ArticleNature communications2017
Prevalence and detection of low-allele-fraction variants in clinical cancer samples.
Article in Nature communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
122 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Korean Society for Genetic Diagnostics Guidelines for Validation of Next-Generation Sequencing-Based Somatic Variant Detection in Hematologic Malignancies.Annals of laboratory medicine · 2019Guideline
- Nivolumab plus ipilimumab in advanced salivary gland cancer: a phase 2 trial.Nature medicine · 2023Trial
- Biomarker-guided targeted therapy in platinum-resistant ovarian cancer (AMBITION; KGOG 3045): a multicentre, open-label, five-arm, uncontrolled, umbrella trial.Journal of gynecologic oncology · 2022Trial
- Impact of Tumor Genomic Profile on Adjuvant Chemotherapy Efficacy in Resected Pancreatic Adenocarcinoma: Results From the PRODIGE-24/CCTG PA6 Study.Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2026Article
- Extra-appendiceal low-grade mucinous neoplasm-like lesions: clinicopathologic and molecular characteristics.Histopathology · 2026Article
- Relative Mutant Allele Frequency Role in ctDNA-Guided Anti-Epidermal Growth Factor Receptor Rechallenge in Metastatic Colorectal Cancer.JCO precision oncology · 2026Article
- Towards an ecosystem of clinical decision support tools for precision cancer medicine.NPJ precision oncology · 2026Review
- High-throughput radiation sensitivity screening of 3D-head and neck squamous cell carcinoma (HNSCC) organoids using an automated radiation modulator (ARM).Materials today. Bio · 2026Article
- Genomic characterization of uterine adenomatoid tumors reveals recurrent alterations in KMT5A and KMT2C.Clinical epigenetics · 2026Article
- Expert recommendations for PIK3CA testing in HR+/HER2- locally advanced and metastatic breast cancer.NPJ breast cancer · 2026Review
- RiSpy: a feature selection-based fingerprinting framework for accurate identification of genome-edited rice lines.Briefings in bioinformatics · 2026Article
- EXaCT-2: an augmented and customizable oncology-focused whole exome sequencing platform.NPJ precision oncology · 2026Article
- A radio-genomics biomarker for precision epidermal growth factor receptor mutation targeting therapy in non-small cell lung cancer.Scientific reports · 2026Article
- Multidimensional tumor heterogeneity and its role in therapeutic resistance.Frontiers in immunology · 2026Review
- Durable response to ALK inhibition in low-allele-frequencyFrontiers in oncology · 2026Article
- Emerging role of low-frequency somatic mutations in cancer relapse: from early detection to precision oncology.Frontiers in oncology · 2026Review
- Synth4bench: generating synthetic data for benchmarking tumor-only somatic variant calling algorithms.Frontiers in bioinformatics · 2026Article
- Real-world effectiveness and prognostic factors of platinum rechallenge in advanced urothelial cancer.BMC cancer · 2025Article
- How to Read a Next-Generation Sequencing Report for AML and MDS? What Hematologists Need to Know.Journal of clinical medicine · 2025Review
- Evaluation of false positive and false negative errors in targeted next generation sequencing.Genome biology · 2025Article
62 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
31 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate detection of genomic alterations using high-throughput sequencing is an essential component of precision cancer medicine. We characterize the variant allele fractions (VAFs) of somatic single nucleotide variants and indels across 5095 clinical samples profiled using a custom panel, CancerSCAN. Our results demonstrate that a significant fraction of clinically actionable variants have low VAFs, often due to low tumor purity and treatment-induced mutations. The percentages of mutations under 5% VAF across hotspots in EGFR, KRAS, PIK3CA, and BRAF are 16%, 11%, 12%, and 10%, respectively, with 24% for EGFR T790M and 17% for PIK3CA E545. For clinical relevance, we describe two patients for whom targeted therapy achieved remission despite low VAF mutations. We also characterize the read depths necessary to achieve sensitivity and specificity comparable to current laboratory assays. These results show that capturing low VAF mutations at hotspots by sufficient sequencing coverage and carefully tuned algorithms is imperative for a clinical assay.
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