Q (sonnet-5.5): In MSS colorectal cancer, what is the frequency of BRAF oncogenic mutations (as defined by OncoKB)? Use the 2017 MSK study for this. Can you give me a table of all these mutations, with frequency, count and denominator?

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

▶ list_studies
{
 "search": "colorectal MSK 2017"
}

◀ 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":"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"}]}

▶ get_study_guide
{
 "study_id": "crc_msk_2017"
}

◀ result
# Study Guide: Metastatic Colorectal Cancer (MSK, Cancer Cell 2018)

**Study ID:** `crc_msk_2017`
**Cancer Type:** coadread
**Description:** Targeted sequencing of 1134 metastatic colorectal tumor/normal pairs.

## Cohort Statistics
- **Patients:** 1,099
- **Samples:** 1,135

## Available Data Types

- **COPY_NUMBER_ALTERATION**: Putative copy-number alterations from GISTIC
- **MUTATION_EXTENDED**: Mutations
- **STRUCTURAL_VARIANT**: Structural variants

## Gene Panels

- **IMPACT410**: 911 samples
- **IMPACT341**: 214 samples
- **IMPACT468**: 9 samples

## Available Clinical Attributes

| Attribute | Samples with Data |
|-----------|------------------|
| TIME_FROM_MET_DX_SEQUENCING | 1,134 |
| METASTASES_SITE_FIRST_LIVER | 1,134 |
| PRIMARY_SITE | 1,134 |
| METASTATIC_BIOPSY_SITE | 1,134 |
| MUTATION_COUNT | 1,134 |
| MSI_STATUS | 1,134 |
| SOMATIC_STATUS | 1,134 |
| METASTASES_SITE_FIRST_PERITONEUM_OMENTUM_ABDOMEN | 1,134 |
| METASTASES_SITE_FIRST_BONE | 1,134 |
| METASTASES_SITE_FIRST_GYN | 1,134 |
| METASTASES_SITE_FIRST_LN | 1,134 |
| TIME_TO_METASTASIS_MONTHS | 1,134 |
| FRACTION_GENOME_ALTERED | 1,134 |
| TMB_NONSYNONYMOUS | 1,134 |
| SPECIMEN_TYPE | 1,134 |
| METASTASES_SITE_FIRST_LUNG | 1,134 |
| STAGE_AT_DIAGNOSIS | 1,134 |
| FIRST_SITE_OF_METS | 1,134 |
| CHEMO_EXP_SEQ_SPECIMEN | 1,134 |
| METASTASES_SITE_FIRST_BRAIN | 1,134 |

## Top Mutated Genes

| Gene | Altered Samples |
|------|----------------|
| APC | 867 |
| TP53 | 824 |
| KRAS | 495 |
| PIK3CA | 229 |
| SMAD4 | 173 |
| FBXW7 | 145 |
| BRAF | 133 |
| TCF7L2 | 124 |
| KMT2D | 107 |
| SOX9 | 107 |

## Sample Types

- **Primary**: 601 samples
- **Metastasis**: 533 samples

## Query Tips for crc_msk_2017

```sql
-- Get all samples in this study
SELECT DISTINCT sample_unique_id, patient_unique_id
FROM clinical_data_derived
WHERE cancer_study_identifier = 'crc_msk_2017';

-- Get mutations for a specific gene
SELECT sample_unique_id, hugo_gene_symbol, mutation_variant, mutation_type
FROM genomic_event_derived
WHERE cancer_study_identifier = 'crc_msk_2017'
    AND hugo_gene_symbol = 'TP53'
    AND variant_type = 'mutation';

-- Get clinical data for specific attributes
SELECT sample_unique_id, attribute_name, attribute_value
FROM clinical_data_derived
WHERE cancer_study_identifier = 'crc_msk_2017'
    AND attribute_name IN ('CANCER_TYPE', 'SAMPLE_TYPE', 'OS_MONTHS');
```


▶ clickhouse_run_select_query
{
 "query": "SELECT attribute_name, attribute_value, count() c FROM clinical_data_derived WHERE cancer_study_identifier='crc_msk_2017' AND (attribute_name ILIKE '%MSI%' OR attribute_name ILIKE '%MSS%' OR attribute_name ILIKE '%SAMPLE_TYPE%') GROUP BY 1,2 ORDER BY 1,3 DESC LIMIT 50"
}

▶ clickhouse_run_select_query
{
 "query": "SELECT driver_filter, count() FROM genomic_event_derived WHERE cancer_study_identifier='crc_msk_2017' AND variant_type='mutation' GROUP BY 1"
}

◀ result
{"rows":[{"attribute_name":"MSI_SCORE","attribute_value":"0","c":146},{"attribute_name":"MSI_SCORE","attribute_value":"0.08","c":41},{"attribute_name":"MSI_SCORE","attribute_value":"0.09","c":28},{"attribute_name":"MSI_SCORE","attribute_value":"0.07","c":21},{"attribute_name":"MSI_SCORE","attribute_value":"0.15","c":21},{"attribute_name":"MSI_SCORE","attribute_value":"0.16","c":16},{"attribute_name":"MSI_SCORE","attribute_value":"0.17","c":16},{"attribute_name":"MSI_SCORE","attribute_value":"0.18","c":11},{"attribute_name":"MSI_SCORE","attribute_value":"0.89","c":10},{"attribute_name":"MSI_SCORE","attribute_value":"0.34","c":10},{"attribute_name":"MSI_SCORE","attribute_value":"0.26","c":10},{"attribute_name":"MSI_SCORE","attribute_value":"0.24","c":10},{"attribute_name":"MSI_SCORE","attribute_value":"0.27","c":9},{"attribute_name":"MSI_SCORE","attribute_value":"0.33","c":9},{"attribute_name":"MSI_SCORE","attribute_value":"0.35","c":9},{"attribute_name":"MSI_SCORE","attribute_value":"0.39","c":9},{"attribute_name":"MSI_SCORE","attribute_value":"0.42","c":9},{"attribute_name":"MSI_SCORE","c":8},{"attribute_name":"MSI_SCORE","attribute_value":"0.59","c":8},{"attribute_name":"MSI_SCORE","attribute_value":"0.19","c":8},{"attribute_name":"MSI_SCORE","attribute_value":"0.49","c":8},{"attribute_name":"MSI_SCORE","attribute_value":"0.22","c":8},{"attribute_name":"MSI_SCORE","attribute_value":"0.1","c":7},{"attribute_name":"MSI_SCORE","attribute_value":"0.47","c":7},{"attribute_name":"MSI_SCORE","attribute_value":"0.55","c":7},{"attribute_name":"MSI_SCORE","attribute_value":"0.38","c":7},{"attribute_name":"MSI_SCORE","attribute_value":"0.31","c":7},{"attribute_name":"MSI_SCORE","attribute_value":"0.57","c":7},{"attribute_name":"MSI_SCORE","attribute_value":"0.5","c":7},{"attribute_name":"MSI_SCORE","attribute_value":"0.14","c":7},{"attribute_name":"MSI_SCORE","attribute_value":"0.25","c":7},{"attribute_name":"MSI_SCORE","attribute_value":"0.67","c":7},{"attribute_name":"MSI_SCORE","attribute_value":"0.45","c":7},{"attribute_name":"MSI_SCORE","attribute_value":"0.65","c":7},{"attribute_name":"MSI_SCORE","attribute_value":"0.3","c":7},{"attribute_name":"MSI_SCORE","attribute_value":"0.84","c":6},{"attribute_name":"MSI_SCORE","attribute_value":"0.36","c":6},{"attribute_name":"MSI_SCORE","attribute_value":"1.1","c":6},{"attribute_name":"MSI_SCORE","attribute_value":"0.28","c":6},{"attribute_name":"MSI_SCORE","attribute_value":"0.85","c":6},{"attribute_name":"MSI_SCORE","attribute_value":"2.07","c":5},{"attribute_name":"MSI_SCORE","attribute_value":"0.76","c":5},{"attribute_name":"MSI_SCORE","attribute_value":"0.77","c":5},{"attribute_name":"MSI_SCORE","attribute_value":"0.54","c":5},{"attribute_name":"MSI_SCORE","attribute_value":"0.52","c":5},{"attribute_name":"MSI_SCORE","attribute_value":"0.88","c":5},{"attribute_name":"MSI_SCORE","attribute_value":"0.53","c":5},{"attribute_name":"MSI_SCORE","attribute_value":"1.04","c":5},{"attribute_name":"MSI_SCORE","att … (90 more chars)

◀ result
{"rows":[{"count()":14656}]}

▶ clickhouse_run_select_query
{
 "query": "SELECT attribute_value, count(DISTINCT sample_unique_id) n, count(DISTINCT patient_unique_id) p FROM clinical_data_derived WHERE cancer_study_identifier='crc_msk_2017' AND attribute_name='MSI_STATUS' GROUP BY 1"
}

◀ result
{"rows":[{"n":327,"p":320},{"attribute_value":"MSS","n":701,"p":677},{"attribute_value":"MSI","n":105,"p":102},{"attribute_value":"Inconclusive","n":1,"p":1}]}

▶ clickhouse_run_select_query
{
 "query": "SELECT driver_filter, count() c FROM genomic_event_derived WHERE cancer_study_identifier='crc_msk_2017' AND variant_type='mutation' GROUP BY driver_filter"
}

◀ result
{"rows":[{"c":14656}]}

▶ clickhouse_run_select_query
{
 "query": "WITH mss AS (SELECT DISTINCT sample_unique_id FROM clinical_data_derived WHERE cancer_study_identifier='crc_msk_2017' AND attribute_name='MSI_STATUS' AND attribute_value='Stable'),
prof AS (SELECT count(DISTINCT sample_unique_id) n FROM mutation_panel_gene_coverage WHERE hugo_gene_symbol='BRAF' AND cancer_study_identifier='crc_msk_2017' AND sample_unique_id IN (SELECT sample_unique_id FROM mss))
SELECT mutation_variant, mutation_type, count(DISTINCT sample_unique_id) altered, (SELECT n FROM prof) profiled, round(altered*100/profiled,2) pct FROM genomic_event_derived WHERE cancer_study_identifier='crc_msk_2017' AND variant_type='mutation' AND mutation_status!='UNCALLED' AND off_panel=0 AND hugo_gene_symbol='BRAF' AND sample_unique_id IN (SELECT sample_unique_id FROM mss) GROUP BY 1,2 ORDER BY altered DESC"
}

◀ result
{"rows":[]}

▶ clickhouse_run_select_query
{
 "query": "WITH mss AS (SELECT DISTINCT sample_unique_id FROM clinical_data_derived WHERE cancer_study_identifier='crc_msk_2017' AND attribute_name='MSI_STATUS' AND attribute_value='MSS'),
prof AS (SELECT count(DISTINCT sample_unique_id) n FROM mutation_panel_gene_coverage WHERE hugo_gene_symbol='BRAF' AND cancer_study_identifier='crc_msk_2017' AND sample_unique_id IN (SELECT sample_unique_id FROM mss))
SELECT mutation_variant, mutation_type, count(DISTINCT sample_unique_id) altered, (SELECT n FROM prof) profiled, round(altered*100/profiled,2) pct FROM genomic_event_derived WHERE cancer_study_identifier='crc_msk_2017' AND variant_type='mutation' AND mutation_status!='UNCALLED' AND off_panel=0 AND hugo_gene_symbol='BRAF' AND sample_unique_id IN (SELECT sample_unique_id FROM mss) GROUP BY 1,2 ORDER BY altered DESC"
}

◀ result
{"rows":[{"mutation_variant":"V600E","mutation_type":"Missense_Mutation","altered":46,"profiled":701,"pct":6.56},{"mutation_variant":"D594G","mutation_type":"Missense_Mutation","altered":7,"profiled":701,"pct":1},{"mutation_variant":"D594N","mutation_type":"Missense_Mutation","altered":3,"profiled":701,"pct":0.43},{"mutation_variant":"T599delinsIP","mutation_type":"In_Frame_Ins","altered":2,"profiled":701,"pct":0.29},{"mutation_variant":"N581S","mutation_type":"Missense_Mutation","altered":2,"profiled":701,"pct":0.29},{"mutation_variant":"G469E","mutation_type":"Missense_Mutation","altered":2,"profiled":701,"pct":0.29},{"mutation_variant":"G469A","mutation_type":"Missense_Mutation","altered":2,"profiled":701,"pct":0.29},{"mutation_variant":"H574Y","mutation_type":"Missense_Mutation","altered":1,"profiled":701,"pct":0.14},{"mutation_variant":"G596R","mutation_type":"Missense_Mutation","altered":1,"profiled":701,"pct":0.14},{"mutation_variant":"Y633C","mutation_type":"Missense_Mutation","altered":1,"profiled":701,"pct":0.14},{"mutation_variant":"A404Cfs*9","mutation_type":"Frame_Shift_Ins","altered":1,"profiled":701,"pct":0.14},{"mutation_variant":"L312P","mutation_type":"Missense_Mutation","altered":1,"profiled":701,"pct":0.14},{"mutation_variant":"N581I","mutation_type":"Missense_Mutation","altered":1,"profiled":701,"pct":0.14},{"mutation_variant":"R354*","mutation_type":"Nonsense_Mutation","altered":1,"profiled":701,"pct":0.14},{"mutation_variant":"F294L","mutation_type":"Missense_Mutation","altered":1,"profiled":701,"pct":0.14},{"mutation_variant":"K601E","mutation_type":"Missense_Mutation","altered":1,"profiled":701,"pct":0.14},{"mutation_variant":"P277Hfs*2","mutation_type":"Frame_Shift_Del","altered":1,"profiled":701,"pct":0.14},{"mutation_variant":"G466V","mutation_type":"Missense_Mutation","altered":1,"profiled":701,"pct":0.14},{"mutation_variant":"Q356K","mutation_type":"Missense_Mutation","altered":1,"profiled":701,"pct":0.14},{"mutation_variant":"E501K","mutation_type":"Missense_Mutation","altered":1,"profiled":701,"pct":0.14},{"mutation_variant":"D594V","mutation_type":"Missense_Mutation","altered":1,"profiled":701,"pct":0.14},{"mutation_variant":"S602Y","mutation_type":"Missense_Mutation","altered":1,"profiled":701,"pct":0.14},{"mutation_variant":"D284Efs*4","mutation_type":"Frame_Shift_Ins","altered":1,"profiled":701,"pct":0.14}]}

▶ clickhouse_run_select_query
{
 "query": "WITH mss AS (SELECT DISTINCT sample_unique_id FROM clinical_data_derived WHERE cancer_study_identifier='crc_msk_2017' AND attribute_name='MSI_STATUS' AND attribute_value='MSS')
SELECT count(DISTINCT sample_unique_id) altered_samples FROM genomic_event_derived WHERE cancer_study_identifier='crc_msk_2017' AND variant_type='mutation' AND mutation_status!='UNCALLED' AND off_panel=0 AND hugo_gene_symbol='BRAF' AND sample_unique_id IN (SELECT sample_unique_id FROM mss)"
}

▶ resolve_and_route
{
 "studyIds": [
  "crc_msk_2017"
 ]
}

◀ result
{"rows":[{"altered_samples":78}]}

◀ result
{"success":true,"message":"Found 1 study. Use the metadata to call the appropriate navigation tool(s).","data":{"totalCount":1,"studiesWithMetadata":[{"studyId":"crc_msk_2017","name":"Metastatic Colorectal Cancer (MSK, Cancer Cell 2018)","sampleCount":1134,"studyViewUrl":"https://www.cbioportal.org/study?id=crc_msk_2017","metadata":{"clinicalAttributeIds":["AGE_AT_DIAGNOSIS","CANCER_TYPE","CANCER_TYPE_DETAILED","CHEMO_EXP_SEQ_SPECIMEN","FIRST_SITE_OF_METS","FRACTION_GENOME_ALTERED","GENE_PANEL","MCRC_TYPE","METASTASECTOMY","METASTASECTOMY_SITE","METASTASES_SITE_FIRST_BONE","METASTASES_SITE_FIRST_BRAIN","METASTASES_SITE_FIRST_GYN","METASTASES_SITE_FIRST_LIVER","METASTASES_SITE_FIRST_LN","METASTASES_SITE_FIRST_LUNG","METASTASES_SITE_FIRST_PELVIS","METASTASES_SITE_FIRST_PERITONEUM_OMENTUM_ABDOMEN","METASTATIC_BIOPSY_SITE","MOLECULAR_SUBTYPE","MSI_SCORE","MSI_STATUS","MUTATION_COUNT","ONCOTREE_CODE","OS_MONTHS","OS_MONTHS_ADDITIONAL","OS_STATUS","OTHER_SITES_OF_METS","PATIENT_GRADE","PRIMARY_SITE","PRIMARY_TUMOR_LOCATION","SAMPLE_COUNT","SAMPLE_TYPE","SEX","SOMATIC_STATUS","SPECIMEN_TYPE","STAGE_AT_DIAGNOSIS","TIME_FROM_MET_DX_SEQUENCING","TIME_TO_METASTASIS_MONTHS","TMB_NONSYNONYMOUS","TUMOR_SAMPLE_HISTOLOGY","VITAL_STATUS"],"molecularProfileIds":["crc_msk_2017_gistic","crc_msk_2017_mutations","crc_msk_2017_structural_variants"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations"]}}]}}

▶ get_studyviewfilter_options
{
 "studyId": "crc_msk_2017",
 "attributeIds": [
  "MSI_STATUS"
 ]
}

◀ result
{"success":true,"message":"Successfully retrieved StudyView filter options","data":{"studyId":"crc_msk_2017","attributes":[{"attributeId":"MSI_STATUS","displayName":"MSI Status","description":"MSI status.","datatype":"STRING","values":["MSI","NA","Inconclusive","MSS"]}]}}

▶ navigate_to_results_view
{
 "studyIds": [
  "crc_msk_2017"
 ],
 "genes": [
  "BRAF: MUT_DRIVER"
 ],
 "tab": "mutations",
 "studyViewFilter": {
  "clinicalDataFilters": [
   {
    "attributeId": "MSI_STATUS",
    "values": [
     {
      "value": "MSS"
     }
    ]
   }
  ]
 }
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/results/mutations?session_id=6ab433b8c2115c492d884974","url":"https://www.cbioportal.org/results/mutations?session_id=6ab433b8c2115c492d884974","data":{"studyIds":["crc_msk_2017"],"studies":[{"studyId":"crc_msk_2017","name":"Metastatic Colorectal Cancer (MSK, Cancer Cell 2018)","sampleCount":1134}],"genes":["BRAF"],"filteredSampleCount":701,"caseSetId":"-1","sessionId":"6ab433b8c2115c492d884974","studyViewUrl":"https://www.cbioportal.org/study?id=crc_msk_2017#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22MSI_STATUS%22%2C%22values%22%3A%5B%7B%22value%22%3A%22MSS%22%7D%5D%7D%5D%7D","pageDescription":"Detailed mutation table with lollipop plot showing mutation positions, types, and frequencies for queried genes."}}

═ answer (success)
I can't give you the OncoKB-defined oncogenic frequency from the database. OncoKB annotations aren't stored there. This study also has no driver annotations of its own. Below are all somatic BRAF mutations in MSS samples, which is a superset of the oncogenic ones. The portal link at the end applies OncoKB and gives the exact oncogenic number.

**Cohort:** Metastatic Colorectal Cancer (MSK, Cancer Cell 2018), `crc_msk_2017`. Counts are per sample. I defined MSS as MSI_STATUS = "MSS", which gives 701 samples, all profiled for BRAF. Samples with MSI, inconclusive or missing MSI status are excluded.

**All BRAF mutations in MSS samples:** 78 of 701 samples (11.1%) carry at least one. Some samples carry more than one mutation, so the rows below add up to more than 78.

| BRAF mutation | Type | Samples | Denominator (MSS, profiled) | Frequency |
|---|---|---|---|---|
| V600E | Missense | 46 | 701 | 6.56% |
| D594G | Missense | 7 | 701 | 1.00% |
| D594N | Missense | 3 | 701 | 0.43% |
| T599delinsIP | In-frame insertion | 2 | 701 | 0.29% |
| N581S | Missense | 2 | 701 | 0.29% |
| G469E | Missense | 2 | 701 | 0.29% |
| G469A | Missense | 2 | 701 | 0.29% |
| H574Y | Missense | 1 | 701 | 0.14% |
| G596R | Missense | 1 | 701 | 0.14% |
| Y633C | Missense | 1 | 701 | 0.14% |
| A404Cfs*9 | Frameshift insertion | 1 | 701 | 0.14% |
| L312P | Missense | 1 | 701 | 0.14% |
| N581I | Missense | 1 | 701 | 0.14% |
| R354* | Nonsense | 1 | 701 | 0.14% |
| F294L | Missense | 1 | 701 | 0.14% |
| K601E | Missense | 1 | 701 | 0.14% |
| P277Hfs*2 | Frameshift deletion | 1 | 701 | 0.14% |
| G466V | Missense | 1 | 701 | 0.14% |
| Q356K | Missense | 1 | 701 | 0.14% |
| E501K | Missense | 1 | 701 | 0.14% |
| D594V | Missense | 1 | 701 | 0.14% |
| S602Y | Missense | 1 | 701 | 0.14% |
| D284Efs*4 | Frameshift insertion | 1 | 701 | 0.14% |

These rows are not all OncoKB-oncogenic. Several are likely passenger or unclassified variants, such as the frameshifts, R354*, F294L, L312P and Q356K. I haven't confirmed OncoKB status for any of them, so treat the table as an upper bound.

To get the OncoKB-filtered numbers:
- [BRAF driver mutations in MSS samples (Mutations tab)](https://www.cbioportal.org/results/mutations?session_id=6ab433b8c2115c492d884974). The query is `BRAF: MUT_DRIVER` on the 701 MSS samples, so the oncogenic and likely oncogenic calls come from OncoKB and hotspot annotations.
- [Study cohort filtered to MSS](https://www.cbioportal.org/study?id=crc_msk_2017#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22MSI_STATUS%22%2C%22values%22%3A%5B%7B%22value%22%3A%22MSS%22%7D%5D%7D%5D%7D)