Q (haiku): What cancer types in MSK-IMPACT have mutations in TP53?

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

▶ list_studies
{
 "search": "MSK-IMPACT"
}

◀ 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 … (36467 more chars)

◀ result
{"result":[{"cancer_study_identifier":"msk_impact_50k_2026","name":"MSK-IMPACT 50K Clinical Sequencing Cohort (MSK, Cancer Cell 2026)","type_of_cancer_id":"mixed","sample_count":54331,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=msk_impact_50k_2026"},{"cancer_study_identifier":"msk_ch_2023","name":"Cancer Therapy and Clonal Hematopoiesis (MSK, Blood Adv 2023)","type_of_cancer_id":"mixed","sample_count":42714,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=msk_ch_2023"},{"cancer_study_identifier":"msk_chord_2024","name":"MSK-CHORD (MSK, Nature 2024)","type_of_cancer_id":"mixed","sample_count":25040,"has_guide":true,"url":"https://www.cbioportal.org/study/summary?id=msk_chord_2024"},{"cancer_study_identifier":"msk_ch_2020","name":"Cancer Therapy and Clonal Hematopoiesis (MSK, Nat Genet 2020)","type_of_cancer_id":"mixed","sample_count":24146,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=msk_ch_2020"},{"cancer_study_identifier":"msk_impact_2017","name":"MSK-IMPACT Clinical Sequencing Cohort (MSK, Nat Med 2017)","type_of_cancer_id":"mixed","sample_count":10945,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=msk_impact_2017"},{"cancer_study_identifier":"crc_msk_2026","name":"Colorectal Adenocarcinoma (MSK, 2026)","type_of_cancer_id":"read","sample_count":7237,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=crc_msk_2026"},{"cancer_study_identifier":"breast_msk_2026","name":"CCNE1 Amplifications in Breast Cancer (MSK, 2026)","type_of_cancer_id":"breast","sample_count":6318,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=breast_msk_2026"},{"cancer_study_identifier":"pancan_mimsi_msk_2024","name":"Mixed Tumors - MiMSI Cohort (MSK, Nat Commun 2024)","type_of_cancer_id":"mixed","sample_count":5033,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=pancan_mimsi_msk_2024"},{"cancer_study_identifier":"breast_msk_2025","name":"Breast Cancer (MSK, Nat Genet 2025)","type_of_cancer_id":"brca","sample_count":3879,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=breast_msk_2025"},{"cancer_study_identifier":"mycf_msk_2026","name":"MYC Family Amplifications in MSK-IMPACT Solid Tumors (MSK, 2026)","type_of_cancer_id":"mixed","sample_count":3442,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=mycf_msk_2026"},{"cancer_study_identifier":"heme_msk_impact_2022","name":"MSK-IMPACT Heme Tumors (MSK, 2022)","type_of_cancer_id":"mixed","sample_count":2383,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=heme_msk_impact_2022"},{"cancer_study_identifier":"pdac_msk_2024","name":"Pancreatic Adenocarcinoma (MSK, Nat Med 2024)","type_of_cancer_id":"pancreas","sample_count":2336,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=pdac_msk_2024"},{"cancer_study_identifier":"prostate_msk_2024","name":"Prostate Cancer (MSK, Clin Cancer Res 2024)","type_of_cancer_id" … (1829 more chars)

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT
    cd.attribute_value AS cancer_type,
    COUNT(DISTINCT ged.sample_unique_id) AS tp53_mutated_samples,
    COUNT(DISTINCT p.sample_unique_id) AS profiled_samples,
    ROUND(tp53_mutated_samples * 100.0 / NULLIF(profiled_samples, 0), 1) AS frequency_pct
FROM genomic_event_derived ged
JOIN cancer_study c ON ged.cancer_study_identifier = c.cancer_study_identifier
JOIN clinical_data_derived cd ON ged.sample_unique_id = cd.sample_unique_id
    AND ged.cancer_study_identifier = cd.cancer_study_identifier
    AND cd.attribute_name = 'CANCER_TYPE'
LEFT JOIN (
    SELECT DISTINCT sample_unique_id, cancer_study_identifier
    FROM mutation_panel_gene_coverage
    WHERE hugo_gene_symbol = 'TP53'
    UNION ALL
    SELECT DISTINCT sample_unique_id, cancer_study_identifier
    FROM mutation_wes_coverage
) p ON ged.sample_unique_id = p.sample_unique_id
    AND ged.cancer_study_identifier = p.cancer_study_identifier
WHERE ged.cancer_study_identifier = 'msk_impact_50k_2026'
    AND ged.hugo_gene_symbol = 'TP53'
    AND ged.variant_type = 'mutation'
    AND ged.mutation_status != 'UNCALLED'
GROUP BY cancer_type
HAVING profiled_samples >= 50
ORDER BY tp53_mutated_samples DESC
",
 "max_rows": 100
}

◀ result
{"rows":[{"cancer_type":"Non-Small Cell Lung Cancer","tp53_mutated_samples":4242,"profiled_samples":4242,"frequency_pct":100},{"cancer_type":"Colorectal Cancer","tp53_mutated_samples":3884,"profiled_samples":3884,"frequency_pct":100},{"cancer_type":"Breast Cancer","tp53_mutated_samples":2835,"profiled_samples":2835,"frequency_pct":100},{"cancer_type":"Pancreatic Cancer","tp53_mutated_samples":1965,"profiled_samples":1965,"frequency_pct":100},{"cancer_type":"Ovarian Cancer","tp53_mutated_samples":1639,"profiled_samples":1639,"frequency_pct":100},{"cancer_type":"Esophagogastric Cancer","tp53_mutated_samples":1310,"profiled_samples":1310,"frequency_pct":100},{"cancer_type":"Bladder Cancer","tp53_mutated_samples":1242,"profiled_samples":1242,"frequency_pct":100},{"cancer_type":"Endometrial Cancer","tp53_mutated_samples":1125,"profiled_samples":1125,"frequency_pct":100},{"cancer_type":"Prostate Cancer","tp53_mutated_samples":947,"profiled_samples":947,"frequency_pct":100},{"cancer_type":"Glioma","tp53_mutated_samples":849,"profiled_samples":849,"frequency_pct":100},{"cancer_type":"Cancer of Unknown Primary","tp53_mutated_samples":802,"profiled_samples":802,"frequency_pct":100},{"cancer_type":"Soft Tissue Sarcoma","tp53_mutated_samples":496,"profiled_samples":496,"frequency_pct":100},{"cancer_type":"Hepatobiliary Cancer","tp53_mutated_samples":473,"profiled_samples":473,"frequency_pct":100},{"cancer_type":"Small Cell Lung Cancer","tp53_mutated_samples":421,"profiled_samples":421,"frequency_pct":100},{"cancer_type":"Melanoma","tp53_mutated_samples":363,"profiled_samples":363,"frequency_pct":100},{"cancer_type":"Head and Neck Cancer","tp53_mutated_samples":328,"profiled_samples":328,"frequency_pct":100},{"cancer_type":"Skin Cancer, Non-Melanoma","tp53_mutated_samples":231,"profiled_samples":231,"frequency_pct":100},{"cancer_type":"Uterine Sarcoma","tp53_mutated_samples":145,"profiled_samples":145,"frequency_pct":100},{"cancer_type":"Thyroid Cancer","tp53_mutated_samples":133,"profiled_samples":133,"frequency_pct":100},{"cancer_type":"Renal Cell Carcinoma","tp53_mutated_samples":121,"profiled_samples":121,"frequency_pct":100},{"cancer_type":"Bone Cancer","tp53_mutated_samples":119,"profiled_samples":119,"frequency_pct":100},{"cancer_type":"Salivary Gland Cancer","tp53_mutated_samples":109,"profiled_samples":109,"frequency_pct":100},{"cancer_type":"Germ Cell Tumor","tp53_mutated_samples":96,"profiled_samples":96,"frequency_pct":100},{"cancer_type":"Appendiceal Cancer","tp53_mutated_samples":94,"profiled_samples":94,"frequency_pct":100},{"cancer_type":"Small Bowel Cancer","tp53_mutated_samples":89,"profiled_samples":89,"frequency_pct":100},{"cancer_type":"Ampullary Cancer","tp53_mutated_samples":73,"profiled_samples":73,"frequency_pct":100},{"cancer_type":"Cervical Cancer","tp53_mutated_samples":50,"profiled_samples":50,"frequency_pct":100}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT
    cd.attribute_value AS cancer_type,
    COUNT(DISTINCT ged.sample_unique_id) AS tp53_mutated_samples,
    COUNT(DISTINCT p.sample_unique_id) AS profiled_samples,
    ROUND(tp53_mutated_samples * 100.0 / NULLIF(profiled_samples, 0), 1) AS frequency_pct
FROM genomic_event_derived ged
JOIN cancer_study c ON ged.cancer_study_identifier = c.cancer_study_identifier
JOIN clinical_data_derived cd ON ged.sample_unique_id = cd.sample_unique_id
    AND ged.cancer_study_identifier = cd.cancer_study_identifier
    AND cd.attribute_name = 'CANCER_TYPE'
INNER JOIN (
    SELECT DISTINCT s.sample_unique_id, s.cancer_study_identifier
    FROM mutation_panel_gene_coverage s
    WHERE s.hugo_gene_symbol = 'TP53' AND s.cancer_study_identifier = 'msk_impact_50k_2026'
    UNION ALL
    SELECT DISTINCT s.sample_unique_id, s.cancer_study_identifier
    FROM mutation_wes_coverage s
    WHERE s.cancer_study_identifier = 'msk_impact_50k_2026'
) p ON ged.sample_unique_id = p.sample_unique_id
    AND ged.cancer_study_identifier = p.cancer_study_identifier
WHERE ged.cancer_study_identifier = 'msk_impact_50k_2026'
    AND ged.hugo_gene_symbol = 'TP53'
    AND ged.variant_type = 'mutation'
    AND ged.mutation_status != 'UNCALLED'
GROUP BY cancer_type
HAVING profiled_samples >= 50
ORDER BY tp53_mutated_samples DESC
",
 "max_rows": 100
}

◀ result
{"rows":[{"cancer_type":"Non-Small Cell Lung Cancer","tp53_mutated_samples":4242,"profiled_samples":4242,"frequency_pct":100},{"cancer_type":"Colorectal Cancer","tp53_mutated_samples":3884,"profiled_samples":3884,"frequency_pct":100},{"cancer_type":"Breast Cancer","tp53_mutated_samples":2835,"profiled_samples":2835,"frequency_pct":100},{"cancer_type":"Pancreatic Cancer","tp53_mutated_samples":1965,"profiled_samples":1965,"frequency_pct":100},{"cancer_type":"Ovarian Cancer","tp53_mutated_samples":1639,"profiled_samples":1639,"frequency_pct":100},{"cancer_type":"Esophagogastric Cancer","tp53_mutated_samples":1310,"profiled_samples":1310,"frequency_pct":100},{"cancer_type":"Bladder Cancer","tp53_mutated_samples":1242,"profiled_samples":1242,"frequency_pct":100},{"cancer_type":"Endometrial Cancer","tp53_mutated_samples":1125,"profiled_samples":1125,"frequency_pct":100},{"cancer_type":"Prostate Cancer","tp53_mutated_samples":947,"profiled_samples":947,"frequency_pct":100},{"cancer_type":"Glioma","tp53_mutated_samples":849,"profiled_samples":849,"frequency_pct":100},{"cancer_type":"Cancer of Unknown Primary","tp53_mutated_samples":802,"profiled_samples":802,"frequency_pct":100},{"cancer_type":"Soft Tissue Sarcoma","tp53_mutated_samples":496,"profiled_samples":496,"frequency_pct":100},{"cancer_type":"Hepatobiliary Cancer","tp53_mutated_samples":473,"profiled_samples":473,"frequency_pct":100},{"cancer_type":"Small Cell Lung Cancer","tp53_mutated_samples":421,"profiled_samples":421,"frequency_pct":100},{"cancer_type":"Melanoma","tp53_mutated_samples":363,"profiled_samples":363,"frequency_pct":100},{"cancer_type":"Head and Neck Cancer","tp53_mutated_samples":328,"profiled_samples":328,"frequency_pct":100},{"cancer_type":"Skin Cancer, Non-Melanoma","tp53_mutated_samples":231,"profiled_samples":231,"frequency_pct":100},{"cancer_type":"Uterine Sarcoma","tp53_mutated_samples":145,"profiled_samples":145,"frequency_pct":100},{"cancer_type":"Thyroid Cancer","tp53_mutated_samples":133,"profiled_samples":133,"frequency_pct":100},{"cancer_type":"Renal Cell Carcinoma","tp53_mutated_samples":121,"profiled_samples":121,"frequency_pct":100},{"cancer_type":"Bone Cancer","tp53_mutated_samples":119,"profiled_samples":119,"frequency_pct":100},{"cancer_type":"Salivary Gland Cancer","tp53_mutated_samples":109,"profiled_samples":109,"frequency_pct":100},{"cancer_type":"Germ Cell Tumor","tp53_mutated_samples":96,"profiled_samples":96,"frequency_pct":100},{"cancer_type":"Appendiceal Cancer","tp53_mutated_samples":94,"profiled_samples":94,"frequency_pct":100},{"cancer_type":"Small Bowel Cancer","tp53_mutated_samples":89,"profiled_samples":89,"frequency_pct":100},{"cancer_type":"Ampullary Cancer","tp53_mutated_samples":73,"profiled_samples":73,"frequency_pct":100},{"cancer_type":"Cervical Cancer","tp53_mutated_samples":50,"profiled_samples":50,"frequency_pct":100}]}

▶ clickhouse_list_table_columns
{
 "table": "mutation_panel_gene_coverage"
}

◀ result
{"columns":[{"name":"sample_unique_id","type":"String"},{"name":"cancer_study_identifier","type":"LowCardinality(String)"},{"name":"hugo_gene_symbol","type":"String"},{"name":"gene_panel_id","type":"LowCardinality(String)"}]}

▶ clickhouse_run_select_query
{
 "query": "
WITH altered AS (
    SELECT cd.attribute_value AS cancer_type,
           COUNT(DISTINCT ged.sample_unique_id) AS tp53_mutated
    FROM genomic_event_derived ged
    JOIN clinical_data_derived cd ON ged.sample_unique_id = cd.sample_unique_id
        AND ged.cancer_study_identifier = cd.cancer_study_identifier
        AND cd.attribute_name = 'CANCER_TYPE'
    WHERE ged.cancer_study_identifier = 'msk_impact_50k_2026'
        AND ged.hugo_gene_symbol = 'TP53'
        AND ged.variant_type = 'mutation'
        AND ged.mutation_status != 'UNCALLED'
    GROUP BY cancer_type
),
profiled AS (
    SELECT cd.attribute_value AS cancer_type,
           COUNT(DISTINCT cd.sample_unique_id) AS profiled_samples
    FROM clinical_data_derived cd
    WHERE cd.cancer_study_identifier = 'msk_impact_50k_2026'
        AND cd.attribute_name = 'CANCER_TYPE'
        AND cd.sample_unique_id IN (
            SELECT DISTINCT sample_unique_id FROM mutation_panel_gene_coverage
            WHERE hugo_gene_symbol = 'TP53' AND cancer_study_identifier = 'msk_impact_50k_2026'
            UNION ALL
            SELECT DISTINCT sample_unique_id FROM mutation_wes_coverage
            WHERE cancer_study_identifier = 'msk_impact_50k_2026'
        )
    GROUP BY cancer_type
)
SELECT a.cancer_type,
       a.tp53_mutated,
       p.profiled_samples,
       ROUND(a.tp53_mutated * 100.0 / NULLIF(p.profiled_samples, 0), 1) AS frequency_pct
FROM altered a
LEFT JOIN profiled p ON a.cancer_type = p.cancer_type
WHERE p.profiled_samples >= 50
ORDER BY a.tp53_mutated DESC
",
 "max_rows": 100
}

◀ result
{"rows":[{"cancer_type":"Non-Small Cell Lung Cancer","tp53_mutated":4242,"profiled_samples":7867,"frequency_pct":53.9},{"cancer_type":"Colorectal Cancer","tp53_mutated":3884,"profiled_samples":5277,"frequency_pct":73.6},{"cancer_type":"Breast Cancer","tp53_mutated":2835,"profiled_samples":6807,"frequency_pct":41.6},{"cancer_type":"Pancreatic Cancer","tp53_mutated":1965,"profiled_samples":2851,"frequency_pct":68.9},{"cancer_type":"Ovarian Cancer","tp53_mutated":1639,"profiled_samples":2140,"frequency_pct":76.6},{"cancer_type":"Esophagogastric Cancer","tp53_mutated":1310,"profiled_samples":1834,"frequency_pct":71.4},{"cancer_type":"Bladder Cancer","tp53_mutated":1242,"profiled_samples":2526,"frequency_pct":49.2},{"cancer_type":"Endometrial Cancer","tp53_mutated":1125,"profiled_samples":2445,"frequency_pct":46},{"cancer_type":"Prostate Cancer","tp53_mutated":947,"profiled_samples":3324,"frequency_pct":28.5},{"cancer_type":"Glioma","tp53_mutated":849,"profiled_samples":2322,"frequency_pct":36.6},{"cancer_type":"Cancer of Unknown Primary","tp53_mutated":802,"profiled_samples":1581,"frequency_pct":50.7},{"cancer_type":"Soft Tissue Sarcoma","tp53_mutated":496,"profiled_samples":2307,"frequency_pct":21.5},{"cancer_type":"Hepatobiliary Cancer","tp53_mutated":473,"profiled_samples":1431,"frequency_pct":33.1},{"cancer_type":"Small Cell Lung Cancer","tp53_mutated":421,"profiled_samples":466,"frequency_pct":90.3},{"cancer_type":"Melanoma","tp53_mutated":363,"profiled_samples":1831,"frequency_pct":19.8},{"cancer_type":"Head and Neck Cancer","tp53_mutated":328,"profiled_samples":657,"frequency_pct":49.9},{"cancer_type":"Skin Cancer, Non-Melanoma","tp53_mutated":231,"profiled_samples":455,"frequency_pct":50.8},{"cancer_type":"Uterine Sarcoma","tp53_mutated":145,"profiled_samples":344,"frequency_pct":42.2},{"cancer_type":"Thyroid Cancer","tp53_mutated":133,"profiled_samples":867,"frequency_pct":15.3},{"cancer_type":"Renal Cell Carcinoma","tp53_mutated":121,"profiled_samples":1209,"frequency_pct":10},{"cancer_type":"Bone Cancer","tp53_mutated":119,"profiled_samples":590,"frequency_pct":20.2},{"cancer_type":"Salivary Gland Cancer","tp53_mutated":109,"profiled_samples":411,"frequency_pct":26.5},{"cancer_type":"Germ Cell Tumor","tp53_mutated":96,"profiled_samples":725,"frequency_pct":13.2},{"cancer_type":"Appendiceal Cancer","tp53_mutated":94,"profiled_samples":274,"frequency_pct":34.3},{"cancer_type":"Small Bowel Cancer","tp53_mutated":89,"profiled_samples":161,"frequency_pct":55.3},{"cancer_type":"Ampullary Cancer","tp53_mutated":73,"profiled_samples":134,"frequency_pct":54.5},{"cancer_type":"Cervical Cancer","tp53_mutated":50,"profiled_samples":351,"frequency_pct":14.2},{"cancer_type":"Gastrointestinal Neuroendocrine Tumor","tp53_mutated":49,"profiled_samples":210,"frequency_pct":23.3},{"cancer_type":"Mesothelioma","tp53_mutated":46,"profiled_samples":408,"frequency_pct":11.3},{"cancer_type":"Gastrointestinal Stromal Tumor","tp53_mutated":35,"profiled_samples":635 … (1234 more chars)

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

◀ result
{"success":true,"message":"Found 1 study. Use the metadata to call the appropriate navigation tool(s).","data":{"totalCount":1,"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"]}}]}}

▶ navigate_to_results_view
{
 "studyIds": [
  "msk_impact_50k_2026"
 ],
 "genes": [
  "TP53"
 ]
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/results/oncoprint?cancer_study_list=msk_impact_50k_2026&gene_list=TP53&case_set_id=msk_impact_50k_2026_all","url":"https://www.cbioportal.org/results/oncoprint?cancer_study_list=msk_impact_50k_2026&gene_list=TP53&case_set_id=msk_impact_50k_2026_all","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":["TP53"],"caseSetId":"msk_impact_50k_2026_all","pageDescription":"Visual summary of alterations in queried genes across samples."}}

═ answer (success)
## TP53 Mutations in MSK-IMPACT 50K by Cancer Type

**TP53 is mutated across 44 cancer types in the MSK-IMPACT 50K cohort.** Here are the cancer types with the highest TP53 mutation frequencies (sample-level):

| Cancer Type | TP53 Mutations | Profiled Samples | Frequency |
|---|---:|---:|---:|
| Small Cell Lung Cancer | 421 | 466 | **90.3%** |
| Ovarian Cancer | 1,639 | 2,140 | **76.6%** |
| Colorectal Cancer | 3,884 | 5,277 | **73.6%** |
| Esophagogastric Cancer | 1,310 | 1,834 | **71.4%** |
| Pancreatic Cancer | 1,965 | 2,851 | **68.9%** |
| Small Bowel Cancer | 89 | 161 | **55.3%** |
| Vaginal Cancer | 32 | 57 | **56.1%** |
| Ampullary Cancer | 73 | 134 | **54.5%** |
| Non-Small Cell Lung Cancer | 4,242 | 7,867 | **53.9%** |
| Skin Cancer, Non-Melanoma | 231 | 455 | **50.8%** |
| Cancer of Unknown Primary | 802 | 1,581 | **50.7%** |
| Head and Neck Cancer | 328 | 657 | **49.9%** |
| Bladder Cancer | 1,242 | 2,526 | **49.2%** |
| Endometrial Cancer | 1,125 | 2,445 | **46.0%** |
| Uterine Sarcoma | 145 | 344 | **42.2%** |
| Breast Cancer | 2,835 | 6,807 | **41.6%** |

**Lower frequencies include:** Appendiceal (34.3%), Hepatobiliary (33.1%), Glioma (36.6%), Salivary Gland (26.5%), and others down to Peripheral Nervous System (1.5%) and CNS Cancer (1.8%).

### Explore the Data

[View TP53 alterations across MSK-IMPACT (OncoPrint)](https://www.cbioportal.org/results/oncoprint?cancer_study_list=msk_impact_50k_2026&gene_list=TP53&case_set_id=msk_impact_50k_2026_all)

This link shows the OncoPrint visualization with TP53 mutations color-coded by alteration type. You can click on individual mutations or filter by cancer type in the StudyView.