Genetic Results, and Organic Acid Test?

[D:Leo333]

Hi All..
Newbie here. I wanted to ask a few questions. I wanted to ask for any insights, help, as I learn more and more of genetics. I wanted to ask if someone could possible help me to marry the organic acid test, with genetic results. Which markers connect to possible snps. Im still learning about snps, methylation etc. It's all new. The Organic Acid test from Great Plains, gives lots of details on the report, what to take to help, but I'm just trying to put the puzzle together with the genetic snp.

A short summary of the report states : reveals the inability to metabolize the proteins leucine, lysine, tryptophan, hydroxylysine due to enzyme deficiencies, mitochondrial dysfunction, and bacterial overgrowth. Adrenal fatigue and low serotonin levels are suspected.

Test result ------------------------ Possible Indications
Slightly High Glyceric -- -- Genetic marker
Slightly High Oxalic -----Excess oxalates
High Fumaric -----Mitochondrial dysfunction
High 3-Methylglutaric ------Leucine metabolism/mitochond
Slightly High 3-Hydroxyglutaric -----Glutaryl CoA deficiency
Slightly High 3-Methylglutaconic -----Leucine metab/mitochon
Slightly Low Vanillylmandelic (VMA) ------Adrenal fatigue
High HVA/VMA Ratio -------Adrenal fatigue
Slightly Low 5-Hydroxyindoleacetic (5-HIAA) -------Slightly low serotonin
High Quinolinic/5-HIAA Ratio -------Adrenal fatigue/tryptophan
High Uracil ------Folic acid deficit
High 3-Hydroxybutyric ------Protein malnutrition/B12
High Acetoacetic ------Protein malnutrition/B12
High Adipic ------Gelatin/”junk food” additive
Slightly High Suberic -----Ketogenic diet
Low Pyridoxic (B6) -----Low vitamin B6
Slightly Low Pantothenic (B5) -----Slightly low vitamin B5
Slightly Low Ascorbic ------Slightly low vitamin C
Low N-Acetylcysteine (NAC) ------Low NAC-antioxidant
High 2-Hydroxybutyric -------Enzyme deficit
Slightly High 2-Hydroxyhippuric -------Aspirin/aspartame

Now my genetic results from the Yasko website were :
RS4680 COMT V158M +/-
RS4633 COMT H62H +/-
RS731236 VDR Taq TT
RS2228570 VDR Fok ff
RS6323 MAO A R297R +/+
RS1801133 MTHFR C677T +/-
RS1805087 MTR A2756G +/+
RS567754 BHMT 2 +/+
RS651852 BHMT 8 +/-
RS234706 CBS C699T +/-
RS1801181 CBS A360A +/-

However the longer more detailed report I received from a different source, does not show the VDR Fok, or Taq TT. Shows normal. I have read about this, find it a bit confusing...

But another snp that wasnt tested from the Yasko site was the NOS snp, which was

NOS2 (rs2297518) +/+
NOS2 (rs2274894) +/+
NOS2 (rs2248814) +/+
NOS3 (rs1800779) +/+
NOS3 (rs3918188) +/-
NOS3 D298E (rs1800783) +/+

Im still learning so Im not sure which is most significant. I also had many ACAT ++, etc. But I guess the ones Yasko lists are more significant etc.

Alright, any puzzle piecing would be appreciated.

 

[Valentijn]

However the longer more detailed report I received from a different source, does not show the VDR Fok, or Taq TT. Shows normal. I have read about this, find it a bit confusing...

Yasko reports one of two basically identical VDR SNPs backwards, so everyone will be +/+ for one, or +/- for both.

But I guess the ones Yasko lists are more significant etc.

No, she lists a lot that don't do anything, or are even slightly beneficial.

 

[D:Leo333]

Thanks. Anyone else with knowledge about the organic acid test + genetics?

 

[alicec]

if someone could possible help me to marry the organic acid test, with genetic results. Which markers connect to possible snps.

There is no direct connection. At best some SNPs may be making a small contribution but the OAT markers reflect the end point of complex metabolic pathways which are influenced by many factors.

Some alternative/additional interpretation of the OAT markers you list.

Elevated glyceric indicates problems with endogenous oxalate production. On very rare occasions this is indeed the result of genetic defects in the relevant enzyme but far more often it reflects an acquired problem with processing of oxalate precursors.

Here and here are threads which discuss some aspects of oxalates.

Elevated 3 OH glutaric. You almost certainly do not have the rare genetic defect of glutaryl CoA deficiency. This marker probably reflects the poor mitochondrial function indicated by several other markers in your test.

Low VMA, high HVA/VMA. This just reflects low conversion of dopamine to noradrenaline which in turn could reflect things like low copper and/or ascorbic acid. The high ratio just reflects the low VMA.

Low 5H1AA, particularly in conjunction with low VMA, could reflect problems with BH4, a common cofactor. The high quinolinic/5HIAA just reflects the low 5HIAA.

Elevated 3 OH butyric and acetoacetic reflect ketosis.

Elevated adipic and suberic reflect problems with fatty acid oxidation - could be lack of B2, carnitine or both.

High 2 OH butyric reflects increased metabolism down the transsulfuration pathway. The body is trying to make more glutathione - ie oxidative stress is present. This would be consistent with oxalate and B6 issues shown in your test.

 

[Journeyman]

Hi All..
Newbie here. I wanted to ask a few questions. I wanted to ask for any insights, help, as I learn more and more of genetics. I wanted to ask if someone could possible help me to marry the organic acid test, with genetic results. Which markers connect to possible snps. Im still learning about snps, methylation etc. It's all new. The Organic Acid test from Great Plains, gives lots of details on the report, what to take to help, but I'm just trying to put the puzzle together with the genetic snp.

A short summary of the report states : reveals the inability to metabolize the proteins leucine, lysine, tryptophan, hydroxylysine due to enzyme deficiencies, mitochondrial dysfunction, and bacterial overgrowth. Adrenal fatigue and low serotonin levels are suspected.

Test result ------------------------ Possible Indications
Slightly High Glyceric -- -- Genetic marker
Slightly High Oxalic -----Excess oxalates
High Fumaric -----Mitochondrial dysfunction
High 3-Methylglutaric ------Leucine metabolism/mitochond
Slightly High 3-Hydroxyglutaric -----Glutaryl CoA deficiency
Slightly High 3-Methylglutaconic -----Leucine metab/mitochon
Slightly Low Vanillylmandelic (VMA) ------Adrenal fatigue
High HVA/VMA Ratio -------Adrenal fatigue
Slightly Low 5-Hydroxyindoleacetic (5-HIAA) -------Slightly low serotonin
High Quinolinic/5-HIAA Ratio -------Adrenal fatigue/tryptophan
High Uracil ------Folic acid deficit
High 3-Hydroxybutyric ------Protein malnutrition/B12
High Acetoacetic ------Protein malnutrition/B12
High Adipic ------Gelatin/”junk food” additive
Slightly High Suberic -----Ketogenic diet
Low Pyridoxic (B6) -----Low vitamin B6
Slightly Low Pantothenic (B5) -----Slightly low vitamin B5
Slightly Low Ascorbic ------Slightly low vitamin C
Low N-Acetylcysteine (NAC) ------Low NAC-antioxidant
High 2-Hydroxybutyric -------Enzyme deficit
Slightly High 2-Hydroxyhippuric -------Aspirin/aspartame

Now my genetic results from the Yasko website were :
RS4680 COMT V158M +/-
RS4633 COMT H62H +/-
RS731236 VDR Taq TT
RS2228570 VDR Fok ff
RS6323 MAO A R297R +/+
RS1801133 MTHFR C677T +/-
RS1805087 MTR A2756G +/+
RS567754 BHMT 2 +/+
RS651852 BHMT 8 +/-
RS234706 CBS C699T +/-
RS1801181 CBS A360A +/-

However the longer more detailed report I received from a different source, does not show the VDR Fok, or Taq TT. Shows normal. I have read about this, find it a bit confusing...

But another snp that wasnt tested from the Yasko site was the NOS snp, which was

NOS2 (rs2297518) +/+
NOS2 (rs2274894) +/+
NOS2 (rs2248814) +/+
NOS3 (rs1800779) +/+
NOS3 (rs3918188) +/-
NOS3 D298E (rs1800783) +/+

Im still learning so Im not sure which is most significant. I also had many ACAT ++, etc. But I guess the ones Yasko lists are more significant etc.

Alright, any puzzle piecing would be appreciated.

Hi Leo,

You're certainly getting off on the right foot by getting both 23&Me and the OAT. I had my 23&Me done years ago and am just now doing the OAT tests...
In any event I want to give you a quick summation of your SNP's and I'm by no means an expert, but I'm sure this will help get you started:

If I'm not mistaken your VDR TAQ result came up as red on the genetic genie interpretaiton? If so it basically means you're predisposed to having low Dopamine levels, which is quite bizarre considering your OAT results that indicate excessive dopamine, or at least an excess of DA relative to NA (Norepinephrine) so if you were looking to 'normalise' this you might consider a Vit D supplement, however I think you'll need the advice of someone expert in OAT interpretation to reconcile this SNP with your OAT result and its high DA levels.... They might, for example, indicate that you have high 'body' dopamine but low neurological levels of it where it affects behaviour etc.

Theres actually a SNP you might be interested in that might also explain this high DA level in spite of the VDR TAQ homozygous mutant. That is; the SNP http://snpedia.com/index.php/Rs1611115 for Dopamine Beta Hydroxylase. (DBH) This is the enzyme responsible for converting DA to NE and as far as I'm aware its the single pathway available to the body..

You and I have near identical folate metabolism SNP's (MTHFR/MTR) though you're homozygous for MTR which iirc means you're body has trouble recycling B12??? Perhaps someone can confirm this?

We have identical COMT SNP's and afaik it means we're in the middle in terms of our minds tendency to breakdown dopamine once its created (COMT is the enzyme that breaks it down and by having the heterozygous mutation the enzyme activity is reduced meaning whatever DA gets created hangs around longer) and COMT is responsible for estrogen breakdown (including xenoestrogens??) so you might want to start eating more cruciferous vegetables which seem a great natural way to detox estrogens from the body.

I look forward to seeing further regarding the interpretation of your OAT... particularly if you have that same Vit D receptor mutation (VDR TAQ) that I have (seems fairly rare) and I'll be posting my results soon too with any luck...

 

[Valentijn]

I look forward to seeing further regarding the interpretation of your OAT... particularly if you have that same Vit D receptor mutation (VDR TAQ) that I have (seems fairly rare) and I'll be posting my results soon too with any luck...

VDR Taq "+/+" is actually the more common SNP and not associated with any negative effects. Yasko reports it backwards. But in any event, VDR Taq/VDR Bsm have a very minor impact. It's unlikely they would have a substantial impact upon dopamine or anything else.