ArticleBritish journal of cancer2014
Clinical massively parallel next-generation sequencing analysis of 409 cancer-related genes for mutations and copy number variations in solid tumours.
Article in British journal of cancer, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers, 1 of them a synthesis that pooled it.
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52 citing papers in PubMed, 1 synthesis or guideline pooled it, 88 citations in OpenAlex.
- Agnostic Pathway/Gene Set Analysis of Genome-Wide Association Data Identifies Associations for Pancreatic Cancer.Journal of the National Cancer Institute · 2019Pooled it
- Evaluation of two highly-multiplexed custom panels for massively parallel semiconductor sequencing on paraffin DNA.PloS one · 2015Trial
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- Precision needle-punch tumor enrichment from paraffin blocks improves the detection of clinically actionable genomic alterations and biomarkers.Frontiers in oncology · 2024Article
- HER2-low expression in patients with advanced or metastatic solid tumors.Annals of oncology : official journal of the European Society for Medical Oncology · 2023Article
- Distinct Gene Mutations Are Associated With Clinicopathologic Features in Urachal Carcinoma.American journal of clinical pathology · 2022Article
- Target Enrichment Approaches for Next-Generation Sequencing Applications in Oncology.Diagnostics (Basel, Switzerland) · 2022Review
- Clinical characteristics and outcomes of phase I cancer patients with CCNE1 amplification: MD Anderson experiences.Scientific reports · 2022Review
- Biomarkers Associated with Lymph Nodal Metastasis in Endometrioid Endometrial Carcinoma.Cancers · 2022Article
- Distinct Somatic Alteration Features Identified by Gene Panel Sequencing in Korean Triple-Negative Breast Cancer with High Ki67 Expression.Diagnostics (Basel, Switzerland) · 2021Article
- Development and Analytical Validation of a Targeted Next-Generation Sequencing Panel to Detect Actionable Mutations for Targeted Therapy.OncoTargets and therapy · 2021Article
- Short somatic alterations at the site of copy number variation in breast cancer.Cancer science · 2021Article
- Integrated clinico-molecular profiling of appendiceal adenocarcinoma reveals a unique grade-driven entity distinct from colorectal cancer.British journal of cancer · 2020Article
- Genome-Wide Association Study Data Reveal Genetic Susceptibility to Chronic Inflammatory Intestinal Diseases and Pancreatic Ductal Adenocarcinoma Risk.Cancer research · 2020Article
- Comprehensive routine diagnostic screening to identify predictive mutations, gene amplifications, and microsatellite instability in FFPE tumor material.BMC cancer · 2020Article
- Identification of biomarkers of immune checkpoint blockade efficacy in recurrent or refractory solid tumor malignancies.Oncotarget · 2020Article
- Simplified molecular classification of lung adenocarcinomas based on EGFR, KRAS, and TP53 mutations.BMC cancer · 2020Article
- Analysis of Copy-Number Variations and Feline Mammary Carcinoma Survival.Scientific reports · 2020Article
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Authors and funding
12 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn a clinical diagnostic laboratory, we evaluated the applicability of the Ion Proton sequencer for screening 409 cancer-related genes in solid tumours.
methodsDNA was extracted from formalin-fixed, paraffin-embedded (FFPE) tissue biopsy specimens of 55 solid tumours (20 with matched normal tissue) and four cell lines and screened for mutations in 409 genes using the Ion Proton system. The mutation profiles of these samples were known based on prior testing using the Ion Torrent Personal Genome Machine (46-gene hotspot panel), Sanger sequencing, or fluorescence in situ hybridisation (FISH). Concordance with retrospective findings and additional mutations were evaluated. Assay sensitivity and reproducibility were established. Gene copy number variations (CNVs) detected were confirmed by molecular inversion probe (MIP) array.
resultsThe average Ion Proton (409-gene panel) sequencing output per run was 8 gigabases with 128 million sequencing reads. Of the 15,992 amplicons in the 409-gene panel, 90% achieved a minimum average sequencing depth of 100X. In 59 samples, the Ion Proton detected 100 of 105 expected single-nucleotide variants (SNVs) and all expected deletions (n=8), insertions (n=5), and CNVs (n=7). Five SNVs were not detected due to failed amplification of targeted regions. In 20 tumours with paired normal tissue, Ion Proton detected 37 additional somatic mutations, several in genes of high prognostic or therapeutic significance, such as MET, ALK, TP53, APC, and PTEN. MIP array analysis confirmed all CNVs detected by Ion Proton.
conclusionsThe Ion Proton (409-gene panel) system was found to be well suited for use in a clinical molecular diagnostic laboratory. It can simultaneously screen 409 genes for a variety of sequence variants in multiple samples using a low input of FFPE DNA with high reproducibility and sensitivity.
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