Hi guys, I'm new to this forum.
Was hoping someone could explain to me in simple terms what the difference between MALDI-TOF and the GOOD Assay is when it comes to methylation detection? I'm trying to do research on how to experimentally identify methylation marks in the D-loop of mtDNA. I understand that both use bisulphite treatment of DNA.
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methylnick
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Posted 17 September 2010 - 01:44 PM
What is the GOOD assay? Do you have a reference?
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Genetics Kid
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Posted 17 September 2010 - 11:19 PM
methylnick, on 17 September 2010 - 01:44 PM, said:
What is the GOOD assay? Do you have a reference?
Yep, http://www.epigenome...=epigenotyping1
Its the technique they're using to map the human methylome. As far as I know, GOOD assay epityping is a modification of the GOOD assay used for SNP detection.
Sauer, S., D. Lechner, et al. (2000). "Full flexibility genotyping of single nucleotide polymorphisms by the GOOD assay." Nucl. Acids Res. 28(23): e100-.
This is probably a silly question but I'm really quite unfamiliar with molecular techniques in epigenetic studies.
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methylnick
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Posted 17 September 2010 - 11:29 PM
Hi there. Thanks for the reference. We are working on the good assay too we just didn't know it was called that!! Haha. I think you are asking if epityper(maldi tof) is better than GOOD. Well that depends. Each primer for good interrogates one cpg. So you can have many in one reaction potentially up to 36 and it can be from many genes too. Epityper focuses on one gene at a time but you are also measuring neighbouring cpgs at the same time. So yeah. It depends
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Posted 17 September 2010 - 11:41 PM
methylnick, on 17 September 2010 - 11:29 PM, said:
Hi there. Thanks for the reference. We are working on the good assay too we just didn't know it was called that!! Haha. I think you are asking if epityper(maldi tof) is better than GOOD. Well that depends. Each primer for good interrogates one cpg. So you can have many in one reaction potentially up to 36 and it can be from many genes too. Epityper focuses on one gene at a time but you are also measuring neighbouring cpgs at the same time. So yeah. It depends
Oh ok, thanks! MALDI-TOF and the GOOD assay are just two of the dozens of protocols for methylation detection out there so it's really difficult to determine which method I would actually need. If I'm looking to sequence the methylation marks of the d-loop in mtDNA (~300bp) for 5 samples, I wouldn't really need a high throughput method like MALDI-TOF would I?
