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MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection


SUMMARY: DNA methylation patterns in a cell are associated with gene expression and the phenotype of a cell, including disease states. Bisulphite PCR sequencing is commonly used to assess the methylation profile of genomic regions between different cells. Here we have developed MethPanel, a computational pipeline with an interactive graphical interface to rapidly analyse multiplex bisulphite PCR sequencing data. MethPanel comprises a complete analysis workflow from genomic alignment to DNA methylation calling and supports an unlimited number of PCR amplicons and input samples. MethPanel offers important and unique features, such as calculation of a epipolymorphism score and bisulphite PCR bias correction capabilities, and is designed so that the methylation data from all samples can be processed in parallel. The outputs are automatically forwarded to a shinyApp for convenient display, visualisation and remotely sharing data with collaborators and clinicians. AVAILABILITY: MethPanel is freely available at SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Type Journal
ISBN 1367-4811 (Electronic) 1367-4803 (Linking)
Authors Luu, P. L.; Ong, P. T.; Loc, T. T. H.; Lam, D.; Pidsley, R.; Stirzaker, C.; Clark, S. J.
Responsible Garvan Author Prof Susan Clark
Publisher Name Bioinformatics
Published Date 2020-12-26
Published Pages btaa1060.
Status Always Electronic
DOI 10.1093/bioinformatics/btaa1060
URL link to publisher's version