ArticleBMC genomics2017
A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
34 citing papers in PubMed.
- Flunarizine changes microRNA expression in cell cultures and in a mouse model of spinal muscular atrophy.Scientific reports · 2026Article
- White paper on best practices for translational research in neuroendocrine neoplasms.Journal of neuroendocrinology · 2025Article
- Insights into the tripartite relationship between cervical cancer, human papillomavirus, and the vaginal microbiome: a mega-analysis.Human genomics · 2025Article
- High-throughput sequencing: a breakthrough in molecular diagnosis for precision medicine.Functional & integrative genomics · 2025Review
- Article
- Reflective Evaluation of Next-Generation Sequencing Data during Early Phase Detection of the Delta Variant.OBM genetics · 2025Article
- Leveraging Next-Generation Sequencing Application from Identity to Purity Profiling of Nucleic Acid-Based Products.Pharmaceutics · 2024Article
- BEERS2: RNA-Seq simulation through high fidelity in silico modeling.Briefings in bioinformatics · 2024Article
- An Overview of Advances in Rare Cancer Diagnosis and Treatment.International journal of molecular sciences · 2024Review
- Review
- Benchmarking second and third-generation sequencing platforms for microbial metagenomics.Scientific data · 2022Article
- Artificial Intelligence, Healthcare, Clinical Genomics, and Pharmacogenomics Approaches in Precision Medicine.Frontiers in genetics · 2022Review
- A Comprehensive Review of Performance of Next-Generation Sequencing Platforms.BioMed research international · 2022Review
- RNA Sequencing Data from Human Intracranial Aneurysm Tissue Reveals a Complex Inflammatory Environment Associated with Rupture.Molecular diagnosis & therapy · 2021Article
- Pervasive transcription of the mitochondrial genome inRNA biology · 2021Article
- CAMPAREE: a robust and configurable RNA expression simulator.BMC genomics · 2021Article
- Method for quick DNA barcode reference library construction.Ecology and evolution · 2021Article
- Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar).BMC genomics · 2021Article
- Article
- Differentiation of Capripox Viruses by Nanopore Sequencing.Vaccines · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
backgroundThough Illumina has largely dominated the RNA-Seq field, the simultaneous availability of Ion Torrent has left scientists wondering which platform is most effective for differential gene expression (DGE) analysis. Previous investigations of this question have typically used reference samples derived from cell lines and brain tissue, and do not involve biological variability. While these comparisons might inform studies of tissue-specific expression, marked by large-scale transcriptional differences, this is not the common use case.
resultsHere we employ a standard treatment/control experimental design, which enables us to evaluate these platforms in the context of the expression differences common in differential gene expression experiments. Specifically, we assessed the hepatic inflammatory response of mice by assaying liver RNA from control and IL-1β treated animals with both the Illumina HiSeq and the Ion Torrent Proton sequencing platforms. We found the greatest difference between the platforms at the level of read alignment, a moderate level of concordance at the level of DGE analysis, and nearly identical results at the level of differentially affected pathways. Interestingly, we also observed a strong interaction between sequencing platform and choice of aligner. By aligning both real and simulated Illumina and Ion Torrent data with the twelve most commonly-cited aligners in the literature, we observed that different aligner and platform combinations were better suited to probing different genomic features; for example, disentangling the source of expression in gene-pseudogene pairs.
conclusionsTaken together, our results indicate that while Illumina and Ion Torrent have similar capacities to detect changes in biology from a treatment/control experiment, these platforms may be tailored to interrogate different transcriptional phenomena through careful selection of alignment software.
Indexed as
Identifiers
What OpenQuestion holds
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.