ArticlePloS one2017
Versatile ion S5XL sequencer for targeted next generation sequencing of solid tumors in a clinical laboratory.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT05372081 (Clinical and Molecular Study With Digital Support of Patients With Inoperable Lung Cancer), which is not on this map. Cited by 17 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Clinical and Molecular Study With Digital Support of Patients With Inoperable Lung Cancer
Who cites it
17 citing papers in PubMed, 26 citations in OpenAlex.
- Comprehensive Genomic Profiling Beyond Driver Testing in Non-Squamous Non-Small Cell Lung Cancer With Known Drivers.Cancer science · 2026Article
- Self-supervised learning can distinguish myelodysplastic neoplasms from clinical mimics using bone marrow biopsies.Blood neoplasia · 2026Article
- Metagenomic detection of protozoan parasites on leafy greens aided by a rapid and efficient DNA extraction protocol.Frontiers in microbiology · 2025Article
- Recent advances in the methods and clinical applications of next-generation sequencing in genomic profiling and precision cancer therapy.EXCLI journal · 2025Review
- PTK7 is a positive allosteric modulator of GPR133 signaling in glioblastoma.Cell reports · 2023Article
- Concurrent development of small lymphocytic lymphoma and lung cancer: A report of two cases and a review of the literature.Journal of clinical and experimental hematopathology : JCEH · 2023Review
- Metagenomics insights into responses of rhizobacteria and their alleviation role in licorice allelopathy.Microbiome · 2023Article
- Utility of targeted next generation sequencing for inborn errors of immunity at a tertiary care centre in North India.Scientific reports · 2022Article
- Design of Personalized Neoantigen RNA Vaccines Against Cancer Based on Next-Generation Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Article
- Comparison of adequacy between transbronchial lung cryobiopsy samples and endobronchial ultrasound-guided transbronchial needle aspiration samples for next-generation sequencing analysis.Thoracic cancer · 2021Article
- Application of Next Generation Sequencing in Laboratory Medicine.Annals of laboratory medicine · 2021Review
- EGFRvIII expression and isocitrate dehydrogenase mutations in patients with glioma.Oncology letters · 2020Article
- Soil potassium is correlated with root secondary metabolites and root-associated core bacteria in licorice of different ages.Plant and soil · 2020Article
- Mutation profiling of anaplastic ependymoma grade III by Ion Proton next generation DNA sequencing.F1000Research · 2019Article
- Detection of Nine Oncogenes Amplification in Lung and Colorectal Cancer Formalin-Fixed Paraffin-Embedded Tissue Samples using Combined Next-Generation Sequencing-Based Script and Digital Droplet Polymerase Chain Reaction.Cancer control : journal of the Moffitt Cancer CenterObservational
- Functional impact of intramolecular cleavage and dissociation of adhesion G protein-coupled receptor GPR133 (ADGRD1) on canonical signaling.The Journal of biological chemistryArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext generation sequencing based tumor tissue genotyping involves complex workflow and a relatively longer turnaround time. Semiconductor based next generation platforms varied from low throughput Ion PGM to high throughput Ion Proton and Ion S5XL sequencer. In this study, we compared Ion PGM and Ion Proton, with a new Ion S5XL NGS system for workflow scalability, analytical sensitivity and specificity, turnaround time and sequencing performance in a clinical laboratory.
methodsEighteen solid tumor samples positive for various mutations as detected previously by Ion PGM and Ion Proton were selected for study. Libraries were prepared using DNA (range10-40ng) from micro-dissected formalin-fixed, paraffin-embedded (FFPE) specimens using the Ion Ampliseq Library Kit 2.0 for comprehensive cancer (CCP), oncomine comprehensive cancer (OCP) and cancer hotspot panel v2 (CHPv2) panel as per manufacturer's instructions. The CHPv2 were sequenced using Ion PGM whereas CCP and OCP were sequenced using Ion Proton respectively. All the three libraries were further sequenced individually (S540) or multiplexed (S530) using Ion S5XL. For S5XL, Ion chef was used to automate template preparation, enrichment of ion spheres and chip loading. Data analysis was performed using Torrent Suite 4.6 software on board S5XL and Ion Reporter. A limit of detection and reproducibility studies was performed using serially diluted DLD1 cell line.
resultsA total of 241 variant calls (235 single nucleotide variants and 6 indels) expected in the studied cohort were successfully detected by S5XL with 100% and 97% concordance with Ion PGM and Proton, respectively. Sequencing run time was reduced from 4.5 to 2.5 hours with output range of 3-5 GB (S530) and 8-9.3Gb (S540). Data analysis time for the Ion S5XL is faster 1 h (S520), 2.5 h (S530) and 5 h (S540) chip, respectively as compared to the Ion PGM (3.5-5 h) and Ion Proton (8h). A limit detection of 5% allelic frequency was established along with high inter-run reproducibility.
conclusionIon S5XL system simplified workflow in a clinical laboratory, was feasible for running smaller and larger panels on the same instrument, had a shorter turnaround time, and showed good concordance for variant calls with similar sensitivity and reproducibility as the Ion PGM and Proton.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.