Extract SNPs from 23andme data to yasko/nutrigenomics notation

[adreno]

I'm a slow metabolizer. And please make the thread you mentioned; I'm interested

 

[Calico13]

I'm a slow metabolizer. And please make the thread you mentioned; I'm interested

I started working on the new thread, offline for now until I get everything together. If you can think of any SNP's you want added, let me know! For now I'm focusing on things like liver pathways, APOE status and whatever else I think is interesting. I want to do more research and add collagen genes and anything related to the detoxification systems and the immune system.

I have to say going through and looking at each gene, I have some weird genotypes. One that hasn't been seen in Caucasians, so I dunno what to think about that. It is on the CYP3A5 gene. Of course there's very little information on it...lol

 

[hixxy]

The way we tend to look at these genes on this forum is as though they are static, making the assumption that all of them are expressed. I guess gene expression is the difference between all these other people with the well known MTHFR polymorphisms and no disease and those of us with disease.

I guess you could say, whatever it was that caused these nasty genes to become expressed is the cause of our disease, while the genes themselves are our potential for disease.

I'm a slow caffeine metaboliser. I've never been able to tolerate much caffeine.

New thread sounds interesting. Be sure to post back here when you create it, so I don't overlook it.

 

[adreno]

I guess you're right about that, hixxy. It's all about epigenetics. That's why I'm starting to think that metabolic testing will provide more useful info than genotype testing.

 

[hixxy]

Indeed. Have you had the HDRI Methylation Panel done yet? I have a consult with my doctor this week, so will be discussing it with him.

 

[adreno]

Indeed. Have you had the HDRI Methylation Panel done yet? I have a consult with my doctor this week, so will be discussing it with him.

No, but I will look into it, once I have the funds.

 

[adreno]

I realize this is getting OT, but I wanted to add that slow metabolizers of caffeine have an increased risk of myocardial infarction, when consuming coffee:

Coffee, CYP1A2 genotype, and risk of myocardial infarction.
http://www.ncbi.nlm.nih.gov/m/pubmed/16522833/

 

[hixxy]

I remember right about the time my health was starting to deteriorate (6 or so years ago) I took some caffeine tablets and ended up at ER with heart instability / crush chest pain. The dose of caffeine tablets was far lower than what should have had that effect.

 

[nandixon]

Positive in that dbSNP orientation is plus. So if dbSNP DOES correlate to positive for that SNP, then I have serious problems in GSTM1. If I crossreference my above posted results with the dbSNP orientation field, it seems they DO correlate. The field will be plus if you are either homozygous or herterozygous positive for the SNP.

I do hope my interpretation is rock solid, as I'm going to take these results to the doctor with me on Friday. It certainly sheds some light on why I have such a horrendous time supplementing almost anything in relation to the methylation cycle. I'm one of these people whose body rejects almost anything you throw at it.

The annoying thing is, recommendations for the 2 COMT homozygous positive SNPs I have is to supplement hydroxocobalamin -- but -- I suspect my glutathione is likely way too low for the enzyme that activates hydroxocobalamin to methylcobalamin to work, therefore this is kind of useless, but supplementing methylcobalamin will overload me with methyl groups.

Such a painful network in interrelated nightmares.

Hi hixxy,

I'm curious to see your GSTM1 results. Here are mine ("normal" call in square brackets):

GSTM1 -/- (CC)[CC] rs12068997
GSTM1 +/+ (GG)[AA] rs4147565
GSTM1 -/- (AA)[AA] rs4147567
GSTM1 +/+ (TT)[AA] rs4147568
GSTM1 -/- (CC)[CC] rs1056806
GSTM1 +/+ (TT)[AA] rs12562055
GSTM1 +/+ (AA)[GG] rs2239892

A lot of positives, too, like you mentioned, but such a grouping may simply represent a haplotype. Perhaps someone knows.

I had a MetaMetrix panel done in 2000. For detoxification of acetaminophen, the glutathione conjugation was only 50% of the lowest normal reference value ("acetaminophen mercapturate" was measured). I'm not sure how much influence GSTM1 has relative to the other glutathione-S-transferases in that particular case.

For anyone else interested, here is a recent (2011) listing of genes for the "glutathione pathway": GSH synthesis (GSS, GCLC, and GCLM); GSH redox status (GSR, GPX1, GPX2, GPX3, GPX4, GPX5, GPX6, and GPX7); GSH S-transferases (GSTA1, GSTA2, GSTA3, GSTA4, GSTA5, GSTM1, GSTM2, GSTM3, GSTM4, GSTM5, GSTO1, GSTO2, GSTP1, GSTT1, GSTT2, and GSTZ1); and GSH conjugate transporters (ABCC1, ABCC2, ABCC3, and ABCC4). From: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044203/

(BTW, hixxy, 23andMe is reporting VDR Taq with the call letters A and G in my report. You have CC . . .?)

 

[qofmiwok]

Interesting. I have exactly the same results as nandixon.

GSTM1 -/- (CC)[CC] rs12068997
GSTM1 +/+ (GG)[AA] rs4147565
GSTM1 -/- (AA)[AA] rs4147567
GSTM1 +/+ (TT)[AA] rs4147568
GSTM1 -/- (CC)[CC] rs1056806
GSTM1 +/+ (TT)[AA] rs12562055
GSTM1 +/+ (AA)[GG] rs2239892

Question, how did you find what is considered "normal"?

Thanks

 

[nandixon]

Hi qofmiwok,

I'm so glad you asked that - in double-checking my results I found that the word processor on my phone inadvertently shifted a column. So my previous post isn't correct. I don't have any variant alleles. The correct results, I hope(!) are:

GSTM1 -/- (CC)[CC] rs12068997
GSTM1 -/- (GG)[GG] rs4147565
GSTM1 -/- (AA)[AA] rs4147567
GSTM1 -/- (TT)[TT] rs4147568
GSTM1 -/- (CC)[CC] rs1056806
GSTM1 -/- (TT)[TT] rs12562055
GSTM1 -/- (AA)[AA] rs2239892

The "normal" calls in square brackets are the ancestral (wild type) alleles from NCBI, e.g., http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=12068997 (I also checked each one with openSNP, too).

So it must be some other glutathione-S-transferase that's causing problems in the MetaMetrix results I mentioned, since all those ancestral alleles seem very dominant in the general population.

If Rich happens to see this maybe he might have an idea. (My GSTA2 rs2608615 is CC, same as Rich's, from a post he made in April, so I guess that one is ok, too.)