MethMarker

MethMarker facilitates the design and optimization of gene-specific DNA methylation assays. Beyond its use as an epigenetic primer-design tool, it provides extensive support for epigenetic biomarker optimization.

For a given gene or genomic region, MethMarker helps design DNA methylation assays for any of the following protocols:

• COBRA (combined bisulfite restriction analysis)
• bisulfite SNuPE (single nucleotide primer extension)
• bisulfite pyrosequencing
• MSP (methylation specific polymerase chain reaction)
• MethyLight
• MeDIP-qPCR
• Other methods (e.g. MassARRAY) via the custom assay feature

Furthermore, if DNA methylation profiles are available for the region of interest, MethMarker can be used to optimize and validate DNA methylation biomarkers that provide robust classification, for example between tumor samples and healthy control tissue. If high-resolution DNA methylation profiles are available for the region of interest (e.g. from bisulfite sequencing, http://biq-analyzer.bioinf.mpi-inf.mpg.de), MethMarker can exploit these data to design biomarker assays that optimally discriminate between cases (e.g. cancer samples) and controls.