ArticleOncotarget2017
Validation and optimization of the Ion Torrent S5 XL sequencer and Oncomine workflow for BRCA1 and BRCA2 genetic testing.
Article in Oncotarget, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Application of SNV Detection Methods for Market Control of Food Products from New Genomic Techniques.International journal of molecular sciences · 2026Review
- Correlation between BRCA1 expression and the advanced stage of triple‑negative breast cancer.Molecular and clinical oncology · 2025Article
- Correlation between circulating tumor DNA and carcinoembryonic antigen levels in patients with metastatic colorectal cancer.Cancer medicine · 2021Article
- Characterization of a novel variant in the HR1 domain ofF1000Research · 2021Article
- A comprehensive custom panel evaluation for routine hereditary cancer testing: improving the yield of germline mutation detection.Journal of translational medicine · 2020Article
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- Evaluation of circulating tumor DNA as a biomarker in pancreatic cancer with liver metastasis.PloS one · 2020Article
- An optimizedJournal of gynecologic oncology · 2020Article
- Early change in circulating tumor DNA as a potential predictor of response to chemotherapy in patients with metastatic colorectal cancer.Scientific reports · 2019Article
- Cancer Panel Assay for Precision Oncology Clinic: Results from a 1-Year Study.Translational oncology · 2019Article
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- Bioinformatics analysis of the prognostic value of CCT6A and associated signalling pathways in breast cancer.Molecular medicine reports · 2019Article
- An Optimized Workflow to Evaluate Estrogen Receptor Gene Mutations in Small Amounts of Cell-Free DNA.The Journal of molecular diagnostics : JMD · 2019Article
- Clinical relevance of circulating tumor DNA assessed through deep sequencing in patients with metastatic colorectal cancer.Cancer medicine · 2019Article
- Article
- Profiling cancer-associated genetic alterations and molecular classification of cancer in Korean gastric cancer patients.Oncotarget · 2017Article
- A Next-Generation Sequencing Primer-How Does It Work and What Can It Do?Academic pathologyReview
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Authors and funding
7 authors.
Funding
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Abstract
In this study, we validated the analytical performance of BRCA1/2 sequencing using Ion Torrent's new bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. Using 43 samples that were previously validated by Illumina's MiSeq platform and/or by Sanger sequencing/multiplex ligation-dependent probe amplification, we amplified the target with the Oncomine™ BRCA Research Assay and sequenced on Ion Torrent S5 XL (Thermo Fisher Scientific, Waltham, MA, USA). We compared two bioinformatics pipelines for optimal processing of S5 XL sequence data: the Torrent Suite with a plug-in Torrent Variant Caller (Thermo Fisher Scientific), and commercial NextGENe software (Softgenetics, State College, PA, USA). All expected 681 single nucleotide variants, 15 small indels, and three copy number variants were correctly called, except one common variant adjacent to a rare variant on the primer-binding site. The sensitivity, specificity, false positive rate, and accuracy for detection of single nucleotide variant and small indels of S5 XL sequencing were 99.85%, 100%, 0%, and 99.99% for the Torrent Variant Caller and 99.85%, 99.99%, 0.14%, and 99.99% for NextGENe, respectively. The reproducibility of variant calling was 100%, and the precision of variant frequency also showed good performance with coefficients of variation between 0.32 and 5.29%. We obtained highly accurate data through uniform and sufficient coverage depth over all target regions and through optimization of the bioinformatics pipeline. We confirmed that our platform is accurate and practical for diagnostic BRCA1/2 testing in a clinical laboratory.
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