ArticleCellular oncology (Dordrecht, Netherlands)2014
Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology.
Article in Cellular oncology (Dordrecht, Netherlands), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 1 of them a synthesis that pooled it.
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Who cites it
30 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Guidelines for cytogenetic investigations in tumours.European journal of human genetics : EJHG · 2016Guideline
- A critical spotlight on the paradigms of FFPE-DNA sequencing.Nucleic acids research · 2023Review
- Pathology review identifies frequent misdiagnoses in recurrent classic Hodgkin lymphoma in a nationwide cohort: implications for clinical and epidemiological studies.Haematologica · 2023Article
- Development and Validation of Targeted Gene Sequencing Panel Based Companion Diagnostic for Korean Patients with Solid Tumors.Cancers · 2021Article
- A Nationwide Study on the Impact of Routine Testing forCancers · 2021Article
- Circulating Tumor DNA as a Preoperative Marker of Recurrence in Patients with Peritoneal Metastases of Colorectal Cancer: A Clinical Feasibility Study.Journal of clinical medicine · 2020Article
- Molecular profiling for precision cancer therapies.Genome medicine · 2020Review
- RAS and BRAF mutations in cell-free DNA are predictive for outcome of cetuximab monotherapy in patients with tissue-tested RAS wild-type advanced colorectal cancer.Molecular oncology · 2019Article
- Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics.Virchows Archiv : an international journal of pathology · 2019Article
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- HPV E4 expression and DNA hypermethylation of CADM1, MAL, and miR124-2 genes in cervical cancer and precursor lesions.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2018Article
- The Utility of Liquid Biopsy in Central Nervous System Malignancies.Current oncology reports · 2018Review
- Targeted sequencing reveals distinct pathogenic variants in Chinese patients with lung adenocarcinoma brain metastases.Oncology letters · 2018Article
- Multicenter validation of cancer gene panel-based next-generation sequencing for translational research and molecular diagnostics.Virchows Archiv : an international journal of pathology · 2018Article
- DNA degrades during storage in formalin-fixed and paraffin-embedded tissue blocks.Virchows Archiv : an international journal of pathology · 2017Article
- Concurrent somatic mutations in driver genes were significantly correlated with lymph node metastasis and pathological types in solid tumors.Oncotarget · 2017Article
- Article
- Capturing Genomic Evolution of Lung Cancers through Liquid Biopsy for Circulating Tumor DNA.Journal of oncology · 2017Review
- Next-generation sequencing of the human TRPV1 gene and the regulating co-players LTB4R and LTB4R2 based on a custom AmpliSeq™ panel.PloS one · 2017Article
- Non-classic EGFR mutations in a cohort of Dutch EGFR-mutated NSCLC patients and outcomes following EGFR-TKI treatment.British journal of cancer · 2016Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
purposeNext generation DNA sequencing (NGS) holds promise for diagnostic applications, yet implementation in routine molecular pathology practice requires performance evaluation on DNA derived from routine formalin-fixed paraffin-embedded (FFPE) tissue specimens. The current study presents a comprehensive analysis of TruSeq Amplicon Cancer Panel-based NGS using a MiSeq Personal sequencer (TSACP-MiSeq-NGS) for somatic mutation profiling.
methodsTSACP-MiSeq-NGS (testing 212 hotspot mutation amplicons of 48 genes) and a data analysis pipeline were evaluated in a retrospective learning/test set approach (n = 58/n = 45 FFPE-tumor DNA samples) against 'gold standard' high-resolution-melting (HRM)-sequencing for the genes KRAS, EGFR, BRAF and PIK3CA. Next, the performance of the validated test algorithm was assessed in an independent, prospective cohort of FFPE-tumor DNA samples (n = 75).
resultsIn the learning set, a number of minimum parameter settings was defined to decide whether a FFPE-DNA sample is qualified for TSACP-MiSeq-NGS and for calling mutations. The resulting test algorithm revealed 82% (37/45) compliance to the quality criteria and 95% (35/37) concordant assay findings for KRAS, EGFR, BRAF and PIK3CA with HRM-sequencing (kappa = 0.92; 95% CI = 0.81-1.03) in the test set. Subsequent application of the validated test algorithm to the prospective cohort yielded a success rate of 84% (63/75), and a high concordance with HRM-sequencing (95% (60/63); kappa = 0.92; 95% CI = 0.84-1.01). TSACP-MiSeq-NGS detected 77 mutations in 29 additional genes.
conclusionTSACP-MiSeq-NGS is suitable for diagnostic gene mutation profiling in oncopathology.
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