My SNPs: weirdness explained

[Valentijn]

Wasn't sensitive enough to, right? A 'no call' means that the chip wasn't sensitive enough to detect that particular SNP. 'Not genotyped' means 23andme did not intend to check for that SNP - it isn't one of the ones they look for.

My understanding is that every chip is looking for certain SNPs. But in the data 23andMe I have from 40+ ME patients, there are a minority of patients where more SNPs where tested, and everyone else has a bunch of no-calls for those SNPs. It's more apparent on certain genes where they were probably doing some exploratory testing, but it happens all over the genome for the same people, which would suggest that they have a slightly different chip version rather than any actual genetic distinction or random factor in detecting the SNPs.

@Gondwanaland , @pogoman : I did download the analyzer you suggested. The only thing I don't like is that they mention the same SNPs over... and over... and over again. I understand that they want to group them by health issue, but I'm doing research and I find myself looking up the same ones again and again.

That does sound rather annoying. I group them by pathway - even when there's some overlap between pathways, it's pretty easy to figure out where a gene fits best.

 

[pogoman]

@Gondwanaland , @pogoman : I did download the analyzer you suggested. The only thing I don't like is that they mention the same SNPs over... and over... and over again. I understand that they want to group them by health issue, but I'm doing research and I find myself looking up the same ones again and again.



-J

yes, there is that grouping of related SNPs which results in duplications across the different categories.

they are doing improvements on V2 so be sure to go to the website and re-open your report every once in awhile to see if there are updates.
I found my report from February? when V2 was first introduced is different from the one now, they corrected at least one green to red SNP.

 

[JaimeS]

@Sidereal - one 100-mg dose of 5-HTP - not serotonin itself. This is one pill from a respected brand - Jarrow, I think. After reading @caledonia's (er... I think it was Caledonia's?) recommendation to sometimes take a pill and divvy it up into 1/125 doses, this was probably high for someone like us, but I didn't know that at the time and took the recommended dose.

I had the same reaction to an herbal blend containing Withania somnifera, which is serotinergic. I had what is considered a 'normal' dose of that as well: just a few grams of powder, and it's typically very benign. I even had it before getting chronically ill and nothing happened to me.

Finally, I get an 'echo' of the same symptoms if I have dark chocolate. Ghostly pressure at the side of my head, increased dizziness and elevated HR.

My serotonin is quite low normally (naturally?) and it REALLY doesn't seem to like an unexpected jump.

-J

 

[Gondwanaland]

took the recommended dose.

Someone said that the recommended dose is based on... the size of the capsule they happened to have on hand to encapsulate the product.

if I have dark chocolate. Ghostly pressure at the side of my head, increased dizziness and elevated HR.

Perhaps look into a low tyramine diet? Are there cases of Parkinson's in your family?

 

[JaimeS]

....no, but I have a pretty rare SNP for juvenile Parkinson's. It's the first one on Valentjin's program.

Grain of salt... grain of salt... grain of salt...

Seriously, I looked up the dose of 5-HTP in several locations and read reports from other people. Some people take less than 100-mg, (say, 60) but most doses were still in that range.

-J

 

[WoolPippi]

Could you please summarize how vit D and dopamine are related?

I can't, I don't remember

It's the part of the cycle in the image I posted, when MTR/MTRR can't give folate/mB12 to the next cycle and syphones it away "to the bottom" of the picture. There Dopamine and vit D are mentioned and other neurotransmitters. I should reread the sources of the images to remember what it's about specifically.
Sorry.

Dr Gominak also talks about vit D. She's a neurologist who found that almost all her patients have vit D shortage, no matter what their neurological disorder.
Vit D receptors are very prevalent in the brain (stem).
I can provide link tomorrow, it's 4 am here and I am on a tablet.

She only mentions Dopamine once though. She says vit D is needed in stomach cells to bind B12. B12 is needed for sleep. As is iron, because iron is a co-factor in making dopamine. Shortage of vit D, B12 and iron commonly co-exist in troubled sleep.

 

[WoolPippi]

Yes, GG gives 2 reports: Methylation and Detox. Detox is actually liver metabolism. That is why I have a link in my sig called "The Liver", because methylation is just one of the liver pathways. Later I also added my Sterling's results, which are paid, but @JaimeS I find it gives much more info than GG (and GG is free anyway).

I always read the Detox profile from GG as being all cell-related, not only liver cells...
That's why I harp on about cells not being able to shed waste.

Do I have this whole thing wrong?

Edit: and is Methylation also only a liver process you think?

 

[Gondwanaland]

I always read the Detox profile from GG as being all cell-related, not only liver cells...
That's why I harp on about cells not being able to shed waste.

Do I have this whole thing wrong?

Edit: and is Methylation also only a liver process you think?

There is a high concentration of CYP proteins in the liver, but these enzymes are also found throughout the body, where they often have specialised roles.

The highest expressed forms in liver are CYPs 3A4, 2C9, 2C8, 2E1, and 1A2, while 2A6, 2D6, 2B6, 2C19 and 3A5 are less abundant and CYPs 2J2, 1A1, and 1B1 are mainly expressed extrahepatically. Expression of each CYP is influenced by a unique combination of mechanisms and factors including genetic polymorphisms, induction by xenobiotics, regulation by cytokines, hormones and during disease states, as well as sex, age, and others. Multiallelic genetic polymorphisms, which strongly depend on ethnicity, play a major role for the function of CYPs 2D6, 2C19, 2C9, 2B6, 3A5 and 2A6, and lead to distinct pharmacogenetic phenotypes termed as poor, intermediate, extensive, and ultrarapid metabolizers.

Same for methylation.

 

[JaimeS]

Re: Vitamin D and dopamine.

There are Vit D receptors on dopamine neurons. It has also been said that Vitamin D helps regulate the genetic expression of dopamine.

There were a flurry of studies in 2012 and 2013 on the fact that Vit D influences dopamine production. Then they related it to schizophrenia and bipolar disorder.

-J