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Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers
Stephan Pabinger1, Karina Ernst1, Walter Pulverer1
1Health & Environment Department, Molecular Diagnostics, AIT-Austrian Institute of Technology, Vienna, Austria.
Plos One
|July 29, 2016
Summary
This study introduces TABSAT, a new tool for analyzing targeted bisulfite sequencing data from Ion Torrent sequencers. TABSAT provides accurate and cost-effective DNA methylation profiling, confirming its reliability against industry standards.
Area of Science:
- Epigenetics and Genomics
- Bioinformatics and Computational Biology
Background:
- Targeted bisulfite sequencing offers a cost-effective method for studying DNA methylation at single CpG resolution.
- Existing platforms lack specific protocols and analysis solutions for targeted bisulfite sequencing on Personal Genome Machines (PGM).
Purpose of the Study:
- To present TABSAT, a novel bioinformatics tool for analyzing targeted bisulfite sequencing data generated on Ion Torrent platforms.
- To validate the accuracy and cost-effectiveness of targeted amplicon bisulfite sequencing for DNA methylation studies.
Main Methods:
- Development of the TABSAT workflow for quality assessment, read mapping using a tailored Bismark version, and visualization of methylation patterns.
- Generation of targeted bisulfite sequencing data from 48 samples, covering 2,544 amplicon targets with a mean coverage of 282X.
- Comparison of TABSAT results with methylation levels from Illumina 450k methylation chips.
Main Results:
- TABSAT successfully analyzes targeted bisulfite sequencing data, deducing specific methylation patterns and enabling sample comparisons.
- High mean coverage (282X) achieved across 2,544 amplicon targets.
- An average Pearson correlation coefficient of 0.91 was obtained when comparing TABSAT results to Illumina 450k methylation chip data, demonstrating high accuracy.
Conclusions:
- Targeted amplicon bisulfite sequencing is an accurate and cost-efficient method for DNA methylation studies.
- TABSAT provides a valuable, platform-independent solution for analyzing targeted bisulfite sequencing data, compatible with Ion Torrent and Illumina MiSeq platforms.
- TABSAT is accessible via the Platomics platform and is freely available under GPLv3.
