Q (sonnet): what other genes are altered in kras mutant crc or luad

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

▶ list_studies
{
 "search": "colorectal"
}

◀ 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)

▶ list_studies
{
 "search": "lung adenocarcinoma"
}

◀ 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":"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":"crc_eo_2020","name":"Colorectal Cancer (MSK, JNCI 2021)","type_of_cancer_id":"bowel","sample_count":1516,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=crc_eo_2020"},{"cancer_study_identifier":"crc_msk_2017","name":"Metastatic Colorectal Cancer (MSK, Cancer Cell 2018)","type_of_cancer_id":"coadread","sample_count":1134,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=crc_msk_2017"},{"cancer_study_identifier":"crc_sysucc_2022","name":"Colorectal Cancer- ChangKang Project (SYSUCC, Nat Commun 2022)","type_of_cancer_id":"coadread","sample_count":1015,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=crc_sysucc_2022"},{"cancer_study_identifier":"coadread_tcga","name":"Colorectal Adenocarcinoma (TCGA, Firehose Legacy)","type_of_cancer_id":"coadread","sample_count":640,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=coadread_tcga"},{"cancer_study_identifier":"coadread_dfci_2016","name":"Colorectal Adenocarcinoma (DFCI, Cell Reports 2016)","type_of_cancer_id":"coadread","sample_count":619,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=coadread_dfci_2016"},{"cancer_study_identifier":"coadread_tcga_pan_can_atlas_2018","name":"Colorectal Adenocarcinoma (TCGA, PanCancer Atlas)","type_of_cancer_id":"coadread","sample_count":594,"has_guide":true,"url":"https://www.cbioportal.org/study/summary?id=coadread_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"crc_apc_impact_2020","name":"Colorectal Cancer (MSK, Gastroenterology 2020)","type_of_cancer_id":"coadread","sample_count":471,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=crc_apc_impact_2020"},{"cancer_study_identifier":"coadread_tcga_pub","name":"Colorectal Adenocarcinoma (TCGA, Nature 2012)","type_of_cancer_id":"coadread","sample_count":276,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=coadread_tcga_pub"},{"cancer_study_identifier":"bowel_colitis_msk_2022","name":"Colorectal Adenocarcinoma (MSK, Nat Commun 2022)","type_of_cancer_id":"bowel","sample_count":179,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=bowel_colitis_msk_2022"},{"cancer_study_identifier":"coadread_cass_2020","name":"Colorectal Cancer (CAS Shanghai, Cancer Cell 2020)","type_of_cancer_id":"coadread","sample_count":146,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=coadread_cass_2020"},{"cancer_study_identifier":"coadread_mskcc","name":"Colorectal Adenocarcinoma Triplets (MSK, Geno … (1887 more chars)

◀ 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 * FROM co_altered_genes_in_study(study = 'coadread_tcga_pan_can_atlas_2018', gene = 'KRAS', top_n = 20)"
}

▶ clickhouse_run_select_query
{
 "query": "SELECT * FROM co_altered_genes_in_study(study = 'luad_tcga_pan_can_atlas_2018', gene = 'KRAS', top_n = 20)"
}

◀ result
{"rows":[{"hugo_gene_symbol":"APC","mutant_altered":182,"mutant_profiled":218,"mutant_pct":83.5,"wildtype_altered":205,"wildtype_profiled":316,"wildtype_pct":64.9,"pct_difference":18.6},{"hugo_gene_symbol":"PIK3CA","mutant_altered":83,"mutant_profiled":218,"mutant_pct":38.1,"wildtype_altered":64,"wildtype_profiled":316,"wildtype_pct":20.3,"pct_difference":17.8},{"hugo_gene_symbol":"BRAF","mutant_altered":6,"mutant_profiled":218,"mutant_pct":2.8,"wildtype_altered":56,"wildtype_profiled":316,"wildtype_pct":17.7,"pct_difference":-14.9},{"hugo_gene_symbol":"COL7A1","mutant_altered":7,"mutant_profiled":218,"mutant_pct":3.2,"wildtype_altered":40,"wildtype_profiled":316,"wildtype_pct":12.7,"pct_difference":-9.5},{"hugo_gene_symbol":"PCBP1","mutant_altered":20,"mutant_profiled":218,"mutant_pct":9.2,"wildtype_altered":5,"wildtype_profiled":316,"wildtype_pct":1.6,"pct_difference":7.6},{"hugo_gene_symbol":"ABCA13","mutant_altered":22,"mutant_profiled":218,"mutant_pct":10.1,"wildtype_altered":55,"wildtype_profiled":316,"wildtype_pct":17.4,"pct_difference":-7.3},{"hugo_gene_symbol":"DOCK3","mutant_altered":11,"mutant_profiled":218,"mutant_pct":5,"wildtype_altered":38,"wildtype_profiled":316,"wildtype_pct":12,"pct_difference":-7},{"hugo_gene_symbol":"YLPM1","mutant_altered":6,"mutant_profiled":218,"mutant_pct":2.8,"wildtype_altered":31,"wildtype_profiled":316,"wildtype_pct":9.8,"pct_difference":-7},{"hugo_gene_symbol":"ZNF469","mutant_altered":11,"mutant_profiled":218,"mutant_pct":5,"wildtype_altered":38,"wildtype_profiled":316,"wildtype_pct":12,"pct_difference":-7},{"hugo_gene_symbol":"CHD7","mutant_altered":7,"mutant_profiled":218,"mutant_pct":3.2,"wildtype_altered":32,"wildtype_profiled":316,"wildtype_pct":10.1,"pct_difference":-6.9},{"hugo_gene_symbol":"ARID1A","mutant_altered":15,"mutant_profiled":218,"mutant_pct":6.9,"wildtype_altered":43,"wildtype_profiled":316,"wildtype_pct":13.6,"pct_difference":-6.7},{"hugo_gene_symbol":"CELSR2","mutant_altered":6,"mutant_profiled":218,"mutant_pct":2.8,"wildtype_altered":30,"wildtype_profiled":316,"wildtype_pct":9.5,"pct_difference":-6.7},{"hugo_gene_symbol":"NRAS","mutant_altered":5,"mutant_profiled":218,"mutant_pct":2.3,"wildtype_altered":28,"wildtype_profiled":316,"wildtype_pct":8.9,"pct_difference":-6.6},{"hugo_gene_symbol":"TMPRSS15","mutant_altered":19,"mutant_profiled":218,"mutant_pct":8.7,"wildtype_altered":7,"wildtype_profiled":316,"wildtype_pct":2.2,"pct_difference":6.5},{"hugo_gene_symbol":"DNAH1","mutant_altered":14,"mutant_profiled":218,"mutant_pct":6.4,"wildtype_altered":40,"wildtype_profiled":316,"wildtype_pct":12.7,"pct_difference":-6.3},{"hugo_gene_symbol":"SCN3A","mutant_altered":9,"mutant_profiled":218,"mutant_pct":4.1,"wildtype_altered":33,"wildtype_profiled":316,"wildtype_pct":10.4,"pct_difference":-6.3},{"hugo_gene_symbol":"CACNA1F","mutant_altered":4,"mutant_profiled":218,"mutant_pct":1.8,"wildtype_altered":25,"wildtype_profiled":316,"wildtype_pct":7.9,"pct_difference":-6.1},{"hugo_gene_symbol" … (505 more chars)

◀ result
{"rows":[{"hugo_gene_symbol":"TP53","mutant_altered":62,"mutant_profiled":168,"mutant_pct":36.9,"wildtype_altered":233,"wildtype_profiled":398,"wildtype_pct":58.5,"pct_difference":-21.6},{"hugo_gene_symbol":"EGFR","mutant_altered":1,"mutant_profiled":168,"mutant_pct":0.6,"wildtype_altered":69,"wildtype_profiled":398,"wildtype_pct":17.3,"pct_difference":-16.7},{"hugo_gene_symbol":"STK11","mutant_altered":38,"mutant_profiled":168,"mutant_pct":22.6,"wildtype_altered":37,"wildtype_profiled":398,"wildtype_pct":9.3,"pct_difference":13.3},{"hugo_gene_symbol":"ATM","mutant_altered":28,"mutant_profiled":168,"mutant_pct":16.7,"wildtype_altered":19,"wildtype_profiled":398,"wildtype_pct":4.8,"pct_difference":11.9},{"hugo_gene_symbol":"MUC16","mutant_altered":84,"mutant_profiled":168,"mutant_pct":50,"wildtype_altered":158,"wildtype_profiled":398,"wildtype_pct":39.7,"pct_difference":10.3},{"hugo_gene_symbol":"NF1","mutant_altered":8,"mutant_profiled":168,"mutant_pct":4.8,"wildtype_altered":58,"wildtype_profiled":398,"wildtype_pct":14.6,"pct_difference":-9.8},{"hugo_gene_symbol":"CSMD1","mutant_altered":48,"mutant_profiled":168,"mutant_pct":28.6,"wildtype_altered":77,"wildtype_profiled":398,"wildtype_pct":19.3,"pct_difference":9.3},{"hugo_gene_symbol":"CNTNAP2","mutant_altered":32,"mutant_profiled":168,"mutant_pct":19,"wildtype_altered":39,"wildtype_profiled":398,"wildtype_pct":9.8,"pct_difference":9.2},{"hugo_gene_symbol":"RIMS2","mutant_altered":32,"mutant_profiled":168,"mutant_pct":19,"wildtype_altered":40,"wildtype_profiled":398,"wildtype_pct":10.1,"pct_difference":8.9},{"hugo_gene_symbol":"LRP1B","mutant_altered":69,"mutant_profiled":168,"mutant_pct":41.1,"wildtype_altered":132,"wildtype_profiled":398,"wildtype_pct":33.2,"pct_difference":7.9},{"hugo_gene_symbol":"LRRC7","mutant_altered":34,"mutant_profiled":168,"mutant_pct":20.2,"wildtype_altered":49,"wildtype_profiled":398,"wildtype_pct":12.3,"pct_difference":7.9},{"hugo_gene_symbol":"TNR","mutant_altered":19,"mutant_profiled":168,"mutant_pct":11.3,"wildtype_altered":76,"wildtype_profiled":398,"wildtype_pct":19.1,"pct_difference":-7.8},{"hugo_gene_symbol":"BRAF","mutant_altered":3,"mutant_profiled":168,"mutant_pct":1.8,"wildtype_altered":38,"wildtype_profiled":398,"wildtype_pct":9.5,"pct_difference":-7.7},{"hugo_gene_symbol":"RP1L1","mutant_altered":37,"mutant_profiled":168,"mutant_pct":22,"wildtype_altered":60,"wildtype_profiled":398,"wildtype_pct":15.1,"pct_difference":6.9},{"hugo_gene_symbol":"ZFHX4","mutant_altered":63,"mutant_profiled":168,"mutant_pct":37.5,"wildtype_altered":122,"wildtype_profiled":398,"wildtype_pct":30.7,"pct_difference":6.8},{"hugo_gene_symbol":"HECTD4","mutant_altered":18,"mutant_profiled":168,"mutant_pct":10.7,"wildtype_altered":16,"wildtype_profiled":398,"wildtype_pct":4,"pct_difference":6.7},{"hugo_gene_symbol":"KMT2C","mutant_altered":15,"mutant_profiled":168,"mutant_pct":8.9,"wildtype_altered":62,"wildtype_profiled":398,"wildtype_pct":15.6,"pct_difference":-6.7},{"hugo_gene_ … (513 more chars)

▶ resolve_and_route
{
 "studyIds": [
  "coadread_tcga_pan_can_atlas_2018",
  "luad_tcga_pan_can_atlas_2018"
 ]
}

◀ 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":"coadread_tcga_pan_can_atlas_2018","name":"Colorectal Adenocarcinoma (TCGA, PanCancer Atlas)","sampleCount":594,"studyViewUrl":"https://www.cbioportal.org/study?id=coadread_tcga_pan_can_atlas_2018","metadata":{"clinicalAttributeIds":["AGE","AJCC_PATHOLOGIC_TUMOR_STAGE","AJCC_STAGING_EDITION","ANEUPLOIDY_SCORE","BUFFA_HYPOXIA_SCORE","CANCER_TYPE","CANCER_TYPE_ACRONYM","CANCER_TYPE_DETAILED","DAYS_LAST_FOLLOWUP","DAYS_TO_BIRTH","DAYS_TO_INITIAL_PATHOLOGIC_DIAGNOSIS","DFS_MONTHS","DFS_STATUS","DSS_MONTHS","DSS_STATUS","ETHNICITY","FORM_COMPLETION_DATE","FRACTION_GENOME_ALTERED","GENETIC_ANCESTRY_LABEL","GRADE","HISTORY_NEOADJUVANT_TRTYN","ICD_10","ICD_O_3_HISTOLOGY","ICD_O_3_SITE","INFORMED_CONSENT_VERIFIED","IN_PANCANPATHWAYS_FREEZE","MSI_SCORE_MANTIS","MSI_SENSOR_SCORE","MUTATION_COUNT","NEW_TUMOR_EVENT_AFTER_INITIAL_TREATMENT","ONCOTREE_CODE","OS_MONTHS","OS_STATUS","OTHER_PATIENT_ID","PATH_M_STAGE","PATH_N_STAGE","PATH_T_STAGE","PERSON_NEOPLASM_CANCER_STATUS","PFS_MONTHS","PFS_STATUS","PRIMARY_LYMPH_NODE_PRESENTATION_ASSESSMENT","PRIOR_DX","RACE","RADIATION_THERAPY","RAGNUM_HYPOXIA_SCORE","SAMPLE_COUNT","SAMPLE_TYPE","SEX","SOMATIC_STATUS","SUBTYPE","TBL_SCORE","TISSUE_PROSPECTIVE_COLLECTION_INDICATOR","TISSUE_RETROSPECTIVE_COLLECTION_INDICATOR","TISSUE_SOURCE_SITE","TISSUE_SOURCE_SITE_CODE","TMB_NONSYNONYMOUS","TUMOR_TISSUE_SITE","TUMOR_TYPE","WEIGHT","WINTER_HYPOXIA_SCORE"],"molecularProfileIds":["coadread_tcga_pan_can_atlas_2018_gistic","coadread_tcga_pan_can_atlas_2018_log2CNA","coadread_tcga_pan_can_atlas_2018_mutations","coadread_tcga_pan_can_atlas_2018_protein_quantification","coadread_tcga_pan_can_atlas_2018_protein_quantification_zscores","coadread_tcga_pan_can_atlas_2018_rna_seq_v2_mrna","coadread_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","coadread_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","coadread_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_ref_normal_Zscores","coadread_tcga_pan_can_atlas_2018_rppa","coadread_tcga_pan_can_atlas_2018_rppa_Zscores","coadread_tcga_pan_can_atlas_2018_structural_variants"],"genericAssayProfiles":["coadread_tcga_pan_can_atlas_2018_armlevel_cna","coadread_tcga_pan_can_atlas_2018_genetic_ancestry","coadread_tcga_pan_can_atlas_2018_methylation_hm27_hm450_merge","coadread_tcga_pan_can_atlas_2018_methylation_hm450"],"heatmapProfileIds":["coadread_tcga_pan_can_atlas_2018_protein_quantification_zscores","coadread_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","coadread_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","coadread_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_ref_normal_Zscores","coadread_tcga_pan_can_atlas_2018_rp … (2852 more chars)

▶ navigate_to_results_view
{
 "studyIds": [
  "coadread_tcga_pan_can_atlas_2018"
 ],
 "genes": [
  "KRAS: MUT",
  "APC",
  "PIK3CA",
  "BRAF",
  "NRAS"
 ],
 "tab": "oncoprint"
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/results/oncoprint?cancer_study_list=coadread_tcga_pan_can_atlas_2018&gene_list=KRAS%3A+MUT%0AAPC%0APIK3CA%0ABRAF%0ANRAS&case_set_id=coadread_tcga_pan_can_atlas_2018_all","url":"https://www.cbioportal.org/results/oncoprint?cancer_study_list=coadread_tcga_pan_can_atlas_2018&gene_list=KRAS%3A+MUT%0AAPC%0APIK3CA%0ABRAF%0ANRAS&case_set_id=coadread_tcga_pan_can_atlas_2018_all","data":{"studyIds":["coadread_tcga_pan_can_atlas_2018"],"studies":[{"studyId":"coadread_tcga_pan_can_atlas_2018","name":"Colorectal Adenocarcinoma (TCGA, PanCancer Atlas)","sampleCount":594}],"genes":["KRAS","APC","PIK3CA","BRAF","NRAS"],"caseSetId":"coadread_tcga_pan_can_atlas_2018_all","pageDescription":"Visual summary of alterations in queried genes across samples."}}

▶ navigate_to_results_view
{
 "studyIds": [
  "luad_tcga_pan_can_atlas_2018"
 ],
 "genes": [
  "KRAS: MUT",
  "STK11",
  "ATM",
  "TP53",
  "EGFR",
  "BRAF"
 ],
 "tab": "oncoprint"
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/results/oncoprint?cancer_study_list=luad_tcga_pan_can_atlas_2018&gene_list=KRAS%3A+MUT%0ASTK11%0AATM%0ATP53%0AEGFR%0ABRAF&case_set_id=luad_tcga_pan_can_atlas_2018_all","url":"https://www.cbioportal.org/results/oncoprint?cancer_study_list=luad_tcga_pan_can_atlas_2018&gene_list=KRAS%3A+MUT%0ASTK11%0AATM%0ATP53%0AEGFR%0ABRAF&case_set_id=luad_tcga_pan_can_atlas_2018_all","data":{"studyIds":["luad_tcga_pan_can_atlas_2018"],"studies":[{"studyId":"luad_tcga_pan_can_atlas_2018","name":"Lung Adenocarcinoma (TCGA, PanCancer Atlas)","sampleCount":566}],"genes":["KRAS","STK11","ATM","TP53","EGFR","BRAF"],"caseSetId":"luad_tcga_pan_can_atlas_2018_all","pageDescription":"Visual summary of alterations in queried genes across samples."}}

═ answer (success)
Here are the direct visualization links for each cohort's OncoPrint, showing KRAS mutation status alongside the top co-altered genes:

- [CRC OncoPrint: KRAS, APC, PIK3CA, BRAF, NRAS](https://www.cbioportal.org/results/oncoprint?cancer_study_list=coadread_tcga_pan_can_atlas_2018&gene_list=KRAS%3A+MUT%0AAPC%0APIK3CA%0ABRAF%0ANRAS&case_set_id=coadread_tcga_pan_can_atlas_2018_all) — 594 samples, Colorectal Adenocarcinoma (TCGA, PanCancer Atlas)
- [LUAD OncoPrint: KRAS, STK11, ATM, TP53, EGFR, BRAF](https://www.cbioportal.org/results/oncoprint?cancer_study_list=luad_tcga_pan_can_atlas_2018&gene_list=KRAS%3A+MUT%0ASTK11%0AATM%0ATP53%0AEGFR%0ABRAF&case_set_id=luad_tcga_pan_can_atlas_2018_all) — 566 samples, Lung Adenocarcinoma (TCGA, PanCancer Atlas)

Note: there are dozens of other CRC (crc_msk_2026, crc_msk_2017, etc.) and LUAD (MSK, OncoSG, CPTAC, etc.) studies available if you'd like this repeated in a different or larger cohort — happy to rerun on any of those.