ArticleFrontiers in genetics2021
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.
Article in Frontiers in genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 26 citations in OpenAlex.
- Cytology smears from endobronchial ultrasound-guided transbronchial needle aspiration as a source of nucleic acids with adequate yield for next-generation sequencing.Journal of thoracic disease · 2026Article
- Sclerosing melanocytic tumors with MAP2K1 in frame deletions and 15q gains: A distinctive pathway of nevogenesis with reproducible morphology.Virchows Archiv : an international journal of pathology · 2026Article
- A Cross-Sectional Study of Variant Interpretation and Reporting of NGS Data Using Tertiary Analysis Software: NavifyOncology and therapy · 2025Article
- PARP Inhibitors in Pancreatic Cancer with Homologous Recombination Repair Gene Mutations: A Single-Institution Experience.Cancers · 2024Article
- Implementation of a High-Accuracy Targeted Gene Expression Panel for Clinical Care.The Journal of molecular diagnostics : JMD · 2024Article
- Coffin-Siris Syndrome and SMARCB1 Mutation Presenting With Schwannomatosis: A Case Report and Literature Review.Cureus · 2024Article
- Neurotrophic tyrosine receptor kinase gene fusions in adult and pediatric patients with solid tumors: a clinicogenomic biobank and record linkage study of expression frequency and patient characteristics from Finland.Acta oncologica (Stockholm, Sweden) · 2024Article
- Deceptive learning in histopathology.Histopathology · 2024Article
- Implementation of an ISO15189 accredited next-generation sequencing service with the fully automated Ion Torrent Genexus: the experience of a clinical diagnostic laboratory.Journal of clinical pathology · 2024Article
- Utility of UV Signature Mutations in the Diagnostic Assessment of Metastatic Head and Neck Carcinomas of Unknown Primary.Head and neck pathology · 2024Article
- Article
- Detection of Hybrid Fusion Transcripts, Aberrant Transcript Expression, and Specific Single Nucleotide Variants in Acute Leukemia and Myeloid Disorders with Recurrent Gene Rearrangements.Pathobiology : journal of immunopathology, molecular and cellular biology · 2024Article
- RET splice site variants in medullary thyroid carcinoma.Frontiers in genetics · 2024Article
- Consensus Recommendations to Optimize the Detection and Reporting ofCurrent oncology (Toronto, Ont.) · 2023Review
- An absolute approach to using whole exome DNA and RNA workflow for cancer biomarker testing.Frontiers in oncology · 2023Article
- Sclerosing Polycystic Adenoma: Conclusive Clinical and Molecular Evidence of Its Neoplastic Nature.Head and neck pathology · 2022Article
- Comprehensive Development and Implementation of Good Laboratory Practice for NGS Based Targeted Panel on Solid Tumor FFPE Tissues in Diagnostics.Diagnostics (Basel, Switzerland) · 2022Article
- Diagnostic Validation of a Comprehensive Targeted Panel for Broad Mutational and Biomarker Analysis in Solid Tumors.Cancers · 2022Article
- Single-cell Characterization of the Cellular Landscape of Acral Melanoma Identifies Novel Targets for Immunotherapy.Clinical cancer research : an official journal of the American Association for Cancer Research · 2022Article
Corrections and comments
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We describe the clinical validation of a targeted DNA and RNA-based next-generation sequencing (NGS) assay at two clinical molecular diagnostic laboratories. This assay employs simultaneous DNA and RNA analysis of all coding exons to detect small variants (single-nucleotide variants, insertions, and deletions) in 148 genes, amplifications in 59 genes, and fusions and splice variants in 55 genes. During independent validations at two sites, 234 individual specimens were tested, including clinical formalin-fixed, paraffin-embedded (FFPE) tumor specimens, reference material, and cell lines. Samples were prepared using the Illumina TruSight Tumor 170 (TST170) kit, sequenced with Illumina sequencers, and the data were analyzed using the TST170 App. At both sites, TST170 had ≥98% success for ≥250× depth for ≥95% of covered positions. Variant calling was accurate and reproducible at allele frequencies ≥5%. Limit of detection studies determined that inputs of ≥50 ng of DNA (with ≥3.3 ng/μl) and ≥50 ng RNA (minimum of 7 copies/ng) were optimal for high analytical sensitivity. The TST170 assay results were highly concordant with prior results using different methods across all variant categories. Optimization of nucleic acid extraction and DNA shearing, and quality control following library preparation is recommended to maximize assay success rates. In summary, we describe the validation of comprehensive and simultaneous DNA and RNA-based NGS testing using TST170 at two clinical sites.
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