Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat

Wong, Nicholas C., Pope, Bernard J., Candiloro, Ida, Korbie, Darren, Trau, Matt, Wong, Stephen Q., Mikeska, Thomas, van Denderen, Bryce J. W., Thompson, Erik W., Eggers, Stefanie, Doyle, Stephen R. and Dobrovic, Alexander (2015) Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat. Gigascience, 4 1: 55.1-55.8. doi:10.1186/s13742-015-0098-x


Author Wong, Nicholas C.
Pope, Bernard J.
Candiloro, Ida
Korbie, Darren
Trau, Matt
Wong, Stephen Q.
Mikeska, Thomas
van Denderen, Bryce J. W.
Thompson, Erik W.
Eggers, Stefanie
Doyle, Stephen R.
Dobrovic, Alexander
Title Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat
Journal name Gigascience   Check publisher's open access policy
ISSN 2047-217X
Publication date 2015-11-26
Sub-type Article (original research)
DOI 10.1186/s13742-015-0098-x
Open Access Status DOI
Volume 4
Issue 1
Start page 55.1
End page 55.8
Total pages 8
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Formatted abstract
Background: DNA methylation is a complex epigenetic marker that can be analyzed using a wide variety of methods. Interpretation and visualization of DNA methylation data can mask complexity in terms of methylation status at each CpG site, cellular heterogeneity of samples and allelic DNA methylation patterns within a given DNA strand. Bisulfite sequencing is considered the gold standard, but visualization of massively parallel sequencing results remains a significant challenge.

Findings: We created a program called Methpat that facilitates visualization and interpretation of bisulfite sequencing data generated by massively parallel sequencing. To demonstrate this, we performed multiplex PCR that targeted 48 regions of interest across 86 human samples. The regions selected included known gene promoters associated with cancer, repetitive elements, known imprinted regions and mitochondrial genomic sequences. We interrogated a range of samples including human cell lines, primary tumours and primary tissue samples. Methpat generates two forms of output: a tab-delimited text file for each sample that summarizes DNA methylation patterns and their read counts for each amplicon, and a HTML file that summarizes this data visually. Methpat can be used with publicly available whole genome bisulfite sequencing and reduced representation bisulfite sequencing datasets with sufficient read depths.

Conclusions: Using Methpat, complex DNA methylation data derived from massively parallel sequencing can be summarized and visualized for biological interpretation. By accounting for allelic DNA methylation states and their abundance in a sample, Methpat can unmask the complexity of DNA methylation and yield further biological insight in existing datasets.
Keyword Bisulfite sequencing
Cancer
DNA methylation
Epialleles
Epigenetics
PCR
Visualization
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 2 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 2 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Fri, 04 Dec 2015, 20:14:37 EST by Mrs Louise Nimwegen on behalf of School of Chemistry & Molecular Biosciences