Invest in ME Conference 12: First Class in Every Way
OverTheHills wraps up our series of articles on this year's 12th Invest in ME International Conference (IIMEC12) in London with some reflections on her experience as a patient attending the conference for the first time.
Discuss the article on the Forums.

Help on my genetic genie results and questions about snp terminology

Discussion in 'Genetic Testing and SNPs' started by sleepingbeautycan, May 6, 2016.

  1. sleepingbeautycan

    sleepingbeautycan

    Messages:
    43
    Likes:
    19
    Here is my genetic genie report:
    upload_2016-5-6_18-23-58.png

    Here is what I THINK I have figured out:
    • The snps predict that I might have stomach permeability issues. Which indeed I did have. I think they are gone with a lot of money spent on supplements.
    • The snps also predict that I might have ammonia issues. I have seen some evidence of this in some blood tests and reactions to foods.
    • The pain that I get in between my shoulder blades may be associated with the ammonia problem. It comes and goes for months at a time, it is reduced when I fast and it gets worse when I eat red meat.
    • I should fix my ammonia issues before attempting to go on meb12 and mefolate.
    Am I right??

    Questions on alleles and snps and terminology

    I have been confused since I opened my genetic report (I have to admit I'm getting better, getting better all the time, can't get much worse). Here are some of my problems:

    I am starting to understand the orientation but sometimes it seems like the risk allele that is listed in my Sterling report has as the options a C and a G or an A and a T. If the gene in SNPedia is minus orientation, do you always switch A->T, T->A, C->G and G->C? Or are there exceptions?

    I had thought that +/+ was a homozygous polymorphism on this site but what about the allele's where the rare/wild one is protective? Is the healthier gene the -/- or the rare gene?
     
  2. alicec

    alicec Senior Member

    Messages:
    1,333
    Likes:
    2,489
    Australia
    You seem to have accepted a number of Yasko's unfounded assumptions in coming to your conclusions. I can see nothing to support them.

    The MTHFR C677T and A1298C variants would slightly slow the enzyme as would MTR A2756G. You are +/- for all these so not a major effect. A small dose of methylfolate and methylB12 respectively could be helpful.

    There's nothing else there of any consequence.

    Some sites assume that the minor allele is risk. This is incorrect. The variant could be protective, in which case the wildtype has the "risk". Many variants of course have no effect so risk is meaningless.

    It is better to think of it as major or wildtype or ancestral, reported as -, and variant reported as +.

    Orientation only matters when the variant changes between G and C or A and T. Then you really do need to check orientation very carefully to know if you have the ancestral or variant allele.

    Otherwise it makes no difference if something is reported as A or T, or as G or C. The terms are interchangeable.

    dsSNP will tell you which is the ancestral and which is the variant allele.
     
    Valentijn likes this.
  3. sleepingbeautycan

    sleepingbeautycan

    Messages:
    43
    Likes:
    19
    Thanks. So on rs1056836, C is the ancenstral, but it is also the risk variant (or less protective variant). So on this site it is referred to as +/+ if you are homozygous C?
     
  4. alicec

    alicec Senior Member

    Messages:
    1,333
    Likes:
    2,489
    Australia
    I just googled that SNP. dsSNP and SNPedia say that G is ancestral and C is minor. They are reporting in the minus (reverse) orientation.

    I don't know what orientation the site you quote is using.

    23andme uses the plus (forward) orientation.
     
  5. sleepingbeautycan

    sleepingbeautycan

    Messages:
    43
    Likes:
    19

See more popular forum discussions.

Share This Page