ArticleThe Journal of molecular diagnostics : JMD2016
Clinical Validation and Implementation of a Targeted Next-Generation Sequencing Assay to Detect Somatic Variants in Non-Small Cell Lung, Melanoma, and Gastrointestinal Malignancies.
Article in The Journal of molecular diagnostics : JMD, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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The trial behind it
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
35 citing papers in PubMed, 69 citations in OpenAlex.
- Targeted next-generation sequencing panel (TruSight Tumor 170) in diffuse glioma: a single institutional experience of 135 cases.Journal of neuro-oncology · 2019Trial
- Advances in the diagnosis and treatment of MET-variant digestive tract tumors.World journal of gastrointestinal oncology · 2024Review
- A unified DNA- and RNA-based NGS strategy for the analysis of multiple types of variants at the dual nucleic acid level in solid tumors.Journal of clinical laboratory analysis · 2023Article
- Mosaicism for ATP2A2 Mutation and Mutant Allelic Fractions Detected by Droplet Digital PCR in Simple Segmental Darier Disease.Acta dermato-venereologica · 2023Article
- Next-generation sequencing in dermatology.Frontiers in medicine · 2023Review
- Dynamics of the Tumor Immune Microenvironment during Neoadjuvant Chemotherapy of High-Grade Serous Ovarian Cancer.Cancers · 2022Article
- Prognostic Biomarkers in Melanoma: Tailoring Treatments to the Patient.The Journal of clinical and aesthetic dermatology · 2021Review
- R-Score: A New Parameter to Assess the Quality of Variants' Calls Assessed by NGS Using Liquid Biopsies.Biology · 2021Article
- MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations.BMC medical genomics · 2021Article
- Guideline-Adherent Clinical Validation of a Comprehensive 170-Gene DNA/RNA Panel for Determination of Small Variants, Copy Number Variations, Splice Variants, and Fusions on a Next-Generation Sequencing Platform in the CLIA Setting.Frontiers in genetics · 2021Article
- A Melanoma-Tailored Next-Generation Sequencing Panel Coupled with a Comprehensive Analysis to Improve Routine Melanoma Genotyping.Targeted oncology · 2020Article
- Application of magnetic nanoparticles in nucleic acid detection.Journal of nanobiotechnology · 2020Review
- Genetic Characterization of Molecular Targets in Korean Patients with Gastrointestinal Stromal Tumors.Journal of gastric cancer · 2020Article
- Identifying a wide range of actionable variants using capture-based ultra-deep targeted sequencing in treatment-naive patients with primary lung adenocarcinoma.International journal of clinical and experimental pathology · 2020Article
- Article
- Preparation of the standard cell lines for reference mutations in cancer gene-panels by genome editing in HEK 293 T/17 cells.Genes and environment : the official journal of the Japanese Environmental Mutagen Society · 2020Article
- Integrating a Next Generation Sequencing Panel into Clinical Practice in Ovarian Cancer.Yonsei medical journal · 2019Article
- Rational "Error Elimination" Approach to Evaluating Molecular Barcoded Next-Generation Sequencing Data Identifies Low-Frequency Mutations in Hematologic Malignancies.The Journal of molecular diagnostics : JMD · 2019Article
- Review
- Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome.Nature communications · 2018Article
Corrections and comments
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Authors and funding
25 authors at 1 institution in 1 country.
Funding
Abstract
We tested and clinically validated a targeted next-generation sequencing (NGS) mutation panel using 80 formalin-fixed, paraffin-embedded (FFPE) tumor samples. Forty non-small cell lung carcinoma (NSCLC), 30 melanoma, and 30 gastrointestinal (12 colonic, 10 gastric, and 8 pancreatic adenocarcinoma) FFPE samples were selected from laboratory archives. After appropriate specimen and nucleic acid quality control, 80 NGS libraries were prepared using the Illumina TruSight tumor (TST) kit and sequenced on the Illumina MiSeq. Sequence alignment, variant calling, and sequencing quality control were performed using vendor software and laboratory-developed analysis workflows. TST generated ≥500× coverage for 98.4% of the 13,952 targeted bases. Reproducible and accurate variant calling was achieved at ≥5% variant allele frequency with 8 to 12 multiplexed samples per MiSeq flow cell. TST detected 112 variants overall, and confirmed all known single-nucleotide variants (n = 27), deletions (n = 5), insertions (n = 3), and multinucleotide variants (n = 3). TST detected at least one variant in 85.0% (68/80), and two or more variants in 36.2% (29/80), of samples. TP53 was the most frequently mutated gene in NSCLC (13 variants; 13/32 samples), gastrointestinal malignancies (15 variants; 13/25 samples), and overall (30 variants; 28/80 samples). BRAF mutations were most common in melanoma (nine variants; 9/23 samples). Clinically relevant NGS data can be obtained from routine clinical FFPE solid tumor specimens using TST, benchtop instruments, and vendor-supplied bioinformatics pipelines.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.