ArticleThe Journal of molecular diagnostics : JMD2014
Validation of a next-generation sequencing assay for clinical molecular oncology.
Article in The Journal of molecular diagnostics : JMD, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers, 2 of them syntheses 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
85 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Molecular Biomarkers for the Evaluation of Colorectal Cancer: Guideline From the American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, and American Society of Clinical Oncology.The Journal of molecular diagnostics : JMD · 2017Guideline
- Molecular Biomarkers for the Evaluation of Colorectal Cancer.American journal of clinical pathology · 2017Guideline
- Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers.PloS one · 2015Trial
- Implementation of an ISO 15189 accredited next generation sequencing service for cell-free total nucleic acid (cfTNA) analysis to facilitate driver mutation reporting in blood: the experience of a clinical diagnostic laboratory.Journal of clinical pathology · 2025Article
- Large-scale analysis of whole genome sequencing data from formalin-fixed paraffin-embedded cancer specimens demonstrates preservation of clinical utility.Nature communications · 2024Article
- Dental DNA Mutations Occurring after Death: A Novel Method for Post-Mortem Interval (PMI) Estimation.International journal of molecular sciences · 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
- Supporting Biomarker-Driven Therapies in Oncology: A Genomic Testing Cost Calculator.The oncologist · 2023Article
- Dental DNA as an Indicator of Post-Mortem Interval (PMI): A Pilot Research.International journal of molecular sciences · 2022Article
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- BRAF mutations may identify a clinically distinct subset of glioblastoma.Scientific reports · 2021Article
- Somatic PIK3R1 variation as a cause of vascular malformations and overgrowth.Genetics in medicine : official journal of the American College of Medical Genetics · 2021Article
- R-Score: A New Parameter to Assess the Quality of Variants' Calls Assessed by NGS Using Liquid Biopsies.Biology · 2021Article
- The electroretinogram in the genomics era: outer retinal disorders.Eye (London, England) · 2021Review
- Development and Analytical Validation of a Targeted Next-Generation Sequencing Panel to Detect Actionable Mutations for Targeted Therapy.OncoTargets and therapy · 2021Article
- Pediatric meningioma: a clinicopathologic and molecular study with potential grading implications.Brain pathology (Zurich, Switzerland) · 2020Article
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- Identification of challenges and a framework for implementation of the AMP/ASCO/CAP classification guidelines for reporting somatic variants.Practical laboratory medicine · 2020Article
- Mutational Mosaics of Cell-Free DNA from Pancreatic Cyst Fluids.Digestive diseases and sciences · 2020Article
25 more citing papers are in PubMed but not listed here.
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Authors and funding
32 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Currently, oncology testing includes molecular studies and cytogenetic analysis to detect genetic aberrations of clinical significance. Next-generation sequencing (NGS) allows rapid analysis of multiple genes for clinically actionable somatic variants. The WUCaMP assay uses targeted capture for NGS analysis of 25 cancer-associated genes to detect mutations at actionable loci. We present clinical validation of the assay and a detailed framework for design and validation of similar clinical assays. Deep sequencing of 78 tumor specimens (≥ 1000× average unique coverage across the capture region) achieved high sensitivity for detecting somatic variants at low allele fraction (AF). Validation revealed sensitivities and specificities of 100% for detection of single-nucleotide variants (SNVs) within coding regions, compared with SNP array sequence data (95% CI = 83.4-100.0 for sensitivity and 94.2-100.0 for specificity) or whole-genome sequencing (95% CI = 89.1-100.0 for sensitivity and 99.9-100.0 for specificity) of HapMap samples. Sensitivity for detecting variants at an observed 10% AF was 100% (95% CI = 93.2-100.0) in HapMap mixes. Analysis of 15 masked specimens harboring clinically reported variants yielded concordant calls for 13/13 variants at AF of ≥ 15%. The WUCaMP assay is a robust and sensitive method to detect somatic variants of clinical significance in molecular oncology laboratories, with reduced time and cost of genetic analysis allowing for strategic patient management.
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