ArticlePloS one2016
Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- The termination of UHRF1-dependent PAF15 ubiquitin signaling is regulated by USP7 and ATAD5.eLife · 2023Article
- Structural basis for the unique multifaceted interaction of DPPA3 with the UHRF1 PHD finger.Nucleic acids research · 2022Article
- Real-world outcome of universal screening for Lynch syndrome in Japanese patients with colorectal cancer highlights the importance of targeting patients with young-onset disease.Molecular and clinical oncology · 2021Article
- Ten Years of EWAS.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Review
- MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection.Bioinformatics (Oxford, England) · 2021Article
- Article
- The impact of DNA demethylation on the upregulation of the NRN1 and TNFAIP3 genes associated with advanced gastric cancer.Journal of molecular medicine (Berlin, Germany) · 2020Article
- A Comparison of Forensic Age Prediction Models Using Data From Four DNA Methylation Technologies.Frontiers in genetics · 2020Article
- EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies.Nucleic acids research · 2019Article
- Inflammation and cancer.Environmental health and preventive medicine · 2018Review
- Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells.Nature communications · 2018Article
- DNA Methylation Signatures Predicting Bevacizumab Efficacy in Metastatic Breast Cancer.Theranostics · 2018Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM). Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. 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. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. 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. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. 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. 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. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage. TABSAT is freely available under a GNU General Public License version 3.0 (GPLv3) at https://github.com/tadkeys/tabsat/ and http://demo.platomics.com/.
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