ArticleInternational journal of molecular sciences2020
Dual Deep Sequencing Improves the Accuracy of Low-Frequency Somatic Mutation Detection in Cancer Gene Panel Testing.
Article in International journal of molecular sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 15 citations in OpenAlex.
- The Role of Somatic Mutation in Hereditary Hemorrhagic Telangiectasia Pathogenesis.Journal of clinical medicine · 2025Review
- Performance of somatic structural variant calling in lung cancer using Oxford Nanopore sequencing technology.BMC genomics · 2024Article
- Dynamic monitoring of UBA1 somatic mutations in patients with relapsing polychondritis.Orphanet journal of rare diseases · 2024Article
- Target-capture full-length double-stranded cDNA long-read sequencing through Nanopore revealed novel intron retention in patient with tuberous sclerosis complex.Frontiers in genetics · 2023Article
- From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research.Life (Basel, Switzerland) · 2022Review
- Poly(A) capture full length cDNA sequencing improves the accuracy and detection ability of transcript quantification and alternative splicing events.Scientific reports · 2022Article
- A comparison of mRNA sequencing (RNA-Seq) library preparation methods for transcriptome analysis.BMC genomics · 2022Article
- Detection of minor variants in Mycobacterium tuberculosis whole genome sequencing data.Briefings in bioinformatics · 2022Article
- Genomics of Tumor Origin and Characteristics for Adenocarcinoma and Malignant Pleural Mesothelioma: A Case Report.Frontiers in oncology · 2022Article
- Target-capture full-length double-strand cDNA sequencing for alternative splicing analysis.RNA biology · 2021Article
- Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Cancer gene panel testing requires accurate detection of somatic mosaic mutations, as the test sample consists of a mixture of cancer cells and normal cells; each minor clone in the tumor also has different somatic mutations. Several studies have shown that the different types of software used for variant calling for next generation sequencing (NGS) can detect low-frequency somatic mutations. However, the accuracy of these somatic variant callers is unknown. We performed cancer gene panel testing in duplicate experiments using three different high-fidelity DNA polymerases in pre-capture amplification steps and analyzed by three different variant callers, Strelka2, Mutect2, and LoFreq. We selected six somatic variants that were detected in both experiments with more than two polymerases and by at least one variant caller. Among them, five single nucleotide variants were verified by CEL nuclease-mediated heteroduplex incision with polyacrylamide gel electrophoresis and silver staining (CHIPS) and Sanger sequencing. In silico analysis indicated that the
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