įunding: This work was supported by the European Union, FP7 small medium focused project 277849 EurHEALTHAgeing ( ).
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This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: All files for testing and running the software are available at and. Received: ApAccepted: JPublished: July 28, 2016Ĭopyright: © 2016 Pabinger et al. PLoS ONE 11(7):Įditor: Matteo Pellegrini, UCLA-DOE Institute for Genomics and Proteomics, UNITED STATES
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(2016) Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers. Ĭitation: Pabinger S, Ernst K, Pulverer W, Kallmeyer R, Valdes AM, Metrustry S, et al.
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TABSAT is freely available under a GNU General Public License version 3.0 (GPLv3) at and. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. We obtained a mean coverage of 282X using 1,196,822 aligned reads. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets.
The obtained profiles are then summarized and compared between samples. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers.
Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM). Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons.
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