Thursday, April 16, 2009

SNPs for cholinesterase inhibitor sensitivity

I've been trying to understand the potential causes of cholinesterase inhibitor sensitivity. My leading theory at this point relates to single nucleotide polymorphisms (SNPs) affecting the genes for encoding and promotion of acetylcholinesterase (ACHE), butyrylcholinesterase (BCHE), and paraoxonase 1 (PON1).

I've found several papers and a couple of books that relate to these genes and talk about polymorphisms which can result in being more susceptible to cholinesterase inhibitors. I've also signed up for 23andMe which hopefully in 8 more weeks or so will allow me to see which version I have of many of them. If, that is, I can figure out the mapping...

First off, it turns out that there are two ways of reporting the alleles for a given SNP: A=T; C=G. SNPedia uses one way, and 23andMe uses the opposite way. A partial explanation of this is at This isn't complicated, but it does make your head hurt more when trying to compare them.

Secondly, the various sources aren't using a consistent naming scheme. I've tried to start making a table to cross reference the names I've found in the papers to the "rs" codes that 23andMe and SNPedia both use (see It's a clunky way to do it, and I'm fantasizing about making something with django to do the job better. So, I'm kinda stuck on that project until I either bite the bullet and do it clunky way, or learn enough django to do it the fancy way and possibly enter a bottomless development hole...

Finally, three SNPs into the project I ran into a possible numbering discrepancy. The paper lists the SNP as position -162 on the PON1 gene. SNPedia doesn't list a SNP there, but lists Rs705381 at position -161. Is it the same one?

How many more of these things are going to almost but not quite line up? Aaaahhhh!

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