methylation analysis - bisulfite sequencing with SOLiD?

[jtjli]

I was reading this article which compares the three sequencing platforms:

http://genomics.ucr.edu/about/reports/SequencerComparison1207_Table.pdf

The table there shows that SOLiD won't work with "methylation (bisulfite)". Does any one know WHY??

[sci_guy]

This is old information. The SOLiD-1 software QC module didn't like the T bias in the bisulphite sequencing reads and called these erroneous clusters. This was fixed in SOLiD-2 and now ABI are developing a very crafty method of bisulphite sequencing incorporating a non-bisulphite treated DNA "address" within the same fragment and read in a paired end strategy. Don't ask me details. The ABI guys were intentionally vague as its still in development.

[snetmcom]

you can get an update on this mate pair strat if you ask.
this method seems to be the most clever/difficult, but it would bypass the issues with refseq that all the platforms have.

[gonzo]

AB has publicly spoken about two ways of doing methylation on SOLiD. One is hemi-methylation, and I am not aware of any protocols or details other than AB's internal work they discussed on that topic. The other utilizes an Invitrogen kit for bi-sulfite conversion (the merger makes that convenient...).

There is nothing about SOLiD that makes it incapable of methylation, AB just hasn't released a supported kit, and I am not aware of a customer who has published their data yet. There is nothing related to the platform that will limit methylation, and it will work fine but lacks AB kit chemistry and published protocols right now.