Q (sonnet):
How many samples in the TCGA PanCancer Atlas breast cancer study have PIK3CA mutations?
In Breast Invasive Carcinoma (TCGA, PanCancer Atlas), 347 of 1,066 profiled samples (32.6%) have a PIK3CA mutation.
Continue this conversation: reply to the user's new message.
break that down by PAM50 subtype please
▶ read_guide
{
"uri": "cbioportal://clinical-data-guide"
}
▶ read_guide
{
"uri": "cbioportal://mutation-frequency-guide"
}
◀ result
# Clinical Data Query Guide
## Overview
Clinical data in cBioPortal is stored at both patient and sample levels. Understanding the distinction is crucial for accurate analysis.
## Data Organization
### Patient-Level vs Sample-Level Data
- **Patient-level**: Demographics, overall survival, disease stage (stored once per patient)
- **Sample-level**: Sample type, sequencing platform, purity (can have multiple per patient)
### Key Tables
- `clinical_patient`: Patient-level clinical attributes
- `clinical_sample`: Sample-level clinical attributes
- `clinical_data_derived`: Pre-joined view combining both levels
- `clinical_attribute_meta`: Metadata about available clinical attributes
## Recommended Approach: Use clinical_data_derived
The `clinical_data_derived` table is pre-joined and optimized for most queries:
```sql
-- Get clinical data for specific attributes
SELECT
sample_unique_id,
patient_unique_id,
attribute_name,
attribute_value
FROM clinical_data_derived
WHERE
cancer_study_identifier = 'your_study_id'
AND attribute_name IN ('CANCER_TYPE', 'SAMPLE_TYPE', 'TMB_NONSYNONYMOUS');
```
## Clinical Attribute Discovery
### Use clinical_attribute_meta for Discovering Available Attributes
**Always start here** to see what clinical attributes are available for a specific study:
```sql
-- Discover available clinical attributes for a study
SELECT
attr_id,
description,
patient_attribute,
cancer_study_id
FROM clinical_attribute_meta
WHERE
cancer_study_id = (
SELECT cancer_study_id
FROM cancer_study
WHERE cancer_study_identifier = 'your_study_id'
)
ORDER BY patient_attribute, attr_id;
```
**Key Fields:**
- **attr_id**: matches attr_id in clinical_sample/clinical_patient tables
- **description**: human-readable description of the attribute
- **patient_attribute**: true = patient attribute, false = sample attribute
- **cancer_study_id**: links to cancer_study table (filter by study)
## Attribute Semantics and Matching
### Case-Insensitive Matching for Attribute Values
Clinical values are free text across studies and may differ only by case. For example, a controlled-looking value such as germline mutation status may appear as `GERMLINE`, `Germline`, or another case variant.
When filtering `clinical_data_derived.attribute_value`, use case-insensitive matching unless you have already profiled the exact values in the target study:
```sql
-- Correct: case-insensitive clinical value filter
SELECT DISTINCT sample_unique_id, patient_unique_id
FROM clinical_data_derived
WHERE cancer_study_identifier = 'your_study_id'
AND attribute_name = 'MUTATION_STATUS'
AND upper(attribute_value) = 'GERMLINE';
```
Do not write `attribute_value = 'GERMLINE'` without first checking all distinct values for that attribute in the study.
### Query the Requested Attribute, Not a Proxy
Do not infer one clinical attribute from a related subtype or marker. Query the actual requested attribute when it … (17073 more chars)
◀ 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)
▶ clickhouse_run_select_query
{
"query": "SELECT DISTINCT attribute_name FROM clinical_data_derived WHERE cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018' AND upper(attribute_name) LIKE '%SUBTYPE%'"
}
◀ result
{"rows":[{"attribute_name":"SUBTYPE"}]}
▶ clickhouse_run_select_query
{
"query": "SELECT DISTINCT attribute_value FROM clinical_data_derived WHERE cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018' AND attribute_name = 'SUBTYPE'"
}
◀ result
{"rows":[{"attribute_value":"BRCA_LumA"},{"attribute_value":"BRCA_Her2"},{"attribute_value":"BRCA_LumB"},{"attribute_value":"BRCA_Normal"},{"attribute_value":"BRCA_Basal"},{}]}
▶ clickhouse_run_select_query
{
"query": "
WITH subtype AS (
SELECT sample_unique_id, attribute_value AS subtype
FROM clinical_data_derived
WHERE cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018'
AND attribute_name = 'SUBTYPE'
AND attribute_value != ''
),
profiled AS (
SELECT DISTINCT sample_unique_id
FROM sample_to_gene_panel_derived
WHERE cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018'
AND alteration_type = 'MUTATION_EXTENDED'
),
altered AS (
SELECT DISTINCT sample_unique_id
FROM genomic_event_derived
WHERE cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018'
AND variant_type = 'mutation'
AND mutation_status != 'UNCALLED'
AND off_panel = 0
AND hugo_gene_symbol = 'PIK3CA'
)
SELECT
s.subtype,
count(DISTINCT p.sample_unique_id) AS profiled_samples,
count(DISTINCT a.sample_unique_id) AS altered_samples,
round(count(DISTINCT a.sample_unique_id) * 100.0 / count(DISTINCT p.sample_unique_id), 1) AS frequency_pct
FROM profiled p
JOIN subtype s USING (sample_unique_id)
LEFT JOIN altered a USING (sample_unique_id)
GROUP BY s.subtype
ORDER BY frequency_pct DESC
"
}
◀ result
{"rows":[]}
▶ clickhouse_run_select_query
{
"query": "
WITH subtype AS (
SELECT sample_unique_id, attribute_value AS subtype
FROM clinical_data_derived
WHERE cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018'
AND attribute_name = 'SUBTYPE'
AND attribute_value != ''
),
profiled AS (
SELECT DISTINCT sample_unique_id
FROM sample_to_gene_panel_derived
WHERE cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018'
AND alteration_type = 'MUTATION_EXTENDED'
),
altered AS (
SELECT DISTINCT sample_unique_id
FROM genomic_event_derived
WHERE cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018'
AND variant_type = 'mutation'
AND mutation_status != 'UNCALLED'
AND off_panel = 0
AND hugo_gene_symbol = 'PIK3CA'
)
SELECT
s.subtype,
count(DISTINCT p.sample_unique_id) AS profiled_samples,
countIf(p.sample_unique_id IN (SELECT sample_unique_id FROM altered)) AS altered_samples,
round(countIf(p.sample_unique_id IN (SELECT sample_unique_id FROM altered)) * 100.0 / count(DISTINCT p.sample_unique_id), 1) AS frequency_pct
FROM profiled p
JOIN subtype s USING (sample_unique_id)
GROUP BY s.subtype
ORDER BY frequency_pct DESC
"
}
◀ result
{"rows":[]}
▶ clickhouse_run_select_query
{
"query": "SELECT count(), uniqExact(sample_unique_id) FROM sample_to_gene_panel_derived WHERE cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018' AND alteration_type = 'MUTATION_EXTENDED'"
}
◀ result
{"rows":[{"count()":1066,"uniqExact(sample_unique_id)":1066}]}
▶ clickhouse_run_select_query
{
"query": "SELECT sample_unique_id FROM sample_to_gene_panel_derived WHERE cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018' LIMIT 3"
}
◀ result
{"rows":[{"sample_unique_id":"brca_tcga_pan_can_atlas_2018_TCGA-A2-A0CM-01"},{"sample_unique_id":"brca_tcga_pan_can_atlas_2018_TCGA-A2-A0D0-01"},{"sample_unique_id":"brca_tcga_pan_can_atlas_2018_TCGA-A2-A0D1-01"}]}
▶ clickhouse_run_select_query
{
"query": "SELECT sample_unique_id FROM clinical_data_derived WHERE cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018' AND attribute_name = 'SUBTYPE' LIMIT 3"
}
◀ result
{"rows":[{},{},{}]}
▶ clickhouse_run_select_query
{
"query": "SELECT sample_unique_id, patient_unique_id, attribute_value FROM clinical_data_derived WHERE cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018' AND attribute_name = 'SUBTYPE' LIMIT 5"
}
▶ clickhouse_list_table_columns
{
"table": "clinical_attribute_meta"
}
◀ result
{"rows":[{"patient_unique_id":"brca_tcga_pan_can_atlas_2018_TCGA-3C-AAAU","attribute_value":"BRCA_LumA"},{"patient_unique_id":"brca_tcga_pan_can_atlas_2018_TCGA-3C-AALI","attribute_value":"BRCA_Her2"},{"patient_unique_id":"brca_tcga_pan_can_atlas_2018_TCGA-3C-AALJ","attribute_value":"BRCA_LumB"},{"patient_unique_id":"brca_tcga_pan_can_atlas_2018_TCGA-3C-AALK","attribute_value":"BRCA_LumA"},{"patient_unique_id":"brca_tcga_pan_can_atlas_2018_TCGA-4H-AAAK","attribute_value":"BRCA_LumA"}]}
◀ result
{"columns":[{"name":"attr_id","type":"String"},{"name":"display_name","type":"String"},{"name":"description","type":"String"},{"name":"datatype","type":"String"},{"name":"patient_attribute","type":"Int32"},{"name":"priority","type":"String"},{"name":"cancer_study_id","type":"Int64"}]}
▶ clickhouse_run_select_query
{
"query": "
WITH subtype AS (
SELECT patient_unique_id, attribute_value AS subtype
FROM clinical_data_derived
WHERE cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018'
AND attribute_name = 'SUBTYPE'
AND attribute_value != ''
),
sample_patient AS (
SELECT DISTINCT sample_unique_id, patient_unique_id
FROM clinical_data_derived
WHERE cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018'
),
profiled AS (
SELECT DISTINCT sample_unique_id
FROM sample_to_gene_panel_derived
WHERE cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018'
AND alteration_type = 'MUTATION_EXTENDED'
),
altered AS (
SELECT DISTINCT sample_unique_id
FROM genomic_event_derived
WHERE cancer_study_identifier = 'brca_tcga_pan_can_atlas_2018'
AND variant_type = 'mutation'
AND mutation_status != 'UNCALLED'
AND off_panel = 0
AND hugo_gene_symbol = 'PIK3CA'
)
SELECT
st.subtype,
count(DISTINCT p.sample_unique_id) AS profiled_samples,
countIf(p.sample_unique_id IN (SELECT sample_unique_id FROM altered)) AS altered_samples,
round(countIf(p.sample_unique_id IN (SELECT sample_unique_id FROM altered)) * 100.0 / count(DISTINCT p.sample_unique_id), 1) AS frequency_pct
FROM profiled p
JOIN sample_patient sp USING (sample_unique_id)
JOIN subtype st USING (patient_unique_id)
GROUP BY st.subtype
ORDER BY frequency_pct DESC
"
}
◀ result
{"rows":[{"subtype":"BRCA_LumA","profiled_samples":499,"altered_samples":237,"frequency_pct":47.5},{"subtype":"BRCA_Her2","profiled_samples":78,"altered_samples":26,"frequency_pct":33.3},{"subtype":"BRCA_LumB","profiled_samples":197,"altered_samples":59,"frequency_pct":29.9},{"subtype":"BRCA_Normal","profiled_samples":36,"altered_samples":8,"frequency_pct":22.2},{"subtype":"BRCA_Basal","profiled_samples":171,"altered_samples":12,"frequency_pct":7}]}
▶ resolve_and_route
{
"studyIds": [
"brca_tcga_pan_can_atlas_2018"
]
}
◀ result
{"success":true,"message":"Found 1 study. Use the metadata to call the appropriate navigation tool(s).","data":{"totalCount":1,"studiesWithMetadata":[{"studyId":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","sampleCount":1084,"studyViewUrl":"https://www.cbioportal.org/study?id=brca_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":["brca_tcga_pan_can_atlas_2018_gistic","brca_tcga_pan_can_atlas_2018_log2CNA","brca_tcga_pan_can_atlas_2018_mutations","brca_tcga_pan_can_atlas_2018_protein_quantification","brca_tcga_pan_can_atlas_2018_protein_quantification_zscores","brca_tcga_pan_can_atlas_2018_rna_seq_v2_mrna","brca_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","brca_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","brca_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_ref_normal_Zscores","brca_tcga_pan_can_atlas_2018_rppa","brca_tcga_pan_can_atlas_2018_rppa_Zscores","brca_tcga_pan_can_atlas_2018_structural_variants"],"genericAssayProfiles":["brca_tcga_pan_can_atlas_2018_armlevel_cna","brca_tcga_pan_can_atlas_2018_genetic_ancestry","brca_tcga_pan_can_atlas_2018_methylation_hm27_hm450_merge","brca_tcga_pan_can_atlas_2018_methylation_hm450","brca_tcga_pan_can_atlas_2018_phosphoprotein_quantification"],"heatmapProfileIds":["brca_tcga_pan_can_atlas_2018_protein_quantification_zscores","brca_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","brca_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","brca_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_ref_normal_Zscores","brca_tcga_pan_can_atlas_2018_rppa_Zscores"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations","mrna","protein","generic_assay_armlevel_cna","generic_assay_genetic_anc … (83 more chars)
▶ get_studyviewfilter_options
{
"studyId": "brca_tcga_pan_can_atlas_2018",
"attributeIds": [
"SUBTYPE"
]
}
◀ result
{"success":true,"message":"Successfully retrieved StudyView filter options","data":{"studyId":"brca_tcga_pan_can_atlas_2018","attributes":[{"attributeId":"SUBTYPE","displayName":"Subtype","description":"Subtype","datatype":"STRING","values":["BRCA_Her2","NA","BRCA_Basal","BRCA_Normal","BRCA_LumA","BRCA_LumB"]}]}}
▶ navigate_to_group_comparison
{
"studyIds": [
"brca_tcga_pan_can_atlas_2018"
],
"tab": "mutations",
"selectedGene": "PIK3CA",
"groups": [
{
"name": "LumA",
"studyViewFilter": {
"clinicalDataFilters": [
{
"attributeId": "SUBTYPE",
"values": [
{
"value": "BRCA_LumA"
}
]
}
]
}
},
{
"name": "LumB",
"studyViewFilter": {
"clinicalDataFilters": [
{
"attributeId": "SUBTYPE",
"values": [
{
"value": "BRCA_LumB"
}
]
}
]
}
},
{
"name": "Her2",
"studyViewFilter": {
"clinicalDataFilters": [
{
"attributeId": "SUBTYPE",
"values": [
{
"value": "BRCA_Her2"
}
]
}
]
}
},
{
"name": "Basal",
"studyViewFilter": {
"clinicalDataFilters": [
{
"attributeId": "SUBTYPE",
"values": [
{
"value": "BRCA_Basal"
}
]
}
]
}
},
{
"name": "Normal",
"studyViewFilter": {
"clinicalDataFilters": [
{
"attributeId": "SUBTYPE",
"values": [
{
"value": "BRCA_Normal"
}
]
}
]
}
}
]
}
◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/comparison/mutations?comparisonId=6a8a10f5e497aad535936938&selectedGene=PIK3CA","url":"https://www.cbioportal.org/comparison/mutations?comparisonId=6a8a10f5e497aad535936938&selectedGene=PIK3CA","data":{"description":"Group comparison (5 custom groups)","studies":["brca_tcga_pan_can_atlas_2018"],"totalGroups":5,"groups":[{"name":"LumA","sampleCount":499},{"name":"LumB","sampleCount":197},{"name":"Her2","sampleCount":78},{"name":"Basal","sampleCount":171},{"name":"Normal","sampleCount":36}],"studyViewUrl":"https://www.cbioportal.org/study?id=brca_tcga_pan_can_atlas_2018","groupUrls":[{"groupName":"LumA","url":"https://www.cbioportal.org/study?id=brca_tcga_pan_can_atlas_2018#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22SUBTYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22BRCA_LumA%22%7D%5D%7D%5D%7D"},{"groupName":"LumB","url":"https://www.cbioportal.org/study?id=brca_tcga_pan_can_atlas_2018#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22SUBTYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22BRCA_LumB%22%7D%5D%7D%5D%7D"},{"groupName":"Her2","url":"https://www.cbioportal.org/study?id=brca_tcga_pan_can_atlas_2018#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22SUBTYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22BRCA_Her2%22%7D%5D%7D%5D%7D"},{"groupName":"Basal","url":"https://www.cbioportal.org/study?id=brca_tcga_pan_can_atlas_2018#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22SUBTYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22BRCA_Basal%22%7D%5D%7D%5D%7D"},{"groupName":"Normal","url":"https://www.cbioportal.org/study?id=brca_tcga_pan_can_atlas_2018#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22SUBTYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22BRCA_Normal%22%7D%5D%7D%5D%7D"}],"pageDescription":"Mutation frequency (protein change) compared across LumA (499) vs LumB (197) vs Her2 (78) vs Basal (171) vs Normal (36)."}}
═ answer (success)
In **Breast Invasive Carcinoma (TCGA, PanCancer Atlas)**, PIK3CA mutation frequency by PAM50 subtype (samples with mutation profiling and a PAM50 call, n=981 of 1,066):
| PAM50 Subtype | Altered / Profiled | Frequency |
|---|---|---|
| Luminal A | 237 / 499 | 47.5% |
| Luminal B | 59 / 197 | 29.9% |
| HER2-enriched | 26 / 78 | 33.3% |
| Basal-like | 12 / 171 | 7.0% |
| Normal-like | 8 / 36 | 22.2% |
PIK3CA mutations are markedly enriched in Luminal A tumors and rare in Basal-like tumors, consistent with the well-known subtype-associated pattern in this cohort. Note: 85 samples (1,066 profiled − 981) lack a PAM50 call and are excluded from this breakdown.
[View PIK3CA mutation comparison across PAM50 subtypes](https://www.cbioportal.org/comparison/mutations?comparisonId=6a8a10f5e497aad535936938&selectedGene=PIK3CA)
For the full cohort overview: [Study View — Breast Invasive Carcinoma (TCGA, PanCancer Atlas)](https://www.cbioportal.org/study?id=brca_tcga_pan_can_atlas_2018)