ArticleThe oncologist2014
Profiling cancer gene mutations in clinical formalin-fixed, paraffin-embedded colorectal tumor specimens using targeted next-generation sequencing.
Article in The oncologist, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 49 citations in OpenAlex.
- Evaluation of two highly-multiplexed custom panels for massively parallel semiconductor sequencing on paraffin DNA.PloS one · 2015Trial
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- Emerging Role of ERBB2 in Targeted Therapy for Metastatic Colorectal Cancer: Signaling Pathways to Therapeutic Strategies.Cancers · 2022Review
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- Targeted Next-Generation Sequencing-Based Multiple Gene Mutation Profiling of Patients with Rectal Adenocarcinoma Receiving or Not Receiving Neoadjuvant Chemoradiotherapy.International journal of molecular sciences · 2022Article
- Preanalytical Variables and Sample Quality Control for Clinical Variant Analysis.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Occurence of RAS reversion in metastatic colorectal cancer patients treated with bevacizumab.Oncotarget · 2021Article
- Tissue gene mutation profiles in patients with colorectal cancer and their clinical implications.Biomedical reports · 2020Article
- Molecular Profiles and Metastasis Markers in Chinese Patients with Gastric Carcinoma.Scientific reports · 2019Article
- Performance validation of an amplicon-based targeted next-generation sequencing assay and mutation profiling of 648 Chinese colorectal cancer patients.Virchows Archiv : an international journal of pathology · 2018Article
- Feasibility study of cancer genome alterations identified by next generation sequencing: ABC study.Japanese journal of clinical oncology · 2018Article
- Targeting HER2 in colorectal cancer: The landscape of amplification and short variant mutations in ERBB2 and ERBB3.Cancer · 2018Article
- Targeted next generation sequencing in Chinese colorectal cancer patients guided anti-EGFR treatment and facilitated precision cancer medicine.Oncotarget · 2017Article
- Comparative mutational landscape analysis of patient-derived tumour xenografts.British journal of cancer · 2017Article
- Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification.International journal of molecular sciences · 2017Review
- Clinical Application of Targeted Next Generation Sequencing for Colorectal Cancers.International journal of molecular sciences · 2016Review
- Molecular predictive markers in tumors of the gastrointestinal tract.World journal of gastrointestinal oncology · 2016Review
- Routine clinical mutation profiling using next generation sequencing and a customized gene panel improves diagnostic precision in myeloid neoplasms.Oncotarget · 2016Review
- Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies.Journal of visualized experiments : JoVE · 2016Article
- Article
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Authors and funding
19 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
purposeThe success of precision oncology relies on accurate and sensitive molecular profiling. The Ion AmpliSeq Cancer Panel, a targeted enrichment method for next-generation sequencing (NGS) using the Ion Torrent platform, provides a fast, easy, and cost-effective sequencing workflow for detecting genomic "hotspot" regions that are frequently mutated in human cancer genes. Most recently, the U.K. has launched the AmpliSeq sequencing test in its National Health Service. This study aimed to evaluate the clinical application of the AmpliSeq methodology.
methodsWe used 10 ng of genomic DNA from formalin-fixed, paraffin-embedded human colorectal cancer (CRC) tumor specimens to sequence 46 cancer genes using the AmpliSeq platform. In a validation study, we developed an orthogonal NGS-based resequencing approach (SimpliSeq) to assess the AmpliSeq variant calls.
resultsValidated mutational analyses revealed that AmpliSeq was effective in profiling gene mutations, and that the method correctly pinpointed "true-positive" gene mutations with variant frequency >5% and demonstrated high-level molecular heterogeneity in CRC. However, AmpliSeq enrichment and NGS also produced several recurrent "false-positive" calls in clinically druggable oncogenes such as PIK3CA.
conclusionAmpliSeq provided highly sensitive and quantitative mutation detection for most of the genes on its cancer panel using limited DNA quantities from formalin-fixed, paraffin-embedded samples. For those genes with recurrent "false-positive" variant calls, caution should be used in data interpretation, and orthogonal verification of mutations is recommended for clinical decision making.
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