ArticleScientific reports2021
High sensitivity sanger sequencing detection of BRAF mutations in metastatic melanoma FFPE tissue specimens.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 25 citations in OpenAlex.
- Review
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- ddPCR Overcomes the CRISPR-Cas13a-Based Technique for the Detection of the BRAF p.V600E Mutation in Liquid Biopsies.International journal of molecular sciences · 2024Article
- Comparative efficiency of differential diagnostic methods for the identification of BRAF V600E gene mutation in papillary thyroid cancer (Review).Experimental and therapeutic medicine · 2024Review
- Improvement of limit of detection in primer extension-based multiplexed mutation assay using capillary electrophoresis.Analytical sciences : the international journal of the Japan Society for Analytical Chemistry · 2024Article
- Genome-wide association analysis of fleece traits in Northwest Xizang white cashmere goat.Frontiers in veterinary science · 2024Article
- Clinicopathological Profile of a Cohort of Patients With Malignant Melanoma in the United Kingdom.Cureus · 2023Article
- Detection of BRAF mutations in malignant melanoma and colorectal cancer by SensiScreen® FFPE BRAF qPCR assay.PloS one · 2023Article
- From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research.Life (Basel, Switzerland) · 2022Review
- First report of inherited protein S deficiency caused by paternalHaematologica · 2022Article
- PEAC: An Ultrasensitive and Cost-Effective MRD Detection System in Non-small Cell Lung Cancer Using Plasma Specimen.Frontiers in medicine · 2022Article
- Characterization and Clinical Utility ofCancers · 2021Article
- Confirming putative variants at ≤ 5% allele frequency using allele enrichment and Sanger sequencing.Scientific reports · 2021Article
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
Mutations in the BRAF gene at or near the p. V600 locus are informative for therapy selection, but current methods for analyzing FFPE tissue DNA generally have a limit of detection of 5% variant allele frequency (VAF), or are limited to the single variant (V600E). These can result in false negatives for samples with low VAFs due to low tumor content or subclonal heterogeneity, or harbor non-V600 mutations. Here, we show that Sanger sequencing using the NuProbe VarTrace BRAF assay, based on the Blocker Displacement Amplification (BDA) technology, is capable of detecting BRAF V600 mutations down to 0.20% VAF from FFPE lymph node tissue samples. Comparison experiments on adjacent tissue sections using BDA Sanger, immunohistochemistry (IHC), digital droplet PCR (ddPCR), and NGS showed 100% concordance among all 4 methods for samples with BRAF mutations at ≥ 1% VAF, though ddPCR did not distinguish the V600K mutation from the V600E mutation. BDA Sanger, ddPCR, and NGS (with orthogonal confirmation) were also pairwise concordant for lower VAF mutations down to 0.26% VAF, but IHC produced a false negative. Thus, we have shown that Sanger sequencing can be effective for rapid detection and quantitation of multiple low VAF BRAF mutations from FFPE samples. BDA Sanger method also enabled detection and quantitation of less frequent, potentially actionable non-V600 mutations as demonstrated by synthetic samples.
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