{"disease": {"name": "Breast cancer", "mondo_id": null, "ncit_id": null, "umls_id": null, "oncotree_code": "brca"}, "updated_at": "2026-09-17", "genome_builds": ["hg19"], "cohort_count": 3, "cohort_count_status": "observed", "cohort_count_unit": "cohorts", "evaluable_patients": null, "evaluable_patients_status": "unknown", "evaluable_patients_unit": "patients", "alteration_types": ["SNV", "small indel", "amplification", "deep deletion"], "genes": [{"gene": "ESR1", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 9, "tested": 1066, "frequency": 0.84, "cohort_count": 2, "frequency_range": {"min": 0.84, "max": 14.07}, "major_variants": ["E380Q (n=2)", "A593D (n=1)", "E523Q (n=1)", "I451_I452del (n=1)", "P222S (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Curated target in the disease briefing.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 9/1066 patients (0.84%).", "Without the 21 hypermutated patients: 6/1045 (0.57%).", "Largest alteration is amplification: 20/1070 (1.87%) in the reference cohort's copy-number profile.", "Observed in 2 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 9, "tested": 1066, "frequency": 0.84, "frequency_excl_hypermutated": 0.57, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 65, "tested": 462, "frequency": 14.07, "frequency_excl_hypermutated": 14.13, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 6.23, "width": 1.0, "reference": 6.23, "scale_max": 30.0}, "headline_alteration": {"kind": "amplification", "altered": 20, "tested": 1070, "frequency": 1.87, "is_mutation": false}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "PGR", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 7, "tested": 1066, "frequency": 0.66, "cohort_count": 2, "frequency_range": {"min": 0.66, "max": 3.5}, "major_variants": ["R740Q (n=1)", "A914V (n=1)", "E596Gfs*13 (n=1)", "E833K (n=1)", "I896M (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Curated target in the disease briefing.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 7/1066 patients (0.66%).", "Without the 21 hypermutated patients: 6/1045 (0.57%).", "Largest alteration is deep deletion: 10/1070 (0.93%) in the reference cohort's copy-number profile.", "Observed in 2 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 7, "tested": 1066, "frequency": 0.66, "frequency_excl_hypermutated": 0.57, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 15, "tested": 429, "frequency": 3.5, "frequency_excl_hypermutated": 3.28, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 3.1, "width": 1.0, "reference": 3.1, "scale_max": 30.0}, "headline_alteration": {"kind": "deep deletion", "altered": 10, "tested": 1070, "frequency": 0.93, "is_mutation": false}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "ERBB2", "alteration_types": ["SNV / small indel", "amplification"], "altered": 30, "tested": 1066, "frequency": 2.81, "cohort_count": 3, "frequency_range": {"min": 2.81, "max": 10.39}, "major_variants": ["L755S (n=5)", "V777L (n=4)", "D769Y (n=2)", "I767M (n=2)", "L755M (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Curated target in the disease briefing.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 30/1066 patients (2.81%).", "Without the 21 hypermutated patients: 24/1045 (2.3%).", "Largest alteration is amplification: 123/1070 (11.5%) in the reference cohort's copy-number profile.", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 30, "tested": 1066, "frequency": 2.81, "frequency_excl_hypermutated": 2.3, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 71, "tested": 2433, "frequency": 2.92, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 48, "tested": 462, "frequency": 10.39, "frequency_excl_hypermutated": 10.43, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 38.33, "width": 1.0, "reference": 38.33, "scale_max": 30.0}, "headline_alteration": {"kind": "amplification", "altered": 123, "tested": 1070, "frequency": 11.5, "is_mutation": false}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "PIK3CA", "alteration_types": ["SNV / small indel", "amplification"], "altered": 346, "tested": 1066, "frequency": 32.46, "cohort_count": 3, "frequency_range": {"min": 32.46, "max": 59.96}, "major_variants": ["H1047R (n=129)", "E545K (n=65)", "E542K (n=43)", "N345K (n=18)", "H1047L (n=13)"], "evidence_confidence": "moderate", "disease_relevance": "Curated target in the disease briefing.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 346/1066 patients (32.46%).", "Without the 21 hypermutated patients: 334/1045 (31.96%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 346, "tested": 1066, "frequency": 32.46, "frequency_excl_hypermutated": 31.96, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 975, "tested": 2433, "frequency": 40.07, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 277, "tested": 462, "frequency": 59.96, "frequency_excl_hypermutated": 59.78, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 100.0, "width": 1.0, "reference": 100.0, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 346, "tested": 1066, "frequency": 32.46, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "AKT1", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 27, "tested": 1066, "frequency": 2.53, "cohort_count": 3, "frequency_range": {"min": 2.53, "max": 6.49}, "major_variants": ["E17K (n=25)", "L52R (n=1)", "V4L (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Curated target in the disease briefing.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 27/1066 patients (2.53%).", "Without the 21 hypermutated patients: 27/1045 (2.58%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 27, "tested": 1066, "frequency": 2.53, "frequency_excl_hypermutated": 2.58, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 98, "tested": 2433, "frequency": 4.03, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 30, "tested": 462, "frequency": 6.49, "frequency_excl_hypermutated": 6.52, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 8.43, "width": 13.2, "reference": 8.43, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 27, "tested": 1066, "frequency": 2.53, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "PTEN", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 58, "tested": 1066, "frequency": 5.44, "cohort_count": 3, "frequency_range": {"min": 3.9, "max": 14.29}, "major_variants": ["R130Q (n=4)", "R130* (n=2)", "T319* (n=2)", "K267Rfs*9 (n=2)", "N48Tfs*6 (n=2)"], "evidence_confidence": "moderate", "disease_relevance": "Curated target in the disease briefing.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 58/1066 patients (5.44%).", "Without the 21 hypermutated patients: 48/1045 (4.59%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 58, "tested": 1066, "frequency": 5.44, "frequency_excl_hypermutated": 4.59, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 95, "tested": 2433, "frequency": 3.9, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 66, "tested": 462, "frequency": 14.29, "frequency_excl_hypermutated": 13.91, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 13.0, "width": 34.63, "reference": 18.13, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 58, "tested": 1066, "frequency": 5.44, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "CDK4", "alteration_types": ["SNV / small indel", "amplification"], "altered": 0, "tested": 1066, "frequency": 0.0, "cohort_count": 1, "frequency_range": {"min": 0.0, "max": 1.08}, "major_variants": [], "evidence_confidence": "moderate", "disease_relevance": "Curated target in the disease briefing.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 0/1066 patients (0.0%).", "Without the 21 hypermutated patients: 0/1045 (0.0%).", "Largest alteration is amplification: 14/1070 (1.31%) in the reference cohort's copy-number profile.", "Observed in 1 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 0, "tested": 1066, "frequency": 0.0, "frequency_excl_hypermutated": 0.0, "counting_unit": "patients", "status": "not_observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 5, "tested": 462, "frequency": 1.08, "frequency_excl_hypermutated": 0.65, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 4.37, "width": 1.0, "reference": 4.37, "scale_max": 30.0}, "headline_alteration": {"kind": "amplification", "altered": 14, "tested": 1070, "frequency": 1.31, "is_mutation": false}, "altered_status": "not_observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "not_observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "CDK6", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 3, "tested": 1066, "frequency": 0.28, "cohort_count": 2, "frequency_range": {"min": 0.28, "max": 0.87}, "major_variants": ["T88A (n=1)", "H139Q (n=1)", "P118S (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Curated target in the disease briefing.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 3/1066 patients (0.28%).", "Without the 21 hypermutated patients: 2/1045 (0.19%).", "Largest alteration is amplification: 6/1070 (0.56%) in the reference cohort's copy-number profile.", "Observed in 2 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 3, "tested": 1066, "frequency": 0.28, "frequency_excl_hypermutated": 0.19, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 4, "tested": 462, "frequency": 0.87, "frequency_excl_hypermutated": 0.87, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 1.87, "width": 1.0, "reference": 1.87, "scale_max": 30.0}, "headline_alteration": {"kind": "amplification", "altered": 6, "tested": 1070, "frequency": 0.56, "is_mutation": false}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "BRCA1", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 27, "tested": 1066, "frequency": 2.53, "cohort_count": 3, "frequency_range": {"min": 1.73, "max": 8.01}, "major_variants": ["Q934* (n=1)", "E9Q (n=1)", "X27_splice (n=1)", "E720* (n=1)", "T688Vfs*12 (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Curated target in the disease briefing.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 27/1066 patients (2.53%).", "Without the 21 hypermutated patients: 23/1045 (2.2%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 27, "tested": 1066, "frequency": 2.53, "frequency_excl_hypermutated": 2.2, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 42, "tested": 2433, "frequency": 1.73, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 37, "tested": 462, "frequency": 8.01, "frequency_excl_hypermutated": 7.61, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 5.77, "width": 20.93, "reference": 8.43, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 27, "tested": 1066, "frequency": 2.53, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "BRCA2", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 29, "tested": 1066, "frequency": 2.72, "cohort_count": 3, "frequency_range": {"min": 1.85, "max": 12.12}, "major_variants": ["Q3206E (n=1)", "Y3308* (n=1)", "L2926* (n=1)", "D1355Y (n=1)", "E260Sfs*15 (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Curated target in the disease briefing.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 29/1066 patients (2.72%).", "Without the 21 hypermutated patients: 24/1045 (2.3%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 29, "tested": 1066, "frequency": 2.72, "frequency_excl_hypermutated": 2.3, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 45, "tested": 2433, "frequency": 1.85, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 56, "tested": 462, "frequency": 12.12, "frequency_excl_hypermutated": 11.96, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 6.17, "width": 34.23, "reference": 9.07, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 29, "tested": 1066, "frequency": 2.72, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "TP53", "alteration_types": ["SNV / small indel", "deep deletion", "amplification"], "altered": 346, "tested": 1066, "frequency": 32.46, "cohort_count": 3, "frequency_range": {"min": 32.46, "max": 55.84}, "major_variants": ["R175H (n=21)", "R273H (n=13)", "R196* (n=8)", "Y220C (n=7)", "R342* (n=7)"], "evidence_confidence": "moderate", "disease_relevance": "Curated target in the disease briefing.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 346/1066 patients (32.46%).", "Without the 21 hypermutated patients: 340/1045 (32.54%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 346, "tested": 1066, "frequency": 32.46, "frequency_excl_hypermutated": 32.54, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 861, "tested": 2433, "frequency": 35.39, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 258, "tested": 462, "frequency": 55.84, "frequency_excl_hypermutated": 55.87, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 100.0, "width": 1.0, "reference": 100.0, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 346, "tested": 1066, "frequency": 32.46, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "TACSTD2", "alteration_types": ["amplification", "deep deletion"], "altered": 0, "tested": 1066, "frequency": 0.0, "cohort_count": 0, "frequency_range": {"min": 0.0, "max": 0.0}, "major_variants": [], "evidence_confidence": "moderate", "disease_relevance": "Curated target in the disease briefing.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 0/1066 patients (0.0%).", "Without the 21 hypermutated patients: 0/1045 (0.0%).", "Largest alteration is amplification: 16/1070 (1.5%) in the reference cohort's copy-number profile.", "Observed in 0 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 0, "tested": 1066, "frequency": 0.0, "frequency_excl_hypermutated": 0.0, "counting_unit": "patients", "status": "not_observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 5.0, "width": 1.0, "reference": 5.0, "scale_max": 30.0}, "headline_alteration": {"kind": "amplification", "altered": 16, "tested": 1070, "frequency": 1.5, "is_mutation": false}, "altered_status": "not_observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "not_observed", "frequency_unit": "percent", "cohort_count_status": "not_observed", "cohort_count_unit": "cohorts"}, {"gene": "GATA3", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 127, "tested": 1066, "frequency": 11.91, "cohort_count": 3, "frequency_range": {"min": 10.97, "max": 13.64}, "major_variants": ["X308_splice (n=21)", "P408Afs*99 (n=13)", "D335Gfs*17 (n=8)", "M293K (n=3)", "S436Lfs*71 (n=2)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 127/1066 patients (11.91%).", "Without the 21 hypermutated patients: 122/1045 (11.67%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 127, "tested": 1066, "frequency": 11.91, "frequency_excl_hypermutated": 11.67, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 267, "tested": 2433, "frequency": 10.97, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 63, "tested": 462, "frequency": 13.64, "frequency_excl_hypermutated": 13.7, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 36.57, "width": 8.9, "reference": 39.7, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 127, "tested": 1066, "frequency": 11.91, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "CDH1", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 127, "tested": 1066, "frequency": 11.91, "cohort_count": 3, "frequency_range": {"min": 9.58, "max": 30.74}, "major_variants": ["Q23* (n=8)", "R63* (n=4)", "P127Afs*41 (n=4)", "E243K (n=3)", "X722_splice (n=3)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 127/1066 patients (11.91%).", "Without the 21 hypermutated patients: 121/1045 (11.58%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 127, "tested": 1066, "frequency": 11.91, "frequency_excl_hypermutated": 11.58, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 233, "tested": 2433, "frequency": 9.58, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 142, "tested": 462, "frequency": 30.74, "frequency_excl_hypermutated": 30.65, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 31.93, "width": 68.07, "reference": 39.7, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 127, "tested": 1066, "frequency": 11.91, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "KMT2C", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 97, "tested": 1066, "frequency": 9.1, "cohort_count": 3, "frequency_range": {"min": 9.1, "max": 27.92}, "major_variants": ["R4478* (n=2)", "E640* (n=2)", "Q1478* (n=2)", "S1334C (n=1)", "E2838K (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 97/1066 patients (9.1%).", "Without the 21 hypermutated patients: 86/1045 (8.23%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 97, "tested": 1066, "frequency": 9.1, "frequency_excl_hypermutated": 8.23, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 277, "tested": 2433, "frequency": 11.39, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 129, "tested": 462, "frequency": 27.92, "frequency_excl_hypermutated": 27.61, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 30.33, "width": 62.74, "reference": 30.33, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 97, "tested": 1066, "frequency": 9.1, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "MAP3K1", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 89, "tested": 1066, "frequency": 8.35, "cohort_count": 3, "frequency_range": {"min": 8.35, "max": 17.75}, "major_variants": ["R273Sfs*27 (n=3)", "R763Cfs*35 (n=3)", "V1346del (n=2)", "L319Tfs*7 (n=2)", "Q1048* (n=2)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 89/1066 patients (8.35%).", "Without the 21 hypermutated patients: 86/1045 (8.23%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 89, "tested": 1066, "frequency": 8.35, "frequency_excl_hypermutated": 8.23, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 236, "tested": 2433, "frequency": 9.7, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 82, "tested": 462, "frequency": 17.75, "frequency_excl_hypermutated": 17.39, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 27.83, "width": 31.34, "reference": 27.83, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 89, "tested": 1066, "frequency": 8.35, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "NCOR1", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 50, "tested": 1066, "frequency": 4.69, "cohort_count": 3, "frequency_range": {"min": 3.53, "max": 14.07}, "major_variants": ["T525Nfs*11 (n=2)", "P7S (n=1)", "E531Q (n=1)", "G1163D (n=1)", "E592* (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 50/1066 patients (4.69%).", "Without the 21 hypermutated patients: 44/1045 (4.21%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 50, "tested": 1066, "frequency": 4.69, "frequency_excl_hypermutated": 4.21, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 86, "tested": 2433, "frequency": 3.53, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 65, "tested": 462, "frequency": 14.07, "frequency_excl_hypermutated": 13.7, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 11.77, "width": 35.13, "reference": 15.63, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 50, "tested": 1066, "frequency": 4.69, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "MAP2K4", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 42, "tested": 1066, "frequency": 3.94, "cohort_count": 3, "frequency_range": {"min": 3.25, "max": 7.79}, "major_variants": ["R281* (n=2)", "S251I (n=2)", "X75_splice (n=2)", "D263Cfs*4 (n=2)", "S184L (n=2)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 42/1066 patients (3.94%).", "Without the 21 hypermutated patients: 42/1045 (4.02%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 42, "tested": 1066, "frequency": 3.94, "frequency_excl_hypermutated": 4.02, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat 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"patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "RUNX1", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 40, "tested": 1066, "frequency": 3.75, "cohort_count": 3, "frequency_range": {"min": 3.33, "max": 5.41}, "major_variants": ["D123Gfs*15 (n=5)", "R169Kfs*44 (n=2)", "D123Gfs*11 (n=2)", "D123Mfs*10 (n=1)", "A244V (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 40/1066 patients (3.75%).", "Without the 21 hypermutated patients: 37/1045 (3.54%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 40, "tested": 1066, "frequency": 3.75, "frequency_excl_hypermutated": 3.54, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 81, "tested": 2433, "frequency": 3.33, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 25, "tested": 462, "frequency": 5.41, "frequency_excl_hypermutated": 5.22, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 11.1, "width": 6.93, "reference": 12.5, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 40, "tested": 1066, "frequency": 3.75, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "ARID1A", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 39, "tested": 1066, "frequency": 3.66, "cohort_count": 3, "frequency_range": {"min": 3.66, "max": 17.75}, "major_variants": ["X960_splice (n=2)", "R1989* (n=2)", "Q528* (n=2)", "Q944* (n=1)", "R2143C (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 39/1066 patients (3.66%).", "Without the 21 hypermutated patients: 35/1045 (3.35%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 39, "tested": 1066, "frequency": 3.66, "frequency_excl_hypermutated": 3.35, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 114, "tested": 2433, "frequency": 4.69, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 82, "tested": 462, "frequency": 17.75, "frequency_excl_hypermutated": 17.39, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 12.2, "width": 46.97, "reference": 12.2, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 39, "tested": 1066, "frequency": 3.66, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "HUWE1", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 38, "tested": 1066, "frequency": 3.56, "cohort_count": 1, "frequency_range": {"min": 3.56, "max": 3.56}, "major_variants": ["S3122F (n=1)", "A889T (n=1)", "R3174H (n=1)", "D882N (n=1)", "R3786Q (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 38/1066 patients (3.56%).", "Without the 21 hypermutated patients: 26/1045 (2.49%).", "Observed in 1 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 38, "tested": 1066, "frequency": 3.56, "frequency_excl_hypermutated": 2.49, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 11.87, "width": 1.0, "reference": 11.87, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 38, "tested": 1066, "frequency": 3.56, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "NF1", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 37, "tested": 1066, "frequency": 3.47, "cohort_count": 3, "frequency_range": {"min": 3.47, "max": 20.56}, "major_variants": ["Q209* (n=1)", "W571* (n=1)", "R366* (n=1)", "E524Q (n=1)", "R2119Qfs*10 (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 37/1066 patients (3.47%).", "Without the 21 hypermutated patients: 32/1045 (3.06%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 37, "tested": 1066, "frequency": 3.47, "frequency_excl_hypermutated": 3.06, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 91, "tested": 2433, "frequency": 3.74, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 95, "tested": 462, "frequency": 20.56, "frequency_excl_hypermutated": 20.43, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 11.57, "width": 56.96, "reference": 11.57, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 37, "tested": 1066, "frequency": 3.47, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "CACNA1E", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 37, "tested": 1066, "frequency": 3.47, "cohort_count": 1, "frequency_range": {"min": 3.47, "max": 3.47}, "major_variants": ["R384C (n=2)", "R1396C (n=1)", "G2125V (n=1)", "Q110K (n=1)", "X391_splice (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 37/1066 patients (3.47%).", "Without the 21 hypermutated patients: 30/1045 (2.87%).", "Largest alteration is amplification: 79/1070 (7.38%) in the reference cohort's copy-number profile.", "Observed in 1 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 37, "tested": 1066, "frequency": 3.47, "frequency_excl_hypermutated": 2.87, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 24.6, "width": 1.0, "reference": 24.6, "scale_max": 30.0}, "headline_alteration": {"kind": "amplification", "altered": 79, "tested": 1070, "frequency": 7.38, "is_mutation": false}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "MDN1", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 36, "tested": 1066, "frequency": 3.38, "cohort_count": 1, "frequency_range": {"min": 3.38, "max": 3.38}, "major_variants": ["L423F (n=1)", "K4830N (n=1)", "E2201Q (n=1)", "D2612H (n=1)", "D5539G (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 36/1066 patients (3.38%).", "Without the 21 hypermutated patients: 27/1045 (2.58%).", "Observed in 1 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 36, "tested": 1066, "frequency": 3.38, "frequency_excl_hypermutated": 2.58, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 11.27, "width": 1.0, "reference": 11.27, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 36, "tested": 1066, "frequency": 3.38, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "RELN", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 34, "tested": 1066, "frequency": 3.19, "cohort_count": 1, "frequency_range": {"min": 3.19, "max": 3.19}, "major_variants": ["G3444E (n=1)", "R1385I (n=1)", "F1269C (n=1)", "G2175S (n=1)", "D1175H (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 34/1066 patients (3.19%).", "Without the 21 hypermutated patients: 26/1045 (2.49%).", "Observed in 1 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 34, "tested": 1066, "frequency": 3.19, "frequency_excl_hypermutated": 2.49, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 10.63, "width": 1.0, "reference": 10.63, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 34, "tested": 1066, "frequency": 3.19, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "TBX3", "alteration_types": ["SNV / small indel", "deep deletion", "amplification"], "altered": 33, "tested": 1066, "frequency": 3.1, "cohort_count": 3, "frequency_range": {"min": 3.1, "max": 13.2}, "major_variants": ["H187Y (n=2)", "Y265Lfs*12 (n=1)", "P134S (n=1)", "M184Gfs*25 (n=1)", "K175* (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 33/1066 patients (3.1%).", "Without the 21 hypermutated patients: 30/1045 (2.87%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 33, "tested": 1066, "frequency": 3.1, "frequency_excl_hypermutated": 2.87, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 122, "tested": 2433, "frequency": 5.01, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 61, "tested": 462, "frequency": 13.2, "frequency_excl_hypermutated": 13.04, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 10.33, "width": 33.67, "reference": 10.33, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 33, "tested": 1066, "frequency": 3.1, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "MYCBP2", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 33, "tested": 1066, "frequency": 3.1, "cohort_count": 1, "frequency_range": {"min": 3.1, "max": 3.1}, "major_variants": ["K2740M (n=1)", "I3077V (n=1)", "Q3845* (n=1)", "S143* (n=1)", "H3616Y (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 33/1066 patients (3.1%).", "Without the 21 hypermutated patients: 24/1045 (2.3%).", "Observed in 1 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 33, "tested": 1066, "frequency": 3.1, "frequency_excl_hypermutated": 2.3, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 10.33, "width": 1.0, "reference": 10.33, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 33, "tested": 1066, "frequency": 3.1, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "SPEN", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 32, "tested": 1066, "frequency": 3.0, "cohort_count": 2, "frequency_range": {"min": 3.0, "max": 15.8}, "major_variants": ["N1429K (n=1)", "P2059Kfs*3 (n=1)", "F609Lfs*2 (n=1)", "E2846K (n=1)", "E2201Q (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 32/1066 patients (3.0%).", "Without the 21 hypermutated patients: 23/1045 (2.2%).", "Observed in 2 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 32, "tested": 1066, "frequency": 3.0, "frequency_excl_hypermutated": 2.2, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 73, "tested": 462, "frequency": 15.8, "frequency_excl_hypermutated": 15.43, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 10.0, "width": 42.67, "reference": 10.0, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 32, "tested": 1066, "frequency": 3.0, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "KMT2D", "alteration_types": ["SNV / small indel", "amplification"], "altered": 32, "tested": 1066, "frequency": 3.0, "cohort_count": 3, "frequency_range": {"min": 3.0, "max": 20.56}, "major_variants": ["K1686Nfs*36 (n=2)", "T1681N (n=1)", "P3246Tfs*5 (n=1)", "E3587V (n=1)", "A2119Rfs*36 (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 32/1066 patients (3.0%).", "Without the 21 hypermutated patients: 22/1045 (2.11%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 32, "tested": 1066, "frequency": 3.0, "frequency_excl_hypermutated": 2.11, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 176, "tested": 2433, "frequency": 7.23, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 95, "tested": 462, "frequency": 20.56, "frequency_excl_hypermutated": 20.43, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 10.0, "width": 58.53, "reference": 10.0, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 32, "tested": 1066, "frequency": 3.0, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "PRUNE2", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 31, "tested": 1066, "frequency": 2.91, "cohort_count": 1, "frequency_range": {"min": 2.91, "max": 2.91}, "major_variants": ["S576N (n=1)", "H2092Y (n=1)", "D830V (n=1)", "V2775M (n=1)", "S2432F (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 31/1066 patients (2.91%).", "Without the 21 hypermutated patients: 22/1045 (2.11%).", "Observed in 1 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 31, "tested": 1066, "frequency": 2.91, "frequency_excl_hypermutated": 2.11, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 9.7, "width": 1.0, "reference": 9.7, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 31, "tested": 1066, "frequency": 2.91, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "FOXA1", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 31, "tested": 1066, "frequency": 2.91, "cohort_count": 2, "frequency_range": {"min": 2.91, "max": 14.72}, "major_variants": ["S250F (n=3)", "I176M (n=3)", "D226G (n=2)", "S194Afs*127 (n=1)", "I450M (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 31/1066 patients (2.91%).", "Without the 21 hypermutated patients: 28/1045 (2.68%).", "Observed in 2 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 31, "tested": 1066, "frequency": 2.91, "frequency_excl_hypermutated": 2.68, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 68, "tested": 462, "frequency": 14.72, "frequency_excl_hypermutated": 14.35, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 9.7, "width": 39.37, "reference": 9.7, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 31, "tested": 1066, "frequency": 2.91, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "FAT1", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 31, "tested": 1066, "frequency": 2.91, "cohort_count": 2, "frequency_range": {"min": 2.91, "max": 16.88}, "major_variants": ["S2060F (n=2)", "T2261M (n=1)", "D2373N (n=1)", "K1044R (n=1)", "D2076N (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 31/1066 patients (2.91%).", "Without the 21 hypermutated patients: 22/1045 (2.11%).", "Observed in 2 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 31, "tested": 1066, "frequency": 2.91, "frequency_excl_hypermutated": 2.11, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": 78, "tested": 462, "frequency": 16.88, "frequency_excl_hypermutated": 16.52, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 9.7, "width": 46.57, "reference": 9.7, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 31, "tested": 1066, "frequency": 2.91, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "VPS13C", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 30, "tested": 1066, "frequency": 2.81, "cohort_count": 1, "frequency_range": {"min": 2.81, "max": 2.81}, "major_variants": ["T3732M (n=2)", "V3571I (n=1)", "E1451K (n=1)", "A840D (n=1)", "A1513S (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 30/1066 patients (2.81%).", "Without the 21 hypermutated patients: 20/1045 (1.91%).", "Observed in 1 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 30, "tested": 1066, "frequency": 2.81, "frequency_excl_hypermutated": 1.91, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 9.37, "width": 1.0, "reference": 9.37, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 30, "tested": 1066, "frequency": 2.81, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "TEX15", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 30, "tested": 1066, "frequency": 2.81, "cohort_count": 1, "frequency_range": {"min": 2.81, "max": 2.81}, "major_variants": ["L2764F (n=1)", "S1432T (n=1)", "P1734L (n=1)", "T208K (n=1)", "E57Q (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 30/1066 patients (2.81%).", "Without the 21 hypermutated patients: 26/1045 (2.49%).", "Largest alteration is deep deletion: 39/1070 (3.64%) in the reference cohort's copy-number profile.", "Observed in 1 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 30, "tested": 1066, "frequency": 2.81, "frequency_excl_hypermutated": 2.49, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 12.13, "width": 1.0, "reference": 12.13, "scale_max": 30.0}, "headline_alteration": {"kind": "deep deletion", "altered": 39, "tested": 1070, "frequency": 3.64, "is_mutation": false}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "MYH9", "alteration_types": ["SNV / small indel", "amplification", "deep 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"processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 30/1066 patients (2.81%).", "Without the 21 hypermutated patients: 24/1045 (2.3%).", "Observed in 2 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 30, "tested": 1066, "frequency": 2.81, "frequency_excl_hypermutated": 2.3, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 87, "tested": 2433, "frequency": 3.58, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 9.37, "width": 2.56, "reference": 9.37, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 30, "tested": 1066, "frequency": 2.81, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "MXRA5", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 30, "tested": 1066, "frequency": 2.81, "cohort_count": 1, "frequency_range": {"min": 2.81, "max": 2.81}, "major_variants": ["G798S (n=1)", "G473S (n=1)", "M273I (n=1)", "A1492G (n=1)", "E266* (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 30/1066 patients (2.81%).", "Without the 21 hypermutated patients: 22/1045 (2.11%).", "Observed in 1 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 30, "tested": 1066, "frequency": 2.81, "frequency_excl_hypermutated": 2.11, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 9.37, "width": 1.0, "reference": 9.37, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 30, "tested": 1066, "frequency": 2.81, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "LYST", "alteration_types": ["SNV / small indel", "amplification"], "altered": 30, "tested": 1066, "frequency": 2.81, "cohort_count": 1, "frequency_range": {"min": 2.81, "max": 2.81}, "major_variants": ["Q3352P (n=1)", "Q2237* (n=1)", "E1095K (n=1)", "V1744F (n=1)", "C2828* (n=1)"], 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OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 30/1066 patients (2.81%).", "Without the 21 hypermutated patients: 21/1045 (2.01%).", "Largest alteration is amplification: 103/1070 (9.63%) in the reference cohort's copy-number profile.", "Observed in 1 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 30, "tested": 1066, "frequency": 2.81, "frequency_excl_hypermutated": 2.01, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, 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"patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "FCGBP", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 30, "tested": 1066, "frequency": 2.81, "cohort_count": 1, "frequency_range": {"min": 2.81, "max": 2.81}, "major_variants": ["N4225Tfs*173 (n=2)", "L1156R (n=1)", "G4218S (n=1)", "V3268I (n=1)", "E2651K (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not 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data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 30/1066 patients (2.81%).", "Without the 21 hypermutated patients: 23/1045 (2.2%).", "Observed in 1 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 30, "tested": 1066, "frequency": 2.81, "frequency_excl_hypermutated": 2.2, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 9.37, "width": 1.0, "reference": 9.37, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 30, "tested": 1066, "frequency": 2.81, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "DYNC1H1", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 30, "tested": 1066, "frequency": 2.81, "cohort_count": 1, "frequency_range": {"min": 2.81, "max": 2.81}, "major_variants": ["K4418N (n=1)", "E1786K (n=1)", "V3797L (n=1)", "E4439G (n=1)", "V88I (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most 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"cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 30/1066 patients (2.81%).", "Without the 21 hypermutated patients: 19/1045 (1.82%).", "Observed in 1 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 30, "tested": 1066, "frequency": 2.81, "frequency_excl_hypermutated": 1.82, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 9.37, "width": 1.0, "reference": 9.37, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 30, "tested": 1066, "frequency": 2.81, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", 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"https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 30/1066 patients (2.81%).", "Without the 21 hypermutated patients: 25/1045 (2.39%).", "Observed in 1 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 30, "tested": 1066, "frequency": 2.81, "frequency_excl_hypermutated": 2.39, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 9.37, "width": 1.0, "reference": 9.37, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 30, "tested": 1066, "frequency": 2.81, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "AKAP9", "alteration_types": ["SNV / small indel", "amplification", "deep deletion"], "altered": 30, "tested": 1066, "frequency": 2.81, "cohort_count": 2, "frequency_range": {"min": 2.81, "max": 5.88}, "major_variants": ["G3802* (n=1)", "E756Kfs*9 (n=1)", "T1942I (n=1)", "S3576Y (n=1)", "E3074Q (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's 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"https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 30/1066 patients (2.81%).", "Without the 21 hypermutated patients: 24/1045 (2.3%).", "Observed in 2 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 30, "tested": 1066, "frequency": 2.81, "frequency_excl_hypermutated": 2.3, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 143, "tested": 2433, "frequency": 5.88, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 9.37, "width": 10.23, "reference": 9.37, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 30, "tested": 1066, "frequency": 2.81, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "VPS13B", "alteration_types": ["SNV / small indel", "amplification", 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"processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 29/1066 patients (2.72%).", "Without the 21 hypermutated patients: 22/1045 (2.11%).", "Largest alteration is amplification: 118/1070 (11.03%) in the reference cohort's copy-number profile.", "Observed in 1 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 29, "tested": 1066, "frequency": 2.72, "frequency_excl_hypermutated": 2.11, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": 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"source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 29/1066 patients (2.72%).", "Without the 21 hypermutated patients: 20/1045 (1.91%).", "Observed in 2 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 29, "tested": 1066, "frequency": 2.72, "frequency_excl_hypermutated": 1.91, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 122, "tested": 2433, "frequency": 5.01, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", "coverage_note": null, "source_id": "brca_metabric", "is_reference": false}, {"cohort": "brca_msk_2025", "cohort_name": "MSK breast carcinoma (2025)", "altered": null, "tested": null, "frequency": null, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "not_assayed", "assayed": false, "assay_note": "Not on this cohort's gene panel.", "evaluable": false, "coverage": "527/527", "coverage_note": null, "source_id": "brca_msk_2025", "is_reference": false}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 9.07, "width": 7.63, "reference": 9.07, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 29, "tested": 1066, "frequency": 2.72, "is_mutation": true}, "altered_status": "observed", "altered_unit": "patients", "tested_status": "observed", "tested_unit": "patients", "frequency_status": "observed", "frequency_unit": "percent", "cohort_count_status": "observed", "cohort_count_unit": "cohorts"}, {"gene": "PIK3R1", "alteration_types": ["SNV / small indel", "deep deletion", "amplification"], "altered": 29, "tested": 1066, "frequency": 2.72, "cohort_count": 3, "frequency_range": {"min": 2.47, "max": 6.49}, "major_variants": ["K567_L570del (n=3)", "K575_T576dup (n=1)", "E468_E469insGLYE (n=1)", "K459_S460dup (n=1)", "L380del (n=1)"], "evidence_confidence": "moderate", "disease_relevance": "Among the most frequently mutated genes in the reference cohort.", "targetability": "See the disease briefing's target table; not inferred from frequency.", "approved_drugs_other_diseases": [], "neuroblastoma_trials": [], "limitations": ["Non-silent calls in the study's sequenced sample list; patients, not samples.", "Cohort rows are not pooled; a zero is a measured absence in that profile, a dot is a gene the panel did not carry."], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 29/1066 patients (2.72%).", "Without the 21 hypermutated patients: 25/1045 (2.39%).", "Observed in 3 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 29, "tested": 1066, "frequency": 2.72, "frequency_excl_hypermutated": 2.39, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": 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false}], "derived_insights": ["Reference cohort: TCGA PanCancer Atlas breast (2018), 29/1066 patients (2.72%).", "Without the 21 hypermutated patients: 20/1045 (1.91%).", "Observed in 2 of 3 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "brca_tcga_pan_can_atlas_2018", "cohort_name": "TCGA PanCancer Atlas breast (2018)", "altered": 29, "tested": 1066, "frequency": 2.72, "frequency_excl_hypermutated": 1.91, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "1066/1084", "coverage_note": null, "source_id": "brca_tcga_pan_can_atlas_2018", "is_reference": true}, {"cohort": "brca_metabric", "cohort_name": "METABRIC (Nature 2012, Nat Commun 2016)", "altered": 157, "tested": 2433, "frequency": 6.45, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "2433/2509", 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"brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": 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["brca_msk_2025"], "source_ids": ["brca_msk_2025_gistic"], "evidence_confidence": "moderate", "details": null}, {"event_type": "copy_number", "gene": "GATA3", "denominator_note": "Patients in the cohort's copy-number sample list.", "partner_gene": null, "alteration": "amplification", "event_label": "GATA3 amplification", "genomic_coordinate": null, "observed": 10, "observed_status": "observed", "observed_unit": "patients", "tested": 462, "tested_status": "observed", "tested_unit": "patients", "frequency": 2.16, "frequency_status": "observed", "frequency_unit": "percent", "cohorts": ["brca_msk_2025"], "source_ids": ["brca_msk_2025_gistic"], "evidence_confidence": "moderate", "details": null}, {"event_type": "copy_number", "gene": "FCGBP", "denominator_note": "Patients in the cohort's copy-number sample list.", "partner_gene": null, "alteration": "amplification", "event_label": "FCGBP amplification", "genomic_coordinate": null, "observed": 23, "observed_status": "observed", "observed_unit": "patients", "tested": 1070, "tested_status": "observed", "tested_unit": "patients", "frequency": 2.15, "frequency_status": "observed", "frequency_unit": "percent", "cohorts": ["brca_tcga_pan_can_atlas_2018"], "source_ids": ["brca_tcga_pan_can_atlas_2018_gistic"], "evidence_confidence": "moderate", "details": null}, {"event_type": "copy_number", "gene": "MAP2K4", "denominator_note": "Patients in the cohort's copy-number sample list.", "partner_gene": null, "alteration": "deep deletion", "event_label": "MAP2K4 deep deletion", "genomic_coordinate": null, "observed": 46, "observed_status": "observed", "observed_unit": "patients", "tested": 2173, "tested_status": "observed", "tested_unit": "patients", "frequency": 2.12, "frequency_status": "observed", "frequency_unit": "percent", "cohorts": ["brca_metabric"], "source_ids": ["brca_metabric_cna"], "evidence_confidence": "moderate", "details": null}, {"event_type": "copy_number", "gene": "PTEN", "denominator_note": "Patients in the cohort's copy-number sample list.", "partner_gene": null, "alteration": "deep deletion", "event_label": "PTEN deep deletion", "genomic_coordinate": null, "observed": 44, "observed_status": "observed", "observed_unit": "patients", "tested": 2173, "tested_status": "observed", "tested_unit": "patients", "frequency": 2.02, "frequency_status": "observed", "frequency_unit": "percent", "cohorts": ["brca_metabric"], "source_ids": ["brca_metabric_cna"], "evidence_confidence": "moderate", "details": null}], "modality_summary": [{"modality": "SNV / small indel", "available_cohorts": 3, "total_cohorts": 3}, {"modality": "Copy number (discrete)", "available_cohorts": 3, "total_cohorts": 3}, {"modality": "Structural variant (present, not read)", "available_cohorts": 2, "total_cohorts": 3}], "chromosome_summary": [], "cohorts": [{"name": "TCGA PanCancer Atlas breast (2018)", "source": "cBioPortal", "accession": "brca_tcga_pan_can_atlas_2018", "patients": {"value": 1066, "status": "observed", "unit": "patients"}, "samples": {"value": 1066, "status": "observed", "unit": "samples"}, "disease_subtype": "Breast Invasive Carcinoma (TCGA, PanCancer Atlas)", "assay_type": "exome or genome", "sequencing_method": "WES (1066)", "genome_build": "hg19", "alteration_types_available": ["SNV", "small indel", "amplification", "deep deletion", "structural variant (profile present, not read)"], "genes_assayed": "all coding genes", "primary_or_metastatic": null, "age_group": null, "retrieved_at": "2026-09-17", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "source_record_id": "brca_tcga_pan_can_atlas_2018", "is_demo": false, "assay_coverage": {"patients_with_calls": 1066, "patients_in_roster": 1066, "frequencies_computed": true, "samples_sequenced": 1066, "samples_in_study": 1084, "hypermutated_patients": 21, "median_mutations_per_sample": 37.0, "reason": null}}, {"name": "METABRIC (Nature 2012, Nat Commun 2016)", "source": "cBioPortal", "accession": "brca_metabric", "patients": {"value": 2433, "status": "observed", "unit": "patients"}, "samples": {"value": 2433, "status": "observed", "unit": "samples"}, "disease_subtype": "Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016)", "assay_type": "targeted panel", "sequencing_method": "METABRIC_173 (2433)", "genome_build": "hg19", "alteration_types_available": ["SNV", "small indel", "amplification", "deep deletion"], "genes_assayed": "panel genes only; per-gene denominators", "primary_or_metastatic": null, "age_group": null, "retrieved_at": "2026-09-17", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "source_record_id": "brca_metabric", "is_demo": false, "assay_coverage": {"patients_with_calls": 2433, "patients_in_roster": 2433, "frequencies_computed": true, "samples_sequenced": 2433, "samples_in_study": 2509, "hypermutated_patients": 0, "median_mutations_per_sample": 5, "reason": null}}, {"name": "MSK breast carcinoma (2025)", "source": "cBioPortal", "accession": "brca_msk_2025", "patients": {"value": 462, "status": "observed", "unit": "patients"}, "samples": {"value": 527, "status": "observed", "unit": "samples"}, "disease_subtype": "Breast Carcinoma (MSK, NPJ Precis Oncol 2025)", "assay_type": "targeted panel", "sequencing_method": "IMPACT468 (283), IMPACT505 (124), IMPACT410 (81), IMPACT341 (39)", "genome_build": "hg19", "alteration_types_available": ["SNV", "small indel", "amplification", "deep deletion", "structural variant (profile present, not read)"], "genes_assayed": "panel genes only; per-gene denominators", "primary_or_metastatic": null, "age_group": null, "retrieved_at": "2026-09-17", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "source_record_id": "brca_msk_2025", "is_demo": false, "assay_coverage": {"patients_with_calls": 462, "patients_in_roster": 462, "frequencies_computed": true, "samples_sequenced": 527, "samples_in_study": 527, "hypermutated_patients": 2, "median_mutations_per_sample": 16, "reason": null}}], "sources": [{"source_name": "cBioPortal · TCGA PanCancer Atlas breast (2018)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018", "source_record_id": "brca_tcga_pan_can_atlas_2018", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · METABRIC (Nature 2012, Nat Commun 2016)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_metabric", "source_record_id": "brca_metabric", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}, {"source_name": "cBioPortal · MSK breast carcinoma (2025)", "source_url": "https://www.cbioportal.org/study/summary?id=brca_msk_2025", "source_record_id": "brca_msk_2025", "source_version": null, "retrieved_at": "2026-09-17", "processing_version": null, "normalization_method": "patient-level, non-silent calls, panel-aware denominator", "genome_build": "hg19", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "is_demo": false}], "limitations": ["A cBioPortal public-API snapshot retrieved 2026-09-17; the page does not refresh source data at request time.", "Counts are patients with at least one non-silent call in the study's sequenced sample list; silent, intronic and UTR calls are excluded.", "For targeted-panel cohorts each gene divides by the patients whose panel carried it; a gene absent from the panel is shown as not assayed, not as zero.", "Copy-number rows use discrete calls (2 = high-level amplification, −2 = deep deletion) against the cohort's copy-number sample list, which is a different roster from the sequenced one.", "Cohorts are not pooled. Cross-study patient overlap has not been checked and no disease-wide frequency is reported.", "Structural variants and fusions are not read in this snapshot even where the study carries a profile; germline variants, mutational signatures, TMB and MSI are not reported.", "The gene set is the briefing's curated targets plus the reference cohort's most frequently mutated genes; it is not genome-wide."], "answer_block": ["In TCGA PanCancer Atlas breast (2018) (1066 sequenced patients, exome or genome), the most frequently altered of the 47 genes shown are PIK3CA 32.46%, TP53 32.46%, GATA3 11.91%, CDH1 11.91%, ERBB2 11.5% (amplification). Each figure divides by the patients on whom that gene could be called.", "21 of 1066 patients are hypermutated (more than 370 non-silent mutations, ten times the cohort median of 37); every gene's frequency without them is beside the headline.", "Of the briefing's 12 curated targets, 5 are altered in under 2% of this cohort (ESR1, PGR, CDK4, CDK6, TACSTD2): targets by expression, dependency or drug label, not by mutation. Frequency is not targetability, in either direction.", "3 cohorts are shown and none are pooled; overlap between them has not been checked and there is no disease-wide percentage."], "key_findings": [{"finding": "PIK3CA is mutated in 346 of 1066 patients in TCGA PanCancer Atlas breast (2018).", "numerator": 346, "denominator": 1066, "frequency": 32.46, "cohorts": 3, "evidence_confidence": "moderate", "source": "brca_tcga_pan_can_atlas_2018", "retrieved_at": "2026-09-17"}, {"finding": "TP53 is mutated in 346 of 1066 patients in TCGA PanCancer Atlas breast (2018).", "numerator": 346, "denominator": 1066, "frequency": 32.46, "cohorts": 3, "evidence_confidence": "moderate", "source": "brca_tcga_pan_can_atlas_2018", "retrieved_at": "2026-09-17"}, {"finding": "GATA3 is mutated in 127 of 1066 patients in TCGA PanCancer Atlas breast (2018).", "numerator": 127, "denominator": 1066, "frequency": 11.91, "cohorts": 3, "evidence_confidence": "moderate", "source": "brca_tcga_pan_can_atlas_2018", "retrieved_at": "2026-09-17"}], "research_gaps": [{"kind": "Structural variants", "text": "Read the structural-variant profiles the studies carry; fusions are the defining event in several of these diseases."}, {"kind": "Context", "text": "Stage, subtype, age and treatment line are not attached to any count; the cohorts differ on all four."}, {"kind": "Interpretation", "text": "Activating versus inactivating, actionable versus not, and evidence level are not inferred here; the briefing's target table carries the drug and trial facts."}], "observations": [], "data_status": "PUBLIC SOURCE SNAPSHOT", "is_demo": false, "reference_cohort": "brca_tcga_pan_can_atlas_2018", "region_events": [], "matrix": [{"label": "ESR1", "kind": "SNV / small indel", "gene": "ESR1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 0.84, "altered": 9, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 14.07, "altered": 65, "tested": 462, "note": null}]}, {"label": "ESR1", "kind": "amplification", "gene": "ESR1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 1.87, "altered": 20, "tested": 1070, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_metabric", "status": "observed", "frequency": 2.3, "altered": 50, "tested": 2173, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 2.16, "altered": 10, "tested": 462, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}]}, {"label": "PGR", "kind": "SNV / small indel", "gene": "PGR", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 0.66, "altered": 7, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 3.5, "altered": 15, "tested": 429, "note": null}]}, {"label": "ERBB2", "kind": "SNV / small indel", "gene": "ERBB2", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.81, "altered": 30, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 2.92, "altered": 71, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 10.39, "altered": 48, "tested": 462, "note": null}]}, {"label": "ERBB2", "kind": "amplification", "gene": "ERBB2", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 11.5, "altered": 123, "tested": 1070, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_metabric", "status": "observed", "frequency": 15.74, "altered": 342, "tested": 2173, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 14.5, "altered": 67, "tested": 462, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}]}, {"label": "PIK3CA", "kind": "SNV / small indel", "gene": "PIK3CA", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 32.46, "altered": 346, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 40.07, "altered": 975, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 59.96, "altered": 277, "tested": 462, "note": null}]}, {"label": "PIK3CA", "kind": "amplification", "gene": "PIK3CA", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 3.18, "altered": 34, "tested": 1070, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_metabric", "status": "observed", "frequency": 4.51, "altered": 98, "tested": 2173, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 3.25, "altered": 15, "tested": 462, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}]}, {"label": "AKT1", "kind": "SNV / small indel", "gene": "AKT1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.53, "altered": 27, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 4.03, "altered": 98, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 6.49, "altered": 30, "tested": 462, "note": null}]}, {"label": "PTEN", "kind": "SNV / small indel", "gene": "PTEN", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 5.44, "altered": 58, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 3.9, "altered": 95, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 14.29, "altered": 66, "tested": 462, "note": null}]}, {"label": "PTEN", "kind": "deep deletion", "gene": "PTEN", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 5.14, "altered": 55, "tested": 1070, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_metabric", "status": "observed", "frequency": 2.02, "altered": 44, "tested": 2173, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 1.52, "altered": 7, "tested": 462, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}]}, {"label": "CDK4", "kind": "SNV / small indel", "gene": "CDK4", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "not_observed", "frequency": 0.0, "altered": 0, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 1.08, "altered": 5, "tested": 462, "note": null}]}, {"label": "CDK6", "kind": "SNV / small indel", "gene": "CDK6", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 0.28, "altered": 3, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 0.87, "altered": 4, "tested": 462, "note": null}]}, {"label": "BRCA1", "kind": "SNV / small indel", "gene": "BRCA1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.53, "altered": 27, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 1.73, "altered": 42, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 8.01, "altered": 37, "tested": 462, "note": null}]}, {"label": "BRCA2", "kind": "SNV / small indel", "gene": "BRCA2", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.72, "altered": 29, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 1.85, "altered": 45, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 12.12, "altered": 56, "tested": 462, "note": null}]}, {"label": "TP53", "kind": "SNV / small indel", "gene": "TP53", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 32.46, "altered": 346, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 35.39, "altered": 861, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 55.84, "altered": 258, "tested": 462, "note": null}]}, {"label": "TACSTD2", "kind": "SNV / small indel", "gene": "TACSTD2", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "not_observed", "frequency": 0.0, "altered": 0, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "GATA3", "kind": "SNV / small indel", "gene": "GATA3", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 11.91, "altered": 127, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 10.97, "altered": 267, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 13.64, "altered": 63, "tested": 462, "note": null}]}, {"label": "GATA3", "kind": "amplification", "gene": "GATA3", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.99, "altered": 32, "tested": 1070, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_metabric", "status": "observed", "frequency": 4.65, "altered": 101, "tested": 2173, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 2.16, "altered": 10, "tested": 462, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}]}, {"label": "CDH1", "kind": "SNV / small indel", "gene": "CDH1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 11.91, "altered": 127, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 9.58, "altered": 233, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 30.74, "altered": 142, "tested": 462, "note": null}]}, {"label": "KMT2C", "kind": "SNV / small indel", "gene": "KMT2C", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 9.1, "altered": 97, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 11.39, "altered": 277, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 27.92, "altered": 129, "tested": 462, "note": null}]}, {"label": "MAP3K1", "kind": "SNV / small indel", "gene": "MAP3K1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 8.35, "altered": 89, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 9.7, "altered": 236, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 17.75, "altered": 82, "tested": 462, "note": null}]}, {"label": "NCOR1", "kind": "SNV / small indel", "gene": "NCOR1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 4.69, "altered": 50, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 3.53, "altered": 86, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 14.07, "altered": 65, "tested": 462, "note": null}]}, {"label": "MAP2K4", "kind": "SNV / small indel", "gene": "MAP2K4", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 3.94, "altered": 42, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 3.25, "altered": 79, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 7.79, "altered": 36, "tested": 462, "note": null}]}, {"label": "MAP2K4", "kind": "deep deletion", "gene": "MAP2K4", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.43, "altered": 26, "tested": 1070, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_metabric", "status": "observed", "frequency": 2.12, "altered": 46, "tested": 2173, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 1.52, "altered": 7, "tested": 462, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}]}, {"label": "RUNX1", "kind": "SNV / small indel", "gene": "RUNX1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 3.75, "altered": 40, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 3.33, "altered": 81, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 5.41, "altered": 25, "tested": 462, "note": null}]}, {"label": "RUNX1", "kind": "amplification", "gene": "RUNX1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 1.21, "altered": 13, "tested": 1070, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_metabric", "status": "observed", "frequency": 2.39, "altered": 52, "tested": 2173, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 0.22, "altered": 1, "tested": 462, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}]}, {"label": "ARID1A", "kind": "SNV / small indel", "gene": "ARID1A", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 3.66, "altered": 39, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 4.69, "altered": 114, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 17.75, "altered": 82, "tested": 462, "note": null}]}, {"label": "HUWE1", "kind": "SNV / small indel", "gene": "HUWE1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 3.56, "altered": 38, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "NF1", "kind": "SNV / small indel", "gene": "NF1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 3.47, "altered": 37, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 3.74, "altered": 91, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 20.56, "altered": 95, "tested": 462, "note": null}]}, {"label": "NF1", "kind": "amplification", "gene": "NF1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.24, "altered": 24, "tested": 1070, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_metabric", "status": "observed", "frequency": 1.61, "altered": 35, "tested": 2173, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 0.43, "altered": 2, "tested": 462, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}]}, {"label": "CACNA1E", "kind": "SNV / small indel", "gene": "CACNA1E", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 3.47, "altered": 37, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "CACNA1E", "kind": "amplification", "gene": "CACNA1E", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 7.38, "altered": 79, "tested": 1070, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_metabric", "status": "observed", "frequency": 20.94, "altered": 455, "tested": 2173, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_msk_2025", "status": "not_observed", "frequency": 0.0, "altered": 0, "tested": 462, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}]}, {"label": "MDN1", "kind": "SNV / small indel", "gene": "MDN1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 3.38, "altered": 36, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "RELN", "kind": "SNV / small indel", "gene": "RELN", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 3.19, "altered": 34, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "TBX3", "kind": "SNV / small indel", "gene": "TBX3", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 3.1, "altered": 33, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 5.01, "altered": 122, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 13.2, "altered": 61, "tested": 462, "note": null}]}, {"label": "MYCBP2", "kind": "SNV / small indel", "gene": "MYCBP2", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 3.1, "altered": 33, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "SPEN", "kind": "SNV / small indel", "gene": "SPEN", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 3.0, "altered": 32, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 15.8, "altered": 73, "tested": 462, "note": null}]}, {"label": "KMT2D", "kind": "SNV / small indel", "gene": "KMT2D", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 3.0, "altered": 32, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 7.23, "altered": 176, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 20.56, "altered": 95, "tested": 462, "note": null}]}, {"label": "PRUNE2", "kind": "SNV / small indel", "gene": "PRUNE2", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.91, "altered": 31, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "FOXA1", "kind": "SNV / small indel", "gene": "FOXA1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.91, "altered": 31, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 14.72, "altered": 68, "tested": 462, "note": null}]}, {"label": "FOXA1", "kind": "amplification", "gene": "FOXA1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 1.5, "altered": 16, "tested": 1070, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_metabric", "status": "observed", "frequency": 2.25, "altered": 49, "tested": 2173, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 1.95, "altered": 9, "tested": 462, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}]}, {"label": "FAT1", "kind": "SNV / small indel", "gene": "FAT1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.91, "altered": 31, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 16.88, "altered": 78, "tested": 462, "note": null}]}, {"label": "VPS13C", "kind": "SNV / small indel", "gene": "VPS13C", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.81, "altered": 30, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "TEX15", "kind": "SNV / small indel", "gene": "TEX15", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.81, "altered": 30, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "TEX15", "kind": "deep deletion", "gene": "TEX15", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 3.64, "altered": 39, "tested": 1070, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_metabric", "status": "observed", "frequency": 0.74, "altered": 16, "tested": 2173, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_msk_2025", "status": "not_observed", "frequency": 0.0, "altered": 0, "tested": 462, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}]}, {"label": "MYH9", "kind": "SNV / small indel", "gene": "MYH9", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.81, "altered": 30, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 3.58, "altered": 87, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "MXRA5", "kind": "SNV / small indel", "gene": "MXRA5", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.81, "altered": 30, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "LYST", "kind": "SNV / small indel", "gene": "LYST", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.81, "altered": 30, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "LYST", "kind": "amplification", "gene": "LYST", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 9.63, "altered": 103, "tested": 1070, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_metabric", "status": "observed", "frequency": 21.54, "altered": 468, "tested": 2173, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_msk_2025", "status": "not_observed", "frequency": 0.0, "altered": 0, "tested": 462, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}]}, {"label": "FCGBP", "kind": "SNV / small indel", "gene": "FCGBP", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.81, "altered": 30, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "FCGBP", "kind": "amplification", "gene": "FCGBP", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.15, "altered": 23, "tested": 1070, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_metabric", "status": "observed", "frequency": 1.24, "altered": 27, "tested": 2173, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_msk_2025", "status": "not_observed", "frequency": 0.0, "altered": 0, "tested": 462, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}]}, {"label": "DYNC1H1", "kind": "SNV / small indel", "gene": "DYNC1H1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.81, "altered": 30, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "BLTP1", "kind": "SNV / small indel", "gene": "BLTP1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.81, "altered": 30, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "AKAP9", "kind": "SNV / small indel", "gene": "AKAP9", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.81, "altered": 30, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 5.88, "altered": 143, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "VPS13B", "kind": "SNV / small indel", "gene": "VPS13B", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.72, "altered": 29, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "VPS13B", "kind": "amplification", "gene": "VPS13B", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 11.03, "altered": 118, "tested": 1070, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_metabric", "status": "observed", "frequency": 20.94, "altered": 455, "tested": 2173, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_msk_2025", "status": "not_observed", "frequency": 0.0, "altered": 0, "tested": 462, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}]}, {"label": "UTRN", "kind": "SNV / small indel", "gene": "UTRN", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.72, "altered": 29, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 5.01, "altered": 122, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "PIK3R1", "kind": "SNV / small indel", "gene": "PIK3R1", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.72, "altered": 29, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 2.47, "altered": 60, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 6.49, "altered": 30, "tested": 462, "note": null}]}, {"label": "MED12", "kind": "SNV / small indel", "gene": "MED12", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.72, "altered": 29, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}, {"cohort": "brca_msk_2025", "status": "observed", "frequency": 6.71, "altered": 31, "tested": 462, "note": null}]}, {"label": "HERC2", "kind": "SNV / small indel", "gene": "HERC2", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.72, "altered": 29, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 6.45, "altered": 157, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "TG", "kind": "SNV / small indel", "gene": "TG", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 2.63, "altered": 28, "tested": 1066, "note": null}, {"cohort": "brca_metabric", "status": "observed", "frequency": 5.55, "altered": 135, "tested": 2433, "note": null}, {"cohort": "brca_msk_2025", "status": "not_assayed", "frequency": null, "altered": null, "tested": null, "note": "Not on this cohort's gene panel."}]}, {"label": "TG", "kind": "amplification", "gene": "TG", "cells": [{"cohort": "brca_tcga_pan_can_atlas_2018", "status": "observed", "frequency": 11.31, "altered": 121, "tested": 1070, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_metabric", "status": "observed", "frequency": 23.1, "altered": 502, "tested": 2173, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}, {"cohort": "brca_msk_2025", "status": "not_observed", "frequency": 0.0, "altered": 0, "tested": 462, "note": "Discrete copy-number call; divides by the cohort's copy-number roster."}]}]}