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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 · Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018)", "source_url": "https://www.cbioportal.org/study/summary?id=vsc_cuk_2018", "source_record_id": "vsc_cuk_2018", "source_version": null, "retrieved_at": "2026-09-18", "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: Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018), 2/15 patients (13.33%).", "Observed in 1 of 1 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "vsc_cuk_2018", "cohort_name": "Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018)", "altered": 2, "tested": 15, "frequency": 13.33, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "15/15", "coverage_note": null, "source_id": "vsc_cuk_2018", "is_reference": true}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 44.43, "width": 1.0, "reference": 44.43, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 2, "tested": 15, "frequency": 13.33, "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": "WDFY4", "alteration_types": ["SNV / small indel"], "altered": 2, "tested": 15, "frequency": 13.33, "cohort_count": 1, "frequency_range": {"min": 13.33, "max": 13.33}, "major_variants": ["S612L (n=1)", "K2219R (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 · Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018)", "source_url": "https://www.cbioportal.org/study/summary?id=vsc_cuk_2018", "source_record_id": "vsc_cuk_2018", "source_version": null, "retrieved_at": "2026-09-18", "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: Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018), 2/15 patients (13.33%).", "Observed in 1 of 1 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "vsc_cuk_2018", "cohort_name": "Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018)", "altered": 2, "tested": 15, "frequency": 13.33, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "15/15", "coverage_note": null, "source_id": "vsc_cuk_2018", "is_reference": true}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 44.43, "width": 1.0, "reference": 44.43, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 2, "tested": 15, "frequency": 13.33, "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": "VPS13A", "alteration_types": ["SNV / small indel"], "altered": 2, "tested": 15, "frequency": 13.33, "cohort_count": 1, "frequency_range": {"min": 13.33, "max": 13.33}, "major_variants": ["E1074K (n=1)", "R254C (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 · Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018)", "source_url": "https://www.cbioportal.org/study/summary?id=vsc_cuk_2018", "source_record_id": "vsc_cuk_2018", "source_version": null, "retrieved_at": "2026-09-18", "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: Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018), 2/15 patients (13.33%).", "Observed in 1 of 1 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "vsc_cuk_2018", "cohort_name": "Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018)", "altered": 2, "tested": 15, "frequency": 13.33, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "15/15", "coverage_note": null, "source_id": "vsc_cuk_2018", "is_reference": true}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 44.43, "width": 1.0, "reference": 44.43, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 2, "tested": 15, "frequency": 13.33, "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": "VGLL1", "alteration_types": ["SNV / small indel"], "altered": 2, "tested": 15, "frequency": 13.33, "cohort_count": 1, "frequency_range": {"min": 13.33, "max": 13.33}, "major_variants": ["T21M (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 · Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018)", "source_url": "https://www.cbioportal.org/study/summary?id=vsc_cuk_2018", "source_record_id": "vsc_cuk_2018", "source_version": null, "retrieved_at": "2026-09-18", "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: Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018), 2/15 patients (13.33%).", "Observed in 1 of 1 cohorts; frequencies are cohort-specific and not pooled."], "cohort_frequencies": [{"cohort": "vsc_cuk_2018", "cohort_name": "Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018)", "altered": 2, "tested": 15, "frequency": 13.33, "frequency_excl_hypermutated": null, "counting_unit": "patients", "status": "observed", "assayed": true, "assay_note": null, "evaluable": true, "coverage": "15/15", "coverage_note": null, "source_id": "vsc_cuk_2018", "is_reference": true}], "hgnc_id": null, "ensembl_id": null, "chromosome": null, "range_plot": {"left": 44.43, "width": 1.0, "reference": 44.43, "scale_max": 30.0}, "headline_alteration": {"kind": "SNV / small indel", "altered": 2, "tested": 15, "frequency": 13.33, "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"}], "variants": [], "genomic_events": [], "modality_summary": [{"modality": "SNV / small indel", "available_cohorts": 1, "total_cohorts": 1}, {"modality": "Copy number (discrete)", "available_cohorts": 0, "total_cohorts": 1}, {"modality": "Structural variant (present, not read)", "available_cohorts": 0, "total_cohorts": 1}], "chromosome_summary": [], "cohorts": [{"name": "Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018)", "source": "cBioPortal", "accession": "vsc_cuk_2018", "patients": {"value": 15, "status": "observed", "unit": "patients"}, "samples": {"value": 15, "status": "observed", "unit": "samples"}, "disease_subtype": "Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018)", "assay_type": "exome or genome", "sequencing_method": "WES (15)", "genome_build": "hg19", "alteration_types_available": ["SNV", "small indel"], "genes_assayed": "all coding genes", "primary_or_metastatic": null, "age_group": null, "retrieved_at": "2026-09-18", "licence": "cBioPortal public data; the study's own data-use terms apply (TCGA: open; TARGET: OCG terms; others as published).", "source_record_id": "vsc_cuk_2018", "is_demo": false, "assay_coverage": {"patients_with_calls": 15, "patients_in_roster": 15, "frequencies_computed": true, "samples_sequenced": 15, "samples_in_study": 15, "hypermutated_patients": 0, "median_mutations_per_sample": 129, "reason": null}}], "sources": [{"source_name": "cBioPortal · Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018)", "source_url": "https://www.cbioportal.org/study/summary?id=vsc_cuk_2018", "source_record_id": "vsc_cuk_2018", "source_version": null, "retrieved_at": "2026-09-18", "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 2026-09-18; 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 Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018) (15 sequenced patients, exome or genome), the most frequently altered of the 50 genes shown are MAML2 40.0%, TP53 33.33%, SPTBN1 33.33%, ODF1 33.33%, NRG3 26.67%. Each figure divides by the patients on whom that gene could be called.", "Of the briefing's 12 curated targets, 5 are altered in under 2% of this cohort (CD274, PDCD1, TERT, KMT2D, PTEN): targets by expression, dependency or drug label, not by mutation. Frequency is not targetability, in either direction.", "1 cohorts are shown and none are pooled; overlap between them has not been checked and there is no disease-wide percentage."], "key_findings": [{"finding": "MAML2 is mutated in 6 of 15 patients in Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018).", "numerator": 6, "denominator": 15, "frequency": 40.0, "cohorts": 1, "evidence_confidence": "moderate", "source": "vsc_cuk_2018", "retrieved_at": "2026-09-18"}, {"finding": "TP53 is mutated in 5 of 15 patients in Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018).", "numerator": 5, "denominator": 15, "frequency": 33.33, "cohorts": 1, "evidence_confidence": "moderate", "source": "vsc_cuk_2018", "retrieved_at": "2026-09-18"}, {"finding": "SPTBN1 is mutated in 5 of 15 patients in Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018).", "numerator": 5, "denominator": 15, "frequency": 33.33, "cohorts": 1, "evidence_confidence": "moderate", "source": "vsc_cuk_2018", "retrieved_at": "2026-09-18"}], "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": "vsc_cuk_2018", "region_events": [], "matrix": [{"label": "TP53", "kind": "SNV / small indel", "gene": "TP53", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 33.33, "altered": 5, "tested": 15, "note": null}]}, {"label": "CDKN2A", "kind": "SNV / small indel", "gene": "CDKN2A", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 6.67, "altered": 1, "tested": 15, "note": null}]}, {"label": "PIK3CA", "kind": "SNV / small indel", "gene": "PIK3CA", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 13.33, "altered": 2, "tested": 15, "note": null}]}, {"label": "HRAS", "kind": "SNV / small indel", "gene": "HRAS", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 6.67, "altered": 1, "tested": 15, "note": null}]}, {"label": "NOTCH1", "kind": "SNV / small indel", "gene": "NOTCH1", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 13.33, "altered": 2, "tested": 15, "note": null}]}, {"label": "EGFR", "kind": "SNV / small indel", "gene": "EGFR", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 6.67, "altered": 1, "tested": 15, "note": null}]}, {"label": "CD274", "kind": "SNV / small indel", "gene": "CD274", "cells": [{"cohort": "vsc_cuk_2018", "status": "not_observed", "frequency": 0.0, "altered": 0, "tested": 15, "note": null}]}, {"label": "PDCD1", "kind": "SNV / small indel", "gene": "PDCD1", "cells": [{"cohort": "vsc_cuk_2018", "status": "not_observed", "frequency": 0.0, "altered": 0, "tested": 15, "note": null}]}, {"label": "TERT", "kind": "SNV / small indel", "gene": "TERT", "cells": [{"cohort": "vsc_cuk_2018", "status": "not_observed", "frequency": 0.0, "altered": 0, "tested": 15, "note": null}]}, {"label": "FAT1", "kind": "SNV / small indel", "gene": "FAT1", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 20.0, "altered": 3, "tested": 15, "note": null}]}, {"label": "KMT2D", "kind": "SNV / small indel", "gene": "KMT2D", "cells": [{"cohort": "vsc_cuk_2018", "status": "not_observed", "frequency": 0.0, "altered": 0, "tested": 15, "note": null}]}, {"label": "PTEN", "kind": "SNV / small indel", "gene": "PTEN", "cells": [{"cohort": "vsc_cuk_2018", "status": "not_observed", "frequency": 0.0, "altered": 0, "tested": 15, "note": null}]}, {"label": "MAML2", "kind": "SNV / small indel", "gene": "MAML2", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 40.0, "altered": 6, "tested": 15, "note": null}]}, {"label": "SPTBN1", "kind": "SNV / small indel", "gene": "SPTBN1", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 33.33, "altered": 5, "tested": 15, "note": null}]}, {"label": "ODF1", "kind": "SNV / small indel", "gene": "ODF1", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 33.33, "altered": 5, "tested": 15, "note": null}]}, {"label": "NRG3", "kind": "SNV / small indel", "gene": "NRG3", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 26.67, "altered": 4, "tested": 15, "note": null}]}, {"label": "FAT2", "kind": "SNV / small indel", "gene": "FAT2", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 26.67, "altered": 4, "tested": 15, "note": null}]}, {"label": "ZFHX3", "kind": "SNV / small indel", "gene": "ZFHX3", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 20.0, "altered": 3, "tested": 15, "note": null}]}, {"label": "ZBTB41", "kind": "SNV / small indel", "gene": "ZBTB41", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 20.0, "altered": 3, "tested": 15, "note": null}]}, {"label": "SLC12A3", "kind": "SNV / small indel", "gene": "SLC12A3", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 20.0, "altered": 3, "tested": 15, "note": null}]}, {"label": "SHROOM3", "kind": "SNV / small indel", "gene": "SHROOM3", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 20.0, "altered": 3, "tested": 15, "note": null}]}, {"label": "SCAF4", "kind": "SNV / small indel", "gene": "SCAF4", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 20.0, "altered": 3, "tested": 15, "note": null}]}, {"label": "PARD3B", "kind": "SNV / small indel", "gene": "PARD3B", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 20.0, "altered": 3, "tested": 15, "note": null}]}, {"label": "NRG1", "kind": "SNV / small indel", "gene": "NRG1", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 20.0, "altered": 3, "tested": 15, "note": null}]}, {"label": "NLGN3", "kind": "SNV / small indel", "gene": "NLGN3", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 20.0, "altered": 3, "tested": 15, "note": null}]}, {"label": "MDN1", "kind": "SNV / small indel", "gene": "MDN1", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 20.0, "altered": 3, "tested": 15, "note": null}]}, {"label": "MAML3", "kind": "SNV / small indel", "gene": "MAML3", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 20.0, "altered": 3, "tested": 15, "note": null}]}, {"label": "LAMA5", "kind": "SNV / small indel", "gene": "LAMA5", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 20.0, "altered": 3, "tested": 15, "note": null}]}, {"label": "KMT2C", "kind": "SNV / small indel", "gene": "KMT2C", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 20.0, "altered": 3, "tested": 15, "note": null}]}, {"label": "KMT2B", "kind": "SNV / small indel", "gene": "KMT2B", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 20.0, "altered": 3, "tested": 15, "note": null}]}, {"label": "FAM193A", "kind": "SNV / small indel", "gene": "FAM193A", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 20.0, "altered": 3, "tested": 15, "note": null}]}, {"label": "F5", "kind": "SNV / small indel", "gene": "F5", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 20.0, "altered": 3, "tested": 15, "note": null}]}, {"label": "DCHS1", "kind": "SNV / small indel", "gene": "DCHS1", "cells": [{"cohort": "vsc_cuk_2018", "status": "observed", "frequency": 20.0, "altered": 3, "tested": 15, "note": null}]}, {"label": "CREBBP", "kind": "SNV / small 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