Protocolpedia - The Encyclopedia Of Lab Protocols

Hello everyone I'm new here and I was wondering if I could get some assistance.
In my research of the literature I thought the differences between the two methods were based on the proximity of the primers to the CpG sites and that BSP primers were designed without including CpG dinucleotides.
I was wondering if someone could clear it up for me and what are the pros and cons of each method. Thank you very much in advance

Hello

I assume by BSP you mean bisulfite PCR and sequencing. If so, the advantages of this over MSP are:

A greater number of CpG residues analysed for methylation when compared with MSP (MSP is only one and that is identified with a methylation specific primer). Bisulfite sequencing looks at every CpG residue across the whole amplicon.

I would also say that primer optimisation is crucial for an MSP assay to work, it is not so crucial for BSP because you will be sequencing through the amplicon anyway.

MSP has it advantages in that it is far more quicker than BSP in terms of hands-on lab time.


hope this helps. I would be interested to see what other people think about this also.

Cheers

Thanks for the reply. I always thought that with MSP one could include a number of Cpg nucleotides in the region being amplified especially in the 3' end primer design to make the primer more specific.
Does this mean we only look at one CpG nucleotide with MSP and if we want to observe several then use BSP?
My confusion started today when I ran across a paper that described the MSP they conducted by using restriction enzyme schussboomers and amplifying the region that the enzymes cut. Thanks once again.

I agree with it, even combined with a BstI restriction of the amplicon, is called site specific; it only lets you look at however many CpGs are in your primers and in a BstI site if you are lucky enough to have one. I wanted to use this method as well to avoid sequencing and cloning but in the end I have determined that sequencing is the only thing I trust and I tend to scoff at papers who use MSP as it is so prone to artifact. Check out my agarose bead protocol in the "bisulfite treatment" thread, pinned above.

Hi, I know most people from cancer field etc. etc. love MSP, but MSP is quite bullshitty. Just one example: Check the papers from Lillycrop et al. in the british journal of nutrition. Lay their rat papers beside eachother. First thing to notice: what the F%%$$#....how can you publish the same results 3 fucking times in the same %^$#@ journal.
Than sequencing 1.6 % difference between 2 groups: MSP says >80%.....Just love MSP dont you?

And what the &$#%^& why measure one CpG if you can run a ABI trace and measure several CpGs?????? semi-quantitatively(with the right software).
come one people: Science is a emperical thingy....so measure the bloody things and dont use proxy things