methBLAST and methPrimerDB: web-tools for PCR based methylation analysis |
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| Authors: | Filip Pattyn Jasmien Hoebeeck Piet Robbrecht Evi Michels Anne De Paepe Guy Bottu David Coornaert Robert Herzog Frank Speleman and Jo Vandesompele |
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| Institution: | (1) Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium;(2) Belgian EMBnet Node, Universit libre de Bruxelles, Boulevard du Triomphe, Campus de la Plaine, building NO-CP 257, 1050 Brussels, Belgium |
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| Abstract: | Background DNA methylation plays an important role in development and tumorigenesis by epigenetic modification and silencing of critical
genes. The development of PCR-based methylation assays on bisulphite modified DNA heralded a breakthrough in speed and sensitivity
for gene methylation analysis. Despite this technological advancement, these approaches require a cumbersome gene by gene
primer design and experimental validation. Bisulphite DNA modification results in sequence alterations (all unmethylated cytosines
are converted into uracils) and a general sequence complexity reduction as cytosines become underrepresented. Consequently,
standard BLAST sequence homology searches cannot be applied to search for specific methylation primers. |
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