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

Phuc-Loi Luu; Phuc-Thinh Ong; Tran Thai Huu Loc; Dilys Lam; Ruth Pidsley; Clare Stirzaker; Susan J Clark

doi:10.1093/bioinformatics/btaa1060

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

Bioinformatics. 2021 Aug 9;37(15):2198-2200. doi: 10.1093/bioinformatics/btaa1060.

Authors

Phuc-Loi Luu^{1

2}, Phuc-Thinh Ong³, Tran Thai Huu Loc⁴, Dilys Lam¹, Ruth Pidsley^{1

2}, Clare Stirzaker^{1

2}, Susan J Clark^{1

2}

Affiliations

¹ Epigenetics Research Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia.
² St Vincent's Clinical School, UNSW, Sydney, NSW 2010, Australia.
³ Center for Population Health Sciences, Hanoi University of Public Health, Hanoi 100000, Vietnam.
⁴ School of Medicine, Vietnam National University, Ho Chi Minh City 70000, Vietnam.

Abstract

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 an 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, visualization and remotely sharing data with collaborators and clinicians.

Availabilityand implementation: MethPanel is freely available at https://github.com/thinhong/MethPanel.

Supplementary information: Supplementary data are available at Bioinformatics online.

Abstract

Grants and funding