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Bisulfite Conversion Efficiency - (Apr/28/2010 )

Does anyone know what is the best way to determine bisulfite conversion efficiency? i.e. would MSP or bisulfite sequencing be used for this?
Also I am trying to optimize bisulfite conversion efficiency of FFPE samples....does anyone have experience with this?


this is difficult to determine properly because the primers you use are designed to bias towards fully converted template.

Efficiency is then measured by cloning and sequencning methods where non-CpG C's sequenced are counted across all the clones sequenced.

Note this is only conversion efficiency of the region you are interested in and PCR amplified, and not necessarily a measure of efficiency across the whole genome. There are some sequence contexts where conversion could be inhibited by GC-content and secondary structures.