Dataset Information

A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression.

ABSTRACT: Though 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.Here 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-1? 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.Taken 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.

SUBMITTER: Lahens NF

PROVIDER: S-EPMC5553782 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression.

Lahens Nicholas F NF Ricciotti Emanuela E Smirnova Olga O Toorens Erik E Kim Eun Ji EJ Baruzzo Giacomo G Hayer Katharina E KE Ganguly Tapan T Schug Jonathan J Grant Gregory R GR

BMC genomics 20170810 1

<h4>Background</h4>Though 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 trans ...[more]

PMID: 28797240

Similar Datasets

Project description:Fast and effective methods are needed for sequencing of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome to track genetic mutations and to identify new and emerging variants during the ongoing pandemic. The objectives were to assess the performance of the SARS-CoV-2 AmpliSeq research panel and S5 plug-in analysis tools for whole-genome sequencing analysis of SARS-CoV-2 and to compare the results with those obtained with the MiSeq-based ARTIC analysis pipeline, using metrics such as depth, coverage, and concordance of single-nucleotide variant (SNV) calls. A total of 191 clinical specimens and a single cultured isolate were extracted and sequenced with AmpliSeq technology and analysis tools. Of the 191 clinical specimens, 83 (with threshold cycle [CT] values of 15.58 to 32.54) were also sequenced using an Illumina MiSeq-based method with the ARTIC analysis pipeline, for direct comparison. A total of 176 of the 191 clinical specimens sequenced on the S5XL system and prepared using the SARS-CoV-2 research panel had nearly complete coverage (>98%) of the viral genome, with an average depth of 5,031×. Similar coverage levels (>98%) were observed for 81/83 primary specimens that were sequenced with both methods tested. The sample with the lowest viral load (CT value of 32.54) achieved 89% coverage using the MiSeq method and failed to sequence with the AmpliSeq method. Consensus sequences produced by each method were identical for 81/82 samples in areas of equal coverage, with a single difference present in one sample. The AmpliSeq approach is as effective as the Illumina-based method using ARTIC v3 amplification for sequencing SARS-CoV-2 directly from patient specimens across a range of viral loads (CT values of 15.56 to 32.54 [median, 22.18]). The AmpliSeq workflow is very easily automated with the Ion Chef and S5 instruments and requires less training and experience with next-generation sequencing sample preparation than the Illumina workflow.

Dataset Information

A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression.

Publications

A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets