/Malignant Fibrous Histiocytoma/High-Grade Spindle Cell Sarcoma","n":226},{"cancer_study_identifier":"msk_met_2021","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Undifferentiated Pleomorphic Sarcoma/Malignant Fibrous Histiocytoma/High-Grade Spindle Cell Sarcoma","n":161},{"cancer_study_identifier":"sarcoma_mskcc_2022","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Undifferentiated Pleomorphic Sarcoma/Maligant Fibrous Histiocytoma/High-Grade Spindle Cell Sarcoma","n":145},{"cancer_study_identifier":"ccrcc_utokyo_2013","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Renal Clear Cell Carcinoma with Sarcomatoid Features","n":106},{"cancer_study_identifier":"sarcoma_msk_2022","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Pleomorphic Liposarcoma","n":64},{"cancer_study_identifier":"msk_impact_50k_2026","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Pleomorphic Carcinoma of the Lung","n":61},{"cancer_study_identifier":"msk_impact_2017","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Undifferentiated Pleomorphic Sarcoma/Malignant Fibrous Histiocytoma/High-Grade Spindle Cell Sarcoma","n":59},{"cancer_study_identifier":"pan_origimed_2020","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Undifferentiated Pleomorphic Sarcoma Malignant Fibrous Histiocytoma","n":55},{"cancer_study_identifier":"sarc_tcga_pan_can_atlas_2018","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Undifferentiated Pleomorphic Sarcoma/Malignant Fibrous Histiocytoma/High-Grade Spindle Cell Sarcoma","n":50},{"cancer_study_identifier":"sarc_tcga","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Undifferentiated Pleomorphic Sarcoma/Malignant Fibrous Histiocytoma/High-Grade Spindle Cell Sarcoma","n":49},{"cancer_study_identifier":"msk_chord_2024","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Pleomorphic Carcinoma of the Lung","n":45},{"cancer_study_identifier":"sarc_tcga_pub","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Undifferentiated Pleomorphic Sarcoma/Malignant Fibrous Histiocytoma/High-Grade Spindle Cell Sarcoma","n":44},{"cancer_study_identifier":"msk_impact_50k_2026","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Sarcomatoid Carcinoma of the Lung","n":30},{"cancer_study_identifier":"msk_impact_50k_2026","attribute_name":"CANCER_TYPE_DETAILED","attribute_value":"Pleomorphic Liposarcoma","n":29},{"cancer_study_identifier":"sarcoma_msk_202 … (2242 more chars)

▶ clickhouse_run_select_query
{
 "query": "
WITH cohort AS (
    SELECT DISTINCT sample_unique_id, attribute_value AS histology
    FROM clinical_data_derived
    WHERE cancer_study_identifier = 'msk_impact_50k_2026'
      AND attribute_name = 'CANCER_TYPE_DETAILED'
      AND attribute_value IN ('Sarcomatoid Carcinoma of the Lung','Pleomorphic Carcinoma of the Lung')
),
altered AS (
    SELECT c.histology, COUNT(DISTINCT ged.sample_unique_id) AS altered_samples
    FROM genomic_event_derived ged
    JOIN cohort c USING (sample_unique_id)
    WHERE ged.cancer_study_identifier = 'msk_impact_50k_2026'
      AND ged.variant_type = 'mutation'
      AND ged.mutation_status != 'UNCALLED'
      AND ged.hugo_gene_symbol = 'BRIP1'
      AND ged.off_panel = 0
    GROUP BY c.histology
),
profiled AS (
    SELECT c.histology, COUNT(DISTINCT stgp.sample_unique_id) AS profiled_samples
    FROM sample_to_gene_panel_derived stgp
    JOIN gene_panel gp ON stgp.gene_panel_id = gp.stable_id
    JOIN gene_panel_list gpl ON gp.internal_id = gpl.internal_id
    JOIN gene g ON gpl.gene_id = g.entrez_gene_id
    JOIN cohort c ON c.sample_unique_id = stgp.sample_unique_id
    WHERE stgp.alteration_type = 'MUTATION_EXTENDED'
      AND g.hugo_gene_symbol = 'BRIP1'
      AND stgp.cancer_study_identifier = 'msk_impact_50k_2026'
    GROUP BY c.histology
)
SELECT p.histology, COALESCE(a.altered_samples,0) AS altered, p.profiled_samples,
       ROUND(COALESCE(a.altered_samples,0)*100.0/p.profiled_samples,2) AS pct
FROM profiled p LEFT JOIN altered a USING (histology)
"
}

◀ result
{"rows":[{"histology":"Pleomorphic Carcinoma of the Lung","altered":1,"profiled_samples":61,"pct":1.64},{"histology":"Sarcomatoid Carcinoma of the Lung","altered":0,"profiled_samples":30,"pct":0}]}

▶ resolve_and_route
{
 "studyIds": [
  "msk_impact_50k_2026",
  "nsclc_tracerx_2017"
 ]
}

◀ result
{"success":true,"message":"Found 2 matching studies. Pick the best match (prefer TCGA → prefer PanCancer Atlas), use its metadata to call the appropriate navigation tool(s) and generate URLs immediately. Present other studies as alternatives.","data":{"totalCount":2,"studiesWithMetadata":[{"studyId":"msk_impact_50k_2026","name":"MSK-IMPACT 50K Clinical Sequencing Cohort (MSK, Cancer Cell 2026)","sampleCount":54331,"studyViewUrl":"https://www.cbioportal.org/study?id=msk_impact_50k_2026","metadata":{"clinicalAttributeIds":["AGE_AT_DX","ANCESTRY_LABEL","CANCER_TYPE","CANCER_TYPE_DETAILED","DISEASE_STATUS","FACETS_PLOIDY","FACETS_PURITY","FACETS_QC","FACETS_SUITE_VERSION","FACETS_WGD","FRACTION_GENOME_ALTERED","GENE_PANEL","HLA-A1","HLA-A2","HLA-B1","HLA-B2","HLA-C1","HLA-C2","HLA_A1_LOH","HLA_A2_LOH","HLA_B1_LOH","HLA_B2_LOH","HLA_C1_LOH","HLA_C2_LOH","HLA_GENOTYPE_AVAILABLE","METASTATIC_SITE","MSI_SCORE","MSI_TYPE","MUTATION_COUNT","N_OTHER_CANCER_TYPES","ONCOTREE_CODE","OS_MONTHS","OS_STATUS","PRIMARY_SITE","PURITY_ESTIMATE_FROM_MUTATIONS","SAMPLE_COUNT","SAMPLE_COVERAGE","SAMPLE_TYPE","SEX","SOMATIC_STATUS","TMB_SCORE","TUMOR_PURITY"],"molecularProfileIds":["msk_impact_50k_2026_gistic","msk_impact_50k_2026_mutations","msk_impact_50k_2026_structural_variants"],"genericAssayProfiles":["msk_impact_50k_2026_armlevel_cna","msk_impact_50k_2026_loh_hla","msk_impact_50k_2026_mutational_signatures_contribution_v2"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations","generic_assay_armlevel_cna","generic_assay_loh_hla","generic_assay_mutational_signature"]}},{"studyId":"nsclc_tracerx_2017","name":"Non-Small Cell Lung Cancer (TRACERx, NEJM & Nature 2017)","sampleCount":447,"studyViewUrl":"https://www.cbioportal.org/study?id=nsclc_tracerx_2017","metadata":{"clinicalAttributeIds":["ADJUVANT_TX","AGE","CANCER_TYPE","CANCER_TYPE_DETAILED","CFDNA_INPUT_NG","CT_SLICE_SPACING","ECOG_SCORE","ETHNICITY","GENOME_DOUBLED","HISTOLOGY","KI_67","LNI","MARGIN_STATUS","MUTATION_COUNT","ONCOTREE_CODE","PERCENTAGE_NECROSIS","PET_TBR","PLEURAL_INVASION","RFS_MONTHS","RFS_STATUS","SAMPLE_CLASS","SAMPLE_COLLECTION_TIMEPOINT","SAMPLE_COUNT","SAMPLE_TYPE","SEX","SMOKING_HISTORY","SMOKING_PACK_YEARS","SOMATIC_STATUS","TMB_NONSYNONYMOUS","TUMOR_SIZE","TUMOR_STAGE","TUMOR_VOLUME","UBIQUITOUS_ASSAY_PANEL","VASCULAR_INVASION"],"molecularProfileIds":["nsclc_tracerx_2017_mutations"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations"]}}]}}

▶ navigate_to_study_view
{
 "studyIds": [
  "msk_impact_50k_2026"
 ],
 "filterJson": {
  "clinicalDataFilters": [
   {
    "attributeId": "CANCER_TYPE_DETAILED",
    "values": [
     {
      "value": "Sarcomatoid Carcinoma of the Lung"
     },
     {
      "value": "Pleomorphic Carcinoma of the Lung"
     }
    ]
   }
  ],
  "geneFilters": [
   {
    "molecularProfileIds": [
     "msk_impact_50k_2026_mutations"
    ],
    "geneQueries": [
     [
      {
       "hugoGeneSymbol": "BRIP1"
      }
     ]
    ]
   }
  ]
 }
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/study/summary?id=msk_impact_50k_2026#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CANCER_TYPE_DETAILED%22%2C%22values%22%3A%5B%7B%22value%22%3A%22Sarcomatoid%20Carcinoma%20of%20the%20Lung%22%7D%2C%7B%22value%22%3A%22Pleomorphic%20Carcinoma%20of%20the%20Lung%22%7D%5D%7D%5D%2C%22geneFilters%22%3A%5B%7B%22geneQueries%22%3A%5B%5B%7B%22hugoGeneSymbol%22%3A%22BRIP1%22%7D%5D%5D%2C%22molecularProfileIds%22%3A%5B%22msk_impact_50k_2026_mutations%22%5D%7D%5D%7D","url":"https://www.cbioportal.org/study/summary?id=msk_impact_50k_2026#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CANCER_TYPE_DETAILED%22%2C%22values%22%3A%5B%7B%22value%22%3A%22Sarcomatoid%20Carcinoma%20of%20the%20Lung%22%7D%2C%7B%22value%22%3A%22Pleomorphic%20Carcinoma%20of%20the%20Lung%22%7D%5D%7D%5D%2C%22geneFilters%22%3A%5B%7B%22geneQueries%22%3A%5B%5B%7B%22hugoGeneSymbol%22%3A%22BRIP1%22%7D%5D%5D%2C%22molecularProfileIds%22%3A%5B%22msk_impact_50k_2026_mutations%22%5D%7D%5D%7D","data":{"studyIds":["msk_impact_50k_2026"],"studies":[{"studyId":"msk_impact_50k_2026","name":"MSK-IMPACT 50K Clinical Sequencing Cohort (MSK, Cancer Cell 2026)","sampleCount":54331}],"tab":"summary","hasFilters":true,"hasPlotsConfig":false,"pageDescription":"Overview of all study data displayed as interactive charts summarizing available clinical and genomic data. Click within a chart to filter. Additional charts may be available in the Charts menu."}}

▶ navigate_to_results_view
{
 "studyIds": [
  "msk_impact_50k_2026"
 ],
 "genes": [
  "BRIP1"
 ],
 "studyViewFilter": {
  "clinicalDataFilters": [
   {
    "attributeId": "CANCER_TYPE_DETAILED",
    "values": [
     {
      "value": "Sarcomatoid Carcinoma of the Lung"
     },
     {
      "value": "Pleomorphic Carcinoma of the Lung"
     }
    ]
   }
  ]
 },
 "tab": "oncoprint"
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/results/oncoprint?session_id=6ab5ca2fe497aad53593c277","url":"https://www.cbioportal.org/results/oncoprint?session_id=6ab5ca2fe497aad53593c277","data":{"studyIds":["msk_impact_50k_2026"],"studies":[{"studyId":"msk_impact_50k_2026","name":"MSK-IMPACT 50K Clinical Sequencing Cohort (MSK, Cancer Cell 2026)","sampleCount":54331}],"genes":["BRIP1"],"filteredSampleCount":91,"caseSetId":"-1","sessionId":"6ab5ca2fe497aad53593c277","studyViewUrl":"https://www.cbioportal.org/study?id=msk_impact_50k_2026#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CANCER_TYPE_DETAILED%22%2C%22values%22%3A%5B%7B%22value%22%3A%22Sarcomatoid%20Carcinoma%20of%20the%20Lung%22%7D%2C%7B%22value%22%3A%22Pleomorphic%20Carcinoma%20of%20the%20Lung%22%7D%5D%7D%5D%7D","pageDescription":"Visual summary of alterations in queried genes across samples."}}

═ answer (success)
## Answer

**No — there is no evidence in cBioPortal for an association between lung carcinosarcoma and BRIP1 mutations, primarily because true "lung carcinosarcoma" is essentially absent as a labeled entity in this database.**

### What I found

1. **Dedicated lung carcinosarcoma cohort:** None. Across all cBioPortal studies, "carcinosarcoma" as a clinical label appears only for breast, ovarian, and uterine cancers (per OncoTree and clinical annotations). The **only** lung sample anywhere in the database annotated as `HISTOLOGY = "Carcinosarcoma"` is a single case in the TRACERx NSCLC study (`nsclc_tracerx_2017`) — and that one sample has **no BRIP1 mutation** on record.

2. **Closest related entities (pulmonary sarcomatoid carcinoma spectrum):** Since true carcinosarcoma is a related but distinct WHO entity from sarcomatoid carcinoma, I checked the closest available lung histologies in the largest cohort (`msk_impact_50k_2026`):

| Histology | BRIP1-mutated | Profiled | Frequency |
|---|---|---|---|
| Pleomorphic Carcinoma of the Lung | 1 | 61 | 1.6% |
| Sarcomatoid Carcinoma of the Lung | 0 | 30 | 0% |

These frequencies (0–1.6%) are **low and unremarkable** — consistent with background BRIP1 mutation rates seen broadly in NSCLC, not indicative of an enrichment or disease-defining association.

### Bottom line
With only 1 true lung carcinosarcoma sample in the entire database (BRIP1-wildtype) and n=0–1 BRIP1 mutations in the closest related sarcomatoid/pleomorphic lung carcinoma groups (total n=91), there is **no statistical basis to claim an association** between lung carcinosarcoma and BRIP1. This is a sample-size/data-availability limitation, not a negative finding — the cohort is simply too small to draw a conclusion either way.

[View BRIP1 in Sarcomatoid/Pleomorphic Lung Carcinoma — OncoPrint](https://www.cbioportal.org/results/oncoprint?session_id=6ab5ca2fe497aad53593c277) (n=91 samples, MSK-IMPACT 50K)

[View same cohort in Study View](https://www.cbioportal.org/study/summary?id=msk_impact_50k_2026#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CANCER_TYPE_DETAILED%22%2C%22values%22%3A%5B%7B%22value%22%3A%22Sarcomatoid%20Carcinoma%20of%20the%20Lung%22%7D%2C%7B%22value%22%3A%22Pleomorphic%20Carcinoma%20of%20the%20Lung%22%7D%5D%7D%5D%2C%22geneFilters%22%3A%5B%7B%22geneQueries%22%3A%5B%5B%7B%22hugoGeneSymbol%22%3A%22BRIP1%22%7D%5D%5D%2C%22molecularProfileIds%22%3A%5B%22msk_impact_50k_2026_mutations%22%5D%7D%5D%7D)

If you're aware of a specific lung carcinosarcoma cohort published outside these MSK/TCGA-derived deployments, let me know the study name and I can check whether it's separately indexed in cBioPortal.