Protocol Online logo
Top : New Forum Archives (2009-): : DNA Methylation and Epigenetics

comparison of bisulfite sequencing and base specific cleavage coupled with Mass - (Jun/03/2009 )

I was just wondering which technique would be better to employ, bisulfite sequencing or the one that employs the base specific cleavage coupled with mass spec analysis of dna fragments

-Muhammad Umer-

we use both, and they both have pro's and con's.

Very hard to say one for the other without more detail on your part.



bisulfite sequencing is simple enough to perform and its result is easier to interpret, although it has its con's as Nick said.


i intend to study the promoter hypermethylation of TSGs in hepatocellular carcinoma. i was just wondering which technique would be more informative.
just to add, i will have to get my sequencing done commercially while MS is available in our lab and procedures are optimized (though not specifically this base specific cleavage-MS analysis methodology, but still)
i was just wondering that even if both have their pros and cons, which would be feasible, economically specially.

-Muhammad Umer-

We have been performing sequenincg but have switched over to base specific cleavage using SEUQENOM for economic reasons, if you are processing many samples as the chip format is 384-samples per run then this is the way to go.

There are pro's and cons, the pro's are it's cheaper than sequencing and supposedly "more representive" than traditional sequencing you need to sequence at least 100 clones to achieve similar accuracy to mass spec, but the big con is, you may not be able to meausre methylation on every CG site in your amplicon of interest because some are too big or too small or non-informative fragments overlap with ones that contain CG's potentiall over or under estimating the methylation


well nick thanks for pointing towards the pros and cons. i would infact choose MS analysis as i dont have enough funds for sequencing.
one more thing, can anybody send me some article etc on the comparison of these two methods, just for the sake of clarity of concepts????

-Muhammad Umer-