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Genetic SNPs Poll

Discussion in 'Genetic Testing and SNPs' started by Soundthealarm21, Jan 5, 2014.

?

What Genetic SNPs have you tested positive for?

  1. COMT V158M

    64.3%
  2. COMT H62H

    64.3%
  3. COMT P199P

    10.7%
  4. VDR Bsm

    67.9%
  5. VDR Taq

    82.1%
  6. MAO A R297R

    78.6%
  7. ACAT1- 02

    10.7%
  8. MTHFR C677T

    57.1%
  9. MTHFR 03 P39P

    21.4%
  10. MTHFR A1298C

    46.4%
  11. MTR A2756G

    25.0%
  12. MTRR

    85.7%
  13. BHMT 1, 02, 04, 08

    75.0%
  14. AHCY 01, 02, 19

    17.9%
  15. CBS C699T

    60.7%
  16. CBS A360A

    39.3%
  17. CBS N212N

    0 vote(s)
    0.0%
  18. SHMT1 C1420T

    39.3%
  19. NOS D298E

    7.1%
  20. I do not have a SNP on the methylation pathway

    0 vote(s)
    0.0%
Multiple votes are allowed.
  1. Soundthealarm21

    Soundthealarm21 Senior Member

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    I think it would do some good to see the commonalities of SNPs within the ME/CFS community. Unfortunately, There is not enough room to put all of the SNPs as options. I condensed the MTRR SNPs to one because there are so many of them. So just vote yes if you have ANY one of them

    If there is a big one that I've missed post it in the comments. Let's see if we can identify some common SNPs that correlate to certain symptoms, treatments, etc.
     
    MeSci and JAH like this.
  2. taniaaust1

    taniaaust1 Senior Member

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    with this poll does anyone know if one can post of some but then edit it later to add more of them in? Right now I dont know the full of what some of mine are, thou know some of the others? eg I dont remember the full thing of my COMT and CBS mutations to know which exactly they are.

    One which Im getting very interested in is the VDR Tag.. its seems rare to see any of us who have our results at the bottom of our posts, not to have this mutation. (I want to know what percent of the normal population carries this mutation so we could maybe compare it).
    ..........

    Valentijin? (or Valentjin?) has put lots of our results onto a spread sheet for comparsion and has been comparing it with a control group of non ME/CFS people and if you are interested in this I suggest to contact him/her (darn brain, sorry Valentijn).. suggest contact him/her anyway if you have ME so your results can be added to it (he's? done a program which pulls out all the more uncommon mutations we have so we can look at those too).. There is a comparison thread somewhere.
     
    Last edited: Jan 5, 2014
    Soundthealarm21 and Valentijn like this.
  3. Soundthealarm21

    Soundthealarm21 Senior Member

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    A big one i'm noticing, thought not with you @taniaaust1 , is BHMT which is the pathway along which phosphatdylcholine is made. Cellular membrane brain health is HUGE.

    Can't say I know an absolute ton about the VDR SNPs other than i'm hetero for both.
     
  4. Valentijn

    Valentijn Activity Level: 3

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    @Soundthealarm21 , @taniaaust1 :

    Here's an excel spreadsheet of results from 11 ME/CFS patients and 11 controls. Orange is homozygous for the Yasko risk (I disagree regarding several) and yellow is heterozygous (usually having little or no impact on functioning, with a couple exceptions). The top 6 are partitioned off and not included in calculations, as they are not directly impacting methylation, but rather are used to determine the impact of supplementing additional methyl groups.

    Missense mutations are in red type. The bolded/underlined/italicized results under VDR indicate a mismatch between Bsm and Taq, which are almost always identical, and may possibly cause big problems when they aren't.

    yasko.gif

    MTHFR status actually looks better in these ME/CFS patients than it does in these controls. However, there are 7 more homozygous results for ME/CFS patients overall, most of which (5) come from MTR and MTRR SNPs. SHMT1 also shows more risky alleles for ME/CFS patients versus controls. I'll try to take a closer look at additional MTR and MTRR SNPs in the next day or two, since there are a lot more relevant ones not listed above.
     
    Radio, taniaaust1, SOC and 3 others like this.
  5. Valentijn

    Valentijn Activity Level: 3

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    It also just occurred to me to count homozygous mutations based on whether or not they're missense mutations, since missense mutations tend to have much more of an impact. ME/CFS patients have 10 methylation missense mutations, versus 5 for controls.

    And 23 heterozygous missense mutations for the ME/CFS patients, versus 26 for controls.
     
    merylg likes this.
  6. Helen

    Helen Senior Member

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    @Soundthealarm21
    Good idea, but shouldn´t a ME/CFS diagnose, according to the Canada criterias, be a must for voting?
     
    Last edited: Jan 6, 2014
    taniaaust1 likes this.
  7. Thinktank

    Thinktank Senior Member

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    Europe + South East Asia
    My snips:
    +/-
    VDR bsm, taq
    MTHFR C677T, 03P39P, A1298C
    MTRR A66G, A664A
    BHMT 1, 02, 04, 08
    SHMT1 C1420T

    Still figuring out how to address the BHMT...

    @Soundthealarm21, what are you taking for BHMT?
     
  8. MeSci

    MeSci ME/CFS since 1995; activity level 6

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    Cornwall, UK
    Great idea - I had wondered whether anyone had collated the data that people had been posting!

    Unfortunately I haven't had all the listed genes tested as I didn't use the same company as most of you (I took advantage of a free gene test in 2007) so I hope my results don't skew things.

    I also had some done that aren't on your list, and don't know if they are relevant but I will list them below:

    ACE Insertion/Deletion
    eNOS/NOS3 G894T
    GSTM1 Present/Deletion
    GSTP1 A313G
    GSTP1 C341T
    IL-6 G(-174)C
    PPARγ2 Pro12Ala
    TNF-α G(-308)A
    VDR Fok
     
    Soundthealarm21 likes this.
  9. Valentijn

    Valentijn Activity Level: 3

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    Here's a spreadsheet of rare and known problematic MTR and MTRR mutations, for 11 ME/CFS patients and 11 controls. A red box indicates prevalence of that genotype is 1-2.5% in the general population, orange is 2.5-5%, and yellow is 5-10%. Known problematic genotypes (downregulations) are underlined, bolded, and italicized.

    MTR-MTRR.gif

    So 10 orange and red (1 - 5%) genotypes for the ME/CFS patients versus 3 orange and 1 red for the controls. And 17 known problematic homozygous mutations for the ME/CFS patients versus 8 for controls.

    It also breaks down as 8 rare problematic MTRR mutations for ME/CFS patients versus 3 for controls. And 3 rare problematic MTR mutations for ME/CFS patients versus 2 for controls.

    There's also 8 problematic MTRR and MTR missense mutations for ME/CFS patients versus 4 for controls.
     
    taniaaust1, SOC, MeSci and 2 others like this.
  10. MeSci

    MeSci ME/CFS since 1995; activity level 6

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    According to my results from Scion/Cellf, 70.6% of the general population have the VDR Taq (rs731236) variation. This CDC page gives a breakdown by race for Americans and has links for variation frequency by age and sex.
     
    taniaaust1 and madietodd like this.
  11. Soundthealarm21

    Soundthealarm21 Senior Member

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    Dallas, TX
    I guess there's no real way to monitor that unfortunately. Hopefully there will be these kinds of studies done by researchers in the future, but for now we'll have to settle with this poll.
     
  12. Soundthealarm21

    Soundthealarm21 Senior Member

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    I'm still starting out on everything. Methylation is the last thing i'm doing. So far it's been diet, gut function/health, and cell membrane health.

    But, I do believe i'm already helping BHMT because I supplement with Phosphatdylcholine daily and I eat a high fat diet. What else i'll do depends on my next doctor's visit which should be either next week or the following depending on when some test results come in.
     
  13. Soundthealarm21

    Soundthealarm21 Senior Member

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    @Radio just posted a study http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3195227/ that talks quite a bit about TNF Alpha and PPAR Gamma though I must say I'm not quite sure I understand them as well as I'd like. What did these results tell you/your doctor?
     
  14. MeSci

    MeSci ME/CFS since 1995; activity level 6

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    Had a quick look at that study. The TNF Alpha stuff seems to be predominantly about
    mice, and I couldn't see anything about PPAR Gamma.

    No point going to a UK doctor about genetic results - waste of time. Info from
    Scion/CellF and Nutrametrix says:

    • ACE deletion in intron 16: bp increase; alterations in levels of total cholesterol and plasma triglycerides; reduction in insulin sensitivity. Advice: exercise, reduce carbs, correct BMI.
    • eNOS G894T: less nitric oxide, so less smooth muscle relaxation; reduced platelet activity. Advice: increase omega-3 intake.
    • GSTM1 deleted: compromised Phase II detoxification and antioxidant activity.
    • GSTP1 A313G and C341T: reduced AO/detox activity.
    • IL-6 G(-174)C but not G(-634)C: increased inflammation but less than if both variations present; undefined implications for heart/cardiovascular health and bone; presumably reduced insulin sensitivity as listed in insulin sensitivity results section as well.
    • PPARγ2 Pro12Ala: associated with lower BMI, improved insulin sensitivity and higher HDL levels - I like this one! :)
    • TNF-α G(-308)A: poss. excess inflammation due to increased levels/activity; undefined implications for heart/cardiovascular health and bone health; presumably reduced insulin sensitivity as listed in insulin sensitivity results section as well
    • VDR Fok1: reduced calcium absorption due to reduced Vitamin D response
     
    taniaaust1 likes this.
  15. Soundthealarm21

    Soundthealarm21 Senior Member

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    I wasn't a fan of the UK doctors when I was there a little less than a year ago for study abroad. It was when my crash happened. It manifested with very severe panic attacks, depression, insomnia, burning ring sensation in my head (I'm assuming brain inflammation), barely being able to walk without completely losing my breath, etc. They wouldn't give me any benzos even though I told them that benzos were the most helpful thing I had tried up to that point (before I knew what I do know now about the things I take for anxiety) and told me to go to therapy. Yeah, definitely not a good experience. (This was before I knew anything about CFS or what was happening).

    I swear I was reading a study in the last couple days that mentioned PPAR gamma. I'll have a look back and see if I can find it. Well, you've got one thing going for you in terms of insulin sensitivity but the other genes seem to knock that down! Lots of genes contradicting each other!
     
  16. MeSci

    MeSci ME/CFS since 1995; activity level 6

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    Sorry if you've said this somewhere, but why are some SNPs bolded and marked with asterisks?
     
  17. SOC

    SOC Senior Member

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    @Valentijn

    I didn't see my data in your chart. Am I not in it, is there an error, or is it an interpretation issue?
    According to Genetic Genie, I'm homzygous for
    MAO A R297R rs6323 TT

    BHMT-08 rs651852 TT

    CBS A360A rs1801181 AA

    I don't see a patient with that combo in your first chart.

    ETA: I also just noticed that your patient group is predominantly female and your control group is predominantly male (I think :confused:). I wonder what effect that has on interpretation.
     
  18. Valentijn

    Valentijn Activity Level: 3

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    Your data is on the new chip with a lot of additional and missing RS numbers compared to the other sets I have, so I can't just cut and paste it into a new column on my Gigantor Excel Spreadsheet of Genetic Doom. Adding your data in one cell at a time for each gene I look at would be very time consuming and impractical.

    And I can't just merge the data, since I can't get full list of the old chip + the new chip into the same column for sorting - Excel is limited to not much over 1,000,000 rows, and I'd need 1,500,000+ to get both sets onto the same column for merging. So pending me figuring out how to merge your data in with the rest, it's not being included currently :oops:
     
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  19. Valentijn

    Valentijn Activity Level: 3

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    Not much ... the only differences would be on the X chromosome, and it's not one that I end up looking at often. Basically the guys are just homozygous for everything :lol:
     
    SOC likes this.
  20. Sea

    Sea Senior Member

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    @Valentijn I don't see mine there either. I'm homozygous for two COMT but the rest of that column isn't me
     

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