Post Orgasmic Illness Syndrome (P.O.I.S.)

General Category => POIS Research => Topic started by: Prospero on January 25, 2021, 12:43:31 PM

Title: Genetic profile results
Post by: Prospero on January 25, 2021, 12:43:31 PM
Hi,

As some people shared parts of their genetic profile regarding methylation and detox, Muon asked me to gather them in a single thread - so here it is.

Please notice that these are really incomplete results and a very little part of our genes. Moreover, many of the gene polymorphisms highlighted here are very common. I guess that interpreting these results in terms of their concrete consequences on health is not an easy task for any of us. It would also certainly be interesting to look to the genes for other issues than methylation and detox.

Methylation results :

COMT V158M rs4680 : 2 +/+ (Prospero, Muon's brother), 5 +/- (CuriousCharacter, Berlin1984, drop247, Iwillbeatthis, rollercoaster), 1 -/- (Kurtosis)
COMT H62H   rs4633 : (always the same as the previous one)
COMT P199P   rs769224 : 4 -/- (Kurtosis, Berlin1884, Iwillbeatthis, rollercoaster)

VDR Bsm   rs1544410 : 2 +/+ (CuriousCharacter, rollercoaster), 1 +/- (Kurtosis), 4 -/- (Prospero, Iwillbeatthis, Berlin1984, drop247)
VDR Taq   rs731236 : 4 +/+ (Prospero, Iwillbeatthis, Berlin1984, drop247), 1 +/- (Kurtosis), 2 -/- (CuriousCharacter, rollercoaster)

MAO A R297R   rs6323 : 2 + (Kurtosis, Iwillbeatthis), 1 - (Berlin1984)

ACAT1-02   rs3741049 : 1 +/- (Iwillbeatthis), 2 -/- (Kurtosis, Berlin1984)

MTHFR C677T   rs1801133 : 3 +/- (Kurtosis, Prospero, drop247), 5 -/- (swell, Berlin1984, Iwillbeatthis, CuriousCharacter, rollercoaster)
MTHFR 03 P39P   rs2066470 : 1 +/- (Iwillbeatthis), 2 -/- (Kurtosis, Berlin1984)
MTHFR A1298C   rs1801131 : 1 +/+ (Iwillbeatthis), 5 +/- (Kurtosis, Prospero, Berlin1984, swell, CuriousCharacter), 2 -/- (drop247, rollercoaster)

MTR A2756G   rs1805087 : 1 +/- (Prospero), 5 -/- (Kurtosis, Berlin1984, Iwillbeatthis, drop247, rollercoaster)

MTRR A66G   rs1801394 : 3 +/+ (Prospero, swell, rollercoaster), 5 +/- (Kurtosis, CuriousCharacter, Berlin1984, drop247, Iwillbeatthis)
MTRR H595Y   rs10380 : 1 +/- (Kurtosis), 1 -/- (Iwillbeatthis)
MTRR K350A   rs162036 : 2 +/- (Kurtosis, Berlin1984), 3 -/- (drop247, Iwillbeatthis, rollercoaster)
MTRR R415T   rs2287780 : 5 -/- (Kurtosis, Iwillbeatthis, drop247, Prospero, rollercoaster)
MTRR A664A   rs1802059 : 2 +/- (Kurtosis, Iwillbeatthis), 1 -/- (Berlin1984)

BHMT-02   rs567754 : 1 +/+ (Berlin1984), 1 +/- (Prospero), 4 -/- (Kurtosis, Iwillbeatthis, drop247, rollercoaster)
BHMT-04   rs617219 : 2 -/- (Kurtosis, Iwillbeatthis)
BHMT-08   rs651852 : 1 +/+ (Berlin1984), 1 +/- (Kurtosis)

AHCY-01   rs819147 : 1 +/- (Kurtosis), 1 -/- (Berlin1984)
AHCY-02   rs819134 : 1 +/- (Kurtosis)
AHCY-19   rs819171 : 1 +/- (Kurtosis), 1 -/- (Berlin1984)

CBS C699T   rs234706 : 4 +/- (Kurtosis, Prospero, Iwillbeatthis, rollercoaster), 2 -/- (Berlin1984, drop247)
CBS A360A   rs1801181 : 2 +/- (Kurtosis, Berlin1984), 1 -/- (Iwillbeatthis)
CBS N212N   rs2298758 : 2 -/- (Kurtosis, Iwillbeatthis)

SHMT1 C1420T   rs1979277 : 1 +/+ (Prospero), 1 +/- (Kurtosis), 2 -/- (drop247, rollercoaster)


Detox results :

CYP1A1*2C A4889G   rs1048943 : 2 -/- (Berlin1984, Iwillbeatthis)
CYP1A1 m3 T3205C   rs4986883 : 2 -/- (Berlin1984, Iwillbeatthis)
CYP1A1 C2453A   rs1799814 : 4 -/- (Prospero, Berlin1984, Iwillbeatthis, rollercoaster)
CYP1A2 164A>C   rs762551 : 3 +/- (Berlin1984, Iwillbeatthis, rollercoaster), 1 -/- (Prospero)
CYP1B1 L432V   rs1056836 : 3 +/+ (Prospero, Iwillbeatthis, rollercoaster), 1 +/- (Berlin1984)
CYP1B1 N453S   rs1800440 : 2 -/- (Berlin1984, Iwillbeatthis)
CYP1B1 R48G   rs10012 : 1 +/- (Berlin1984)

CYP2A6*2 1799T>A rs1801272 : 1 +/- (Iwillbeatthis), 1 -/- (Berlin1984)
CYP2A6*20 rs568811809 : 2 -/- (Berlin1984, Iwillbeatthis)
CYP2C9*2 C430T   rs1799853 : 1 +/- (Iwillbeatthis), 3 -/- (Prospero, Berlin1984, rollercoaster)
CYP2C9*3 A1075C   rs1057910 : 4 -/- (Prospero, Berlin1984, Iwillbeatthis, rollercoaster)
CYP2C19*17   rs12248560 : 1 +/- (Iwillbeatthis), 3 -/- (Prospero, Berlin1984, rollercoaster)
CYP2D6 S486T rs1135840 : 2 +/+ (Berlin1984, Iwillbeatthis)
CYP2D6 100C>T rs1065852 : 1 +/- (Berlin1984)
CYP2D6 2850C>T rs16947 : 1 +/- (Berlin1984)

CYP2E1*1B 9896C>G   rs2070676 : 1 +/- (Prospero), 3 -/- (Berlin1984, Iwillbeatthis, rollercoaster)
CYP2E1*1B 10023G>A rs55897648 : 2 -/- (Berlin1984, Iwillbeatthis)
CYP2E1*4 4768G>A   rs6413419 : 4 -/- (Prospero, Berlin1984, Iwillbeatthis, rollercoaster)

CYP3A4*1B   rs2740574 : 4 -/- (Prospero, Berlin1984, Iwillbeatthis, rollercoaster)
CYP3A4*2 S222P   rs55785340 : 4 -/- (Prospero, Berlin1984, Iwillbeatthis, rollercoaster)
CYP3A4*3 M445T   rs4986910 : 3 -/- (Prospero, Berlin1984, rollercoaster)
CYP3A4*16 T185S   rs12721627 : 4 -/- (Prospero, Berlin1984, Iwillbeatthis, rollercoaster)

GSTP1 I105V   rs1695   : 1 +/+ (Iwillbeatthis), 1 +/- (rollercoaster), 2 -/- (Prospero, Berlin1984)
GSTP1 A114V   rs1138272 : 4 -/- (Prospero, Berlin1984, Iwillbeatthis, rollercoaster)

SOD2 A16V   rs4880   : 2 +/+ (Prospero, Iwillbeatthis), 1 +/- (rollercoaster), 1 -/- (Berlin1984)

NAT1 R187Q   rs4986782 : 4 -/- (Prospero, Berlin1984, Iwillbeatthis, rollercoaster)
NAT1 R64W   rs1805158 : 4 -/- (Prospero, Berlin1984, Iwillbeatthis, rollercoaster)

NAT2 I114T   rs1801280 : 2 +/+ (Iwillbeatthis,rollercoaster), 1 +/- (Berlin1984), 1 -/- (Prospero)
NAT2 R197Q   rs1799930 : 1 +/- (Prospero), 3 -/- (Berlin1984, Iwillbeatthis, rollercoaster)
NAT2 G286E   rs1799931 : 4 -/- (Prospero, Berlin1984, Iwillbeatthis, rollercoaster)
NAT2 R64Q   rs1801279 : 4 -/- (Prospero, Berlin1984, Iwillbeatthis, rollercoaster)
NAT2 K268R   rs1208 : 3 +/+ (Berlin1984, Iwillbeatthis, rollercoaster), 1 -/- (Prospero)




Links to the personal profiles : Kurtosis (M) (https://poiscenter.com/forums/index.php?topic=820.msg8029#msg8029), Berlin1984 (M (https://poiscenter.com/forums/index.php?topic=2684.msg35819#msg35819), D (https://poiscenter.com/forums/index.php?topic=2684.msg37429#msg37429)), Drop247 (M (https://poiscenter.com/forums/index.php?topic=2684.msg35823#msg35823)), Iwillbeatthis (M (https://poiscenter.com/forums/index.php?topic=2684.msg37287#msg37287), D (https://poiscenter.com/forums/index.php?topic=2684.msg37288#msg37288)), Prospero (M, D) (https://poiscenter.com/forums/index.php?topic=2684.msg38803#msg38803), swell (M) (https://poiscenter.com/forums/index.php?topic=2728.msg34079#msg34079), CuriousCharacter (M) (https://poiscenter.com/forums/index.php?topic=2728.msg24633#msg24633), rollercoaster (M, D) (https://poiscenter.com/forums/index.php?topic=3694.msg42131#msg42131), Muon's brother (https://poiscenter.com/forums/index.php?topic=2545.msg38828#msg38828).
Iwillbeatthis' more complete profile. (https://poiscenter.com/forums/index.php?topic=2684.msg39266#msg39266)
Additional genetic information from Trusttheprocess: FOXP3, IL-12B, CD40 etc (https://poiscenter.com/forums/index.php?topic=2456.0)
Title: Re: Genetic profile results
Post by: Prospero on January 25, 2021, 12:57:09 PM
Reserved, for any practical purpose.
Title: Re: Genetic profile results
Post by: Prospero on January 25, 2021, 12:59:40 PM
Reserved 2.
Title: Re: Genetic profile results
Post by: berlin1984 on January 25, 2021, 03:22:03 PM
Thanks a lot for going through the effort!

What I find very interesting (we also had a poll about this here in the forum) that a lot of people in the forum are engineer/science/nerd type of guys. (No idea about the low number of female POISers we have, but would beinteresting too).

Could be a coincidence that people like us are more likely to visit this kind of forum, but could also be a genetic clue for something.
Title: Re: Genetic profile results
Post by: Muon on February 03, 2021, 03:26:04 PM
Thanks for the thread!
Title: Re: Genetic profile results
Post by: Muon on February 28, 2021, 06:23:55 PM
Attachment: FOXP3, IL-12B, CD40 etc: https://poiscenter.com/forums/index.php?topic=2456.0

https://poiscenter.com/forums/index.php?action=dlattach;topic=2456.0;attach=490;image
https://poiscenter.com/forums/index.php?action=dlattach;topic=2456.0;attach=488;image
Title: Re: Genetic profile results
Post by: Quantum on March 01, 2021, 11:47:34 AM
Thanks, Prospero !   I am sure it means a lot of work to create a compilation like this one.
I suppose not everyone is familiar with genetic polymorphisms results.  Could you confirm that, in your chart, a "+" means that the person has the allele that is less common, so that a +/+ means that this individual has 2 genes of the rarer variant ( homozygote SNP )?  Having the rarer variant/allele can potentially mean that a protein in this individual body and metabolism, like an enzyme, a cellular receptor, or another type of protein, is not functioning like in the majority of the human population, because one amino acid, which means one of the building blocks in the chain, is not the same.   A +/- means that one of the the 2 genes someone has for the same loci is the more common variant, and the other one is the rarer one. We all have 2 copies of all our genes, one copy from eahc of our parents. An heterozygote result usually has less impact on the individual's biology, but may be halfway between the common function for the majority of the population and those who have 2 copies of the rarer gene.

 A rarer variant is also called a SNP (Single Nucleotide Permutation), and is found in more than 1% of the population ( if the variant is rarer still, less than 1% , it is rather called a mutation ).
If what I have written above is in line with your notation, Prospero,  a  "-/-" result means that the individual has the more common allele/variant in both of his genes for this loci, for this particular location on a particular gene, so has likely the normal/usual function for whatever is coded by this gene.
A gene loci is usually named by a series of capitalized letters, like "COMT".  You can search these specific gene names on the net to know more about what is known about each one of them.
A "rs" followed by a serie of numbers, like "rs4680" is used to define a specific SNP.  It stands for Reference SNP cluster ID.  For example, rs4680 refers to a specific SNP found in the COMT gene.  It is also called COMT V158M, the V158M part referring to the amino acid change that this nucleotide permutation will produce ( I spare you all the details, but if you are interest in genetics, DNA structure, and how it encodes for amino acids and leads to proteins synthesis, you will surely find all the details over the net)
It is useful to know that all these SNPs can be searched with their rs ID,  There are great internet databases for that.  For example, you can search rs4680 on sites like snpedia.com. ( https://www.snpedia.com/index.php/SNPedia)  Of course, you can also make your search with COMT V158M and will also get the the right information.   You just have to get used to the fact that a single SNP can go by multiple names and types of notation.
Don't worry, if you are not familiar with biology and genetics, it is normal that, at first, all this information seems really confusing and hard to understand.  Just go slowly, and you can always use Wikipedia to search any individual term, and know more about it ( like, "SNP", "mutation", "gene"  "COMT", and even well known SNPs will have their own entry, like "rs4680" - https://en.wikipedia.org/wiki/Rs4680 )
Title: Re: Genetic profile results
Post by: Iwillbeatthis on March 01, 2021, 12:18:13 PM
Yeah I only realised a few days ago that Allele type is very important. Some allele variants are gain of function and others are loss of function depending on which allele is there.

So what I mean is that you can have some homozygous SNPs that are actually a good thing depending on whether the allele type is AA, TT, CC or GG. So just because you have a homozygous gene don't automatically assume it's bad check the scientific literature to see what your allele variant means.

Then you also have things called VNTR repeats that don't have a RS number which also have a big impact on gene function.
Title: Re: Genetic profile results
Post by: Prospero on March 01, 2021, 01:08:27 PM
Could you confirm that, in your chart, a "+" means that the person has the allele that is less common, so that a +/+ means that this individual has 2 genes of the rarer variant ( homozygote SNP )?
Yes.

Thank you for your specifications.
Title: Re: Genetic profile results
Post by: HeatherRaeINHC on March 18, 2021, 06:42:18 PM
I am a certified functional genomic analyst and health coach.  A new client presents with POIS, and that brings me to this forum.

The DNA test I use looks at over 200000 variants in the inflammation and detoxification pathways, beyond the common and usual suspects (COMT, MTHFR, ACHY).  This test uses a proprietary CHiP and is fulfilled at a lab at Rutgers in NJ.  The data is loaded into analytical software and, along with an organic acids test and signs/symptoms questionnaire, gives us very good insights into sources of inflammation.  We're looking at not only variants in enzymes (genes) but toxins and nutritional/biochemical imbalances.

For this client, in the enzymes/genes, I will be looking at several cycles of inflammation/detoxification (Krebs, methylation, sulfation, glucoronidation, urea  ...), the roots of his oxidative stress (hydroxyl radicals, hydrogen peroxide, peroxynitrite, etc), "mast cell activation"/histamine, NOS uncoupling, neurotransmitters, ammonia, and more. 

I suspect mold mycotoxins, and other toxins like glyphosate, aluminum, borrelia, are taking "hits" on my client's immune system (NADPH oxidase, NOX) and blocking detox pathways.

I highly recommend the book, "Toxic" by Dr. Neil Nathan who contributes to "my" research team at NGRI.  Chapter 16 describes our methodology.  My website has additional info, graphics, resources.
Title: Re: Genetic profile results
Post by: HeatherRaeINHC on March 18, 2021, 06:49:00 PM
about the "geek" factor ...  most of my clients are engineers, scientists, ITers; they are analytical, often type A and sensitive males.
I've attached some files (sample organic acids test), graphics of the inflammation pathways, a "zoom in" to the mast cell and histamine pathways.  I can look at the data in many ways. 
Title: Re: Genetic profile results
Post by: drop247 on March 18, 2021, 06:54:23 PM
Hi Heather and welcome to the forum. What kind of time frame are you expecting to have the results of your client's testing? I'd be interested to hear the results.
Title: Re: Genetic profile results
Post by: HeatherRaeINHC on March 18, 2021, 07:00:02 PM
Thanks a lot for going through the effort!

What I find very interesting (we also had a poll about this here in the forum) that a lot of people in the forum are engineer/science/nerd type of guys. (No idea about the low number of female POISers we have, but would beinteresting too).

Could be a coincidence that people like us are more likely to visit this kind of forum, but could also be a genetic clue for something.

GLUTAMATE (quite possibly, GAD genes, and others related)
Title: Re: Genetic profile results
Post by: Iwillbeatthis on March 18, 2021, 07:26:09 PM
I am a certified functional genomic analyst and health coach.  A new client presents with POIS, and that brings me to this forum.


Hi Heather

Does your client have a username on here? I'm interested to see if you are able to fix your clients POIS.

I have done an OAT test, genetic testing but I still find the results confusing, I've attached my results bellow.

Maybe my MAO A genes are causing issues with catecholamines in me?
Title: Re: Genetic profile results
Post by: Cosmic1982 on March 19, 2021, 12:42:21 AM
Hello,

You all seem very good with your knowledge of DNA, I havnt a clue when it comes to science and this question may seem like a stupid one for you all but if you find a link between DNA and the POIS what actions are necessary? Are you able to turn on and off certain DNA strains?
Title: Re: Genetic profile results
Post by: Drew1312 on March 19, 2021, 07:12:42 AM
I am a certified functional genomic analyst and health coach.  A new client presents with POIS, and that brings me to this forum.

The DNA test I use looks at over 200000 variants in the inflammation and detoxification pathways, beyond the common and usual suspects (COMT, MTHFR, ACHY).  This test uses a proprietary CHiP and is fulfilled at a lab at Rutgers in NJ.  The data is loaded into analytical software and, along with an organic acids test and signs/symptoms questionnaire, gives us very good insights into sources of inflammation.  We're looking at not only variants in enzymes (genes) but toxins and nutritional/biochemical imbalances.

For this client, in the enzymes/genes, I will be looking at several cycles of inflammation/detoxification (Krebs, methylation, sulfation, glucoronidation, urea  ...), the roots of his oxidative stress (hydroxyl radicals, hydrogen peroxide, peroxynitrite, etc), "mast cell activation"/histamine, NOS uncoupling, neurotransmitters, ammonia, and more. 

I suspect mold mycotoxins, and other toxins like glyphosate, aluminum, borrelia, are taking "hits" on my client's immune system (NADPH oxidase, NOX) and blocking detox pathways.

I highly recommend the book, "Toxic" by Dr. Neil Nathan who contributes to "my" research team at NGRI.  Chapter 16 describes our methodology.  My website has additional info, graphics, resources.

Hello!Can you tell us what symptoms does he have?
Title: Re: Genetic profile results
Post by: Quantum on March 19, 2021, 08:53:43 AM
Hello,

You all seem very good with your knowledge of DNA, I havnt a clue when it comes to science and this question may seem like a stupid one for you all but if you find a link between DNA and the POIS what actions are necessary? Are you able to turn on and off certain DNA strains?

It is a very good question, Cosmic!

Genomics can help you by giving you personalized information on your SNPs ( small DNA variations) that can lead to some lifestyle adjustments that will help raise your overall well-being.
For example, if you have a SNP with a risk allele ( the "bad" version") causing that a specific enzyme in your body is 60% less active, you can adjust depending on the biological function of this enzyme.  If, for example, the function of this enzyme is to digest a specific type of sugar, you will then avoid eating food containing that specific type of sugar.  You can also take as a supplement the vitamin or other substance that is a co-factor to this enzyme so that you help boost and support his level of activity.  If an alternative pathway is known for the digestion of this specific type of sugar, you can also help this other pathway with supplementing with the cofactors if this other pathway.
It will especially help if you do that for those SNPs for which you have 2 risk alleles on the same gene locus ( we have two copies of all our genes, one copy from each of our 2 parents).  If you happen, on a specific gene locus, to have 2 "bad" versions, risk alleles, then you have a homozygote, +/+ SNP, there, which usually creates more problems than a +/-, half-"bad" version ( one of your parents gave you the usual, "normal" version). 

Genomics is a young science, there is not useful and clear information for all SNPs, and for some, you will not find anything.  But new information is adding each month in the databases. Apart from accumulating good information, another current challenge is to detect the cumulative effect of many different +/- and +/+ SNPs, and find the specific bad effects of a certain specific combination of SNPs

My opinion is that POIS is possibly caused by the cumulative effect of many SNPs.   I also think that all POISers do not all have the exact same kit of risky SNPs, but similar enough to display similar sets of symptoms.  Like I have written already, I think there is more than one type of POIS.  this is reflected in my POIS Types Chart, and their possible relief methods ( see https://poiscenter.com/forums/index.php?topic=2338.msg19448#msg19448 (https://poiscenter.com/forums/index.php?topic=2338.msg19448#msg19448) ).  This would explain why some members get relief from a specific elimination diet, some others from of methylation support, and so on.  It depends on their specific SNPs, leading to specific metabolic problems.

If, let's say, it takes 50 to 80 different risky SNPs to cause POIS, maybe that 30 of them are common to most POIS sufferers, and the other SNPs would account for the different types of POIS ( of course, this is a very speculative hypothesis, it will take many, many years to see if this is the case or not). 

Anyway, I suppose that all those complex syndromes that evade detection by simple blood tests or standard exams will benefit from genomics research.
Title: Re: Genetic profile results
Post by: HeatherRaeINHC on March 19, 2021, 09:30:21 AM
Genomics is a new science, but I think of it as more an art, this identifying root causes of health conditions and how to heal from them.  Many people are so sick that even a whiff of quercetin can make them sicker.  There is no 'cookie cutter' solution.
It really isn't helpful to name/diagnose a dysfunction/disease and work backward into an explanation in order to reverse the condition, though it does help in finding community :)
Genetic variants plus toxins plus nutritional deficiencies plus gut micriobiota imbalances plus poor vagal tone manifest differently in each person.   My client exhibits symptoms of POIS (post-coital fatigue, irritability, brain fog).

Genomics is about far more than diet and food.  It's about inflammation, detoxification which are at the root of chronic health conditions.  It's a powerfully female story. The DNA in the mitochondria, where energy is made, come from your mother only; so for some genes, whether heterozygous or homozygous for a variant, they come from your mother.   

This recent conference addressed the complexity of functional health and healing:
https://forumforintegrativemedicine.org/#front-page-2
I direct clients to MyMedLab where they can order tests themselves (organic acids, glyphosate, heavy metals, mycotoxins, pesticides etc), residential/building mold testing/remediation. 

Voltage is vastly ignored in America; Germans and Russians are far ahead in therapies/treatments using electrical frequencies (we are electromagnetic beings ... eventually, that's where the conversation ends up.)  For energy medicine, see James Oschman's "Energy Medicine" 2nd edition).

I can't offer advice/insights here for individuals.  It takes me hours to analyze the data and work though it with clients.  Software helps!

In short, I look for ways to better "express" my clients' genes:  remove toxins, bolster microbiome, immunity through diet and supplementation, balance the autonomic nervous system.  Therapies will include micro-frequency currents, osteo/chiro manipulations, EFT and whatever the client is open to trying/works for them.
Title: Re: Genetic profile results
Post by: Muon on March 19, 2021, 10:07:13 AM
It's a powerfully female story. The DNA in the mitochondria, where energy is made, come from your mother only; so for some genes, whether heterozygous or homozygous for a variant, they come from your mother.

That could explain the dominance of women presenting health conditions in my family. The concept of resonance frequencies is barely investigated in medical research.
Title: Re: Genetic profile results
Post by: Hopeoneday on March 19, 2021, 03:37:00 PM
Hi, HeatherRaeINHC, we hawe some medical data colected in medical test results treed too.


   
Title: Re: Genetic profile results
Post by: berlin1984 on March 20, 2021, 04:00:54 PM
HeatherRaeINHC, welcome to forum.

Genetic variants plus toxins plus nutritional deficiencies plus gut micriobiota imbalances plus poor vagal tone manifest differently in each person.   

Yes. Finding a single root cause is futile. We (each person individually) need to attack on many angles and find a way to be feeling good enough to make orgasm after effects bearable.

(And the crazy goal of "being able to masturbate 5 times per day without symptoms" is not healthy to be achieved. It's not normal)
Title: Re: Genetic profile results
Post by: Cosmic1982 on March 24, 2021, 03:04:31 AM
Hello,

You all seem very good with your knowledge of DNA, I havnt a clue when it comes to science and this question may seem like a stupid one for you all but if you find a link between DNA and the POIS what actions are necessary? Are you able to turn on and off certain DNA strains?

It is a very good question, Cosmic!

Genomics can help you by giving you personalized information on your SNPs ( small DNA variations) that can lead to some lifestyle adjustments that will help raise your overall well-being.
For example, if you have a SNP with a risk allele ( the "bad" version") causing that a specific enzyme in your body is 60% less active, you can adjust depending on the biological function of this enzyme.  If, for example, the function of this enzyme is to digest a specific type of sugar, you will then avoid eating food containing that specific type of sugar.  You can also take as a supplement the vitamin or other substance that is a co-factor to this enzyme so that you help boost and support his level of activity.  If an alternative pathway is known for the digestion of this specific type of sugar, you can also help this other pathway with supplementing with the cofactors if this other pathway.
It will especially help if you do that for those SNPs for which you have 2 risk alleles on the same gene locus ( we have two copies of all our genes, one copy from each of our 2 parents).  If you happen, on a specific gene locus, to have 2 "bad" versions, risk alleles, then you have a homozygote, +/+ SNP, there, which usually creates more problems than a +/-, half-"bad" version ( one of your parents gave you the usual, "normal" version). 

Genomics is a young science, there is not useful and clear information for all SNPs, and for some, you will not find anything.  But new information is adding each month in the databases. Apart from accumulating good information, another current challenge is to detect the cumulative effect of many different +/- and +/+ SNPs, and find the specific bad effects of a certain specific combination of SNPs

My opinion is that POIS is possibly caused by the cumulative effect of many SNPs.   I also think that all POISers do not all have the exact same kit of risky SNPs, but similar enough to display similar sets of symptoms.  Like I have written already, I think there is more than one type of POIS.  this is reflected in my POIS Types Chart, and their possible relief methods ( see https://poiscenter.com/forums/index.php?topic=2338.msg19448#msg19448 (https://poiscenter.com/forums/index.php?topic=2338.msg19448#msg19448) ).  This would explain why some members get relief from a specific elimination diet, some others from of methylation support, and so on.  It depends on their specific SNPs, leading to specific metabolic problems.

If, let's say, it takes 50 to 80 different risky SNPs to cause POIS, maybe that 30 of them are common to most POIS sufferers, and the other SNPs would account for the different types of POIS ( of course, this is a very speculative hypothesis, it will take many, many years to see if this is the case or not). 

Anyway, I suppose that all those complex syndromes that evade detection by simple blood tests or standard exams will benefit from genomics research.



That's a fascinating read, thank you for giving the time to explain the genome and snp. It does make alot of sense, I have managed to reduce my recovery rate down to 3 weeks now by supplementing and changing my diet. I just wish it would completely go.

Thanks again.
Neil
Title: Does anyone known what post i m talking about?
Post by: Drew1312 on May 13, 2021, 10:23:41 AM
There was a post somewhere and in that post someone replied that  has a client that has pois symptoms and is gonna check some metabolic ( i think) pathways  with the help  of some software.Or does anyone know babout someone who doesn t have poid but had or has a client with pois?
Title: Re: Does anyone known what post i m talking about?
Post by: Progecitor on May 13, 2021, 11:30:34 AM
https://poiscenter.com/forums/index.php?topic=3694.0
Title: Re: Genetic profile results
Post by: swell on June 15, 2021, 03:08:14 PM
First of all Prospero, this is an incredible gem thread.  You even have the SNPs for the P450 family enzymes.  Detoxification/metabolic pathways I think is baseline critical to Pois, even immune system and health.  Though I don't see the 'alleles'?  Once we have all the SNPs and allele's, we can actually find out where our problems lay (not easy, though do'able).  I will gather my SNPs and let you know. 

Cosmic:  This is a new science so probably everyone (and specially myself is new, I knew zero about biology 2 yrs back), so you can easily learnt it.  To your question:  I will make it simple (at risk of over-simplification) so its easily understandable
1.  Our body has many cells. Cells have DNA (the "genetic" code of our body). It is kept closely guarded under lock and key. 
2.  When cells are copied, they can develop defects (SNPs are identification markers for them).  These defects can be important or may not be important (Alleles).
3.  When information needs to be sent, Information stored in DNA is used to make RNA (ribo-nucleuc-acid).  The Covid RNA vaccine works at this level and hence there was all that controversy.
3.  RNA is used to Proteins.  The medications/herbs/compounds we take they affect these proteins.  So you see the defects in our genes are guarded under multiple layers of defense.  The various drugs we take affect these proteins.  They manage the "manifestations" but do not touch the master source of information (for good reasons).  Now genes can be edited (to correct the source of the problem), however due to the severity of repercussions of working at that level, the scope of gene therapy is under research.

So back to your question, you can turn on or off genes (i.e. gene expression) as well you can effect the proteins that are produced (much safer approach), however, until you map things out, balance risk to reward calculation, so hence this would require plenty of work.  You only get 1 life :) and messing with gene is a serious work.  But we can easily (well with plenty of work) map out the defects, and figure out the corresponding molecules that can be beneficial.

if you find a link between DNA and the POIS what actions are necessary? Are you able to turn on and off certain DNA strains?
Title: Re: Genetic profile results
Post by: Prospero on June 15, 2021, 03:58:16 PM
I didn't write the letter of the allele in each case but "+" indicates the less common allele and "-" the more common one (so you can find them with the information +/+, +/-, -/-).
Title: Re: Genetic profile results
Post by: Iwillbeatthis on June 18, 2021, 02:14:38 PM
@Prospero https://uk.iherb.com/pr/Life-Extension-SOD-Booster-30-Vegetarian-Capsules/102528 - Superoxide Dismutase breaks down superoxide so it's a useful supplement when we are SOD2 ++.

http://www.heartfixer.com/AMRI-Nutrigenomics.htm this website has invaluable info for anyone who wants to learn about the methyl cycle genes and how to fix them.

Supplementing with high sulfur compounds like taurine might make you feel good in the short run but in the long run if you have any kind of CBS mutation then you will be causing yourself a whole host of problems.

"CBS (Cystathionine Beta-Synthase) is discussed on pages 48-53 of Dr. Yasko’s book, Genetic Bypass..  You are +/+ (all of your CBS enzymes are abnormal) or +/- (half of your CBS enzymes are abnormal) for one of the two CBS gain-of-function up regulations and you may also be +/+ or +/- for one of the BHMT reduced-function down regulations (which act like CBS up regulations).  Homocysteine (and its Methyl Cycle precursors) is thus being “pulled and pushed” down the trans-sulfuration pathway, in this process generating excessive sulfur break down products (sulfite and sulfate, which stimulate the stress/cortisol “fight or flight” response), glutamate (which leads to glutaminergic excitotoxicity), hydrogen sulfide (which produces brain fog), and too much ammonia (which depletes BH4, leading to insufficient dopamine and serotonin production).

This deficiency in BH4 predisposes eNOS (endothelial nitric oxide synthase) to convert arginine in to free radicals (superoxide and peroxynitrite) as opposed to nitric oxide (atheroprotective vasodilator), predisposing you to hypertension and cardiovascular and inflammatory disease states.  Those of you with reduced function alleles for the antioxidant enzymes SOD (superoxide dismutase), CAT (catalase), GPX (glutathione peroxidase), and PON1 (paraoxonase) may be challenged dealing with this superoxide free radical burden. "

Title: Re: Genetic profile results
Post by: Quantum on July 23, 2021, 09:36:51 AM
Hi everyone,

I have finally received my Whole Genome Sequencing  (WGS) results a few days ago.  It is a lot of information, and I have to take the time to analyze all this, which will take months.  However, I already have found some significant SNPs ( Single Nucleotides Permutations) that are explaining parts of my POIS.

I will share more in the coming months, but for now, I can share the more significant finding I have done so far:   I have 2 SNPs in the CACNA1S gene that are linked in ClinVar ( a database of SNPs) to a channelopathy called Hypokalemic Periodic Paralysis ( HypoKPP), Type 1.  I already suspected that I had a form of HypoKPP.  However, my two SNPs,rs3850625 (Arg1539Cys) and rs12742169 (Leu458His), are not the more usual ones in HypoKPP, so even in this rare disease, I am a less frequent sub-type.

For me, I do not have downright "paralysis", but lethargy, fatigue, and muscle weakness, linked to abnormal potassium levels. A particularity of my presentation is that it takes days to recover.   The more frequent presentation is that the person is totally paralyzed for some muscles or even the whole body, for 20 minutes to a few hours.   But like POIS, this rare disease has many different presentations, almost unique in each patient.
(P.S. : in my case, both of my CACNA1S SNPs are heterozygote, meaning I have 1 defective version and one usual version on each.  However, most HypoKPP mutations are autosomal dominant ( see https://pubmed.ncbi.nlm.nih.gov/34290819/ (https://pubmed.ncbi.nlm.nih.gov/34290819/) ) , meaning that only one defective gene in the pair is enough to have symptoms, although usually less severe. That would explain why I do not have full paralysis, but weakness and extreme fatigue ( I am able to move, but it's a lot more demanding than usual, felt like extreme fatigue )
A current trigger for the attack of PP is exercise or excitement followed by a rest period.  It fits both sexual activity and sport, my two main triggers.  It also explains the delay... my symptoms set in after some rest, not instantly.

I already knew that potassium was good for my POIS, and as you may know, it is part of my pre-pack.  I also take potassium after sport - I have found some years ago that it was helping me recover faster.  However, I was unsure about what type of Periodic Paralysis I have before seeing it in my genetic results.

Be aware that there is a sister channelopathy, with similar symptoms, that is called Hyperkalemic Periodic Paralysis, so taking potassium, in this case, will worsen the symptoms.  So, unless you have your genome results or have a clear diagnosis with a neurologist, potassium is not to be tried, because potassium at high doses can trigger fatal arrhythmia ( a heart problem) !

Hopefully, HypoKPP Type 1, my type, does not come with myotonia ( muscles stiffness, cramps, spasms).  Another gene is related to this type

I have other SNPs that are significant and may contribute to my POIS, like 3 SNPs contributing to low vitamin B12, and another to ammonia elimination being reduced.   Many problems in my genes...but that, I already knew.

If you have a POIS similar to mine, that is, with no cognitive symptoms ( no brain fog, no memory problems, no reduced cognitive abilities during POIS), and have POIS-like symptoms after sport/exercise, and other frequent triggers for other people having PP ( but no me) like cold, eating food with high carb/sugars content, hign salt/sodium intake, and stress, you may take a look at the different types of Periodic Paralysis and see a specialist, or have your genome sequenced, and see if this is relevant for you


So, I think having your whole genome sequencing done can be a very good idea if you are motivated to learn how to dig into it and find some needles in the haystack.  There are great tools now to do it, and sometimes later I will write on the current methods I use to search in my WGS, if anyone is interested.   Also, cost are getting lower and lower.  I got my whole genome sequencing ( yes, whole genome, not only 1% of it like with 23andme or myHeritage ) for $299, and paid for a lifetime subscription to their reports database, a total of $499 I think.  So far, worth it a lot.  I had it done with Nebula Genomics ( good service, but expect 20 to 24 weeks before getting back your results, not the 8 weeks advertised).  Also, I have uploaded my results to sequencing.com for free, and they provide a lot of free tools to search and explore your genome, and some very useful tools at very low cost, like the Genome Explorer Plus, helping you figure out with less work which of your numerous SNPs could be more interesting to analyze.  However, with any method you choose, be prepared to do a lot of work and searching, or else, pay a genetic counselor to do it for you.

For more information on HypoKPP and other forms of Periodic Paralysis, see https://periodicparalysis.org/what-is-periodic-paralysis-2/ (https://periodicparalysis.org/what-is-periodic-paralysis-2/)  and https://rarediseases.info.nih.gov/diseases/6729/hypokalemic-periodic-paralysis (https://rarediseases.info.nih.gov/diseases/6729/hypokalemic-periodic-paralysis)
Title: Re: Genetic profile results
Post by: Prospero on July 23, 2021, 10:22:02 AM
Interesting news, Quantum.
Do you have a double mutation for the SNPs you mentioned? As for me, I'm heterozygous for rs2297902 in the CACNA1S gene, which is one of the SNPs mentioned for HypoKPP, but I doubt it has an effect alone.
As you told us too, your condition regarding potassium is probably quite specific among Poisers. In any case, nice to see that you're digging in your genetic data!
Title: Re: Genetic profile results
Post by: Quantum on July 23, 2021, 11:03:50 AM
Interesting news, Quantum.
Do you have a double mutation for the SNPs you mentioned? As for me, I'm heterozygous for rs2297902 in the CACNA1S gene, which is one of the SNPs mentioned for HypoKPP, but I doubt it has an effect alone.
As you told us too, your condition regarding potassium is probably quite specific among Poisers. In any case, nice to see that you're digging in your genetic data!
Hi Prospero,
Thanks for your very relevant question, because severity is usually greater in homozygous SNPs, that is, variants where both paretnal genes are the defective version.

In my case, both of my CACNA1S SNPs are heterozygote, meaning I have 1 defective version and one usual version on each.  However, most HypoKPP mutations are autosomal dominant ( see https://pubmed.ncbi.nlm.nih.gov/34290819/ (https://pubmed.ncbi.nlm.nih.gov/34290819/) ) , meaning that only one defective gene in the pair is enough to have symptoms, although usually less severe.
That would explain why I do not have full paralysis, but weakness and extreme fatigue ( I am able to move, but it's a lot more demanding than usual, felt like extreme fatigue )

Also, I have 7 SNPs in my KCNJ18 gene, another gene associated with a form of HypoKPP, called thyrotoxic PP, and about 3 of them are homozygous, but they are not reported yet in ClinVar, so I do not know yet what to think of my very badly affected KCNJ18 gene, and what could be its effects.  Further development of SNPs databases will bring me more light on this one. ( For those wondering, each gene is composed of hundreds of pairs of DNA bases, and some specific mutations in some specific positions only are known yet to be associated with medical conditions... for many positions with an alternative version ( SNP), there is no data yet about the possible consequences.  Those 7 SNPs I have in this KCNJ18 gene are not reported yet in databases, so it is not known yet what effect they have, but it is already known that other SNPs in that same gene are associated with a condition, Thyrotoxic PP, so there is some potential problem here. Data will be added with time, as more people will have their genome sequencing done... then, by comparing genes of affected persons with larger populations not affected, you find specific mutations for this condition... that is how databases like ClinVar are developed)

To complicate matters more, I also have another very badly mutated gene with many SNPs, associated with another channelopathy affecting sodium, some I may have a compounding effect here, too soon to tell.  However, loss of sodium leads to higher aldosterone secretion, in order to retain sodium, but at the cost of losing potassium in the urine... which is bad if you have another condition that already causes low potassium, like HypoKalemic PP... so I have to sort out this channelopathic puzzle, in the coming months.  I will do what it takes, including finding a channelopathy specialist to consult if needed.
Title: Re: Genetic profile results
Post by: Iwillbeatthis on July 23, 2021, 04:46:30 PM
Be sure to check your mutations on promethease or somewhere else where it gives the population frequency for each mutation, if you haven't already. As I have found you can have some homozygous mutations which are very common and completely normal to have. Gene reports like MTHFR support can show you have a ton of homozygous mutations that look bad but when I search them on promethease some of them have a 70% frequency in the general population.
Title: Re: Genetic profile results
Post by: Quantum on July 27, 2021, 11:21:28 AM
Be sure to check your mutations on promethease or somewhere else where it gives the population frequency for each mutation, if you haven't already. As I have found you can have some homozygous mutations which are very common and completely normal to have. Gene reports like MTHFR support can show you have a ton of homozygous mutations that look bad but when I search them on promethease some of them have a 70% frequency in the general population.

Good point, IWBT, the frequency is of major interest in determining if our personal conditions are caused by a less frequent variant.
The tools I have access to on the website of the company that sequenced my genome ( Nebula Genomics) give me the frequency, along with much more information.  For others who do not have these data frequencies, they are freely accessible on free websites, like the genomAD browser, at https://gnomad.broadinstitute.org/ (https://gnomad.broadinstitute.org/) 
Title: Re: Genetic profile results
Post by: begonePOIS on August 03, 2021, 10:29:40 PM
Is there any effort ongoing to organize a compilation of genetic profiles (SNP-array, whole ex/gen-ome seq, etc.)? If there are sufficient number of profiles (along with some demographics information), it should be possible to analyze the data together using a case-control design in order to detect potential genetic loci involved in POIS. I'm currently doing my PhD in genetics and would be willing to spend some time on this if the data can be put together.

Edit: By genetic profiles, what I want is the raw genotype calls of all the SNPs tested, not just a summary.
Title: Re: Genetic profile results
Post by: demografx on August 03, 2021, 11:41:32 PM
begonePOIS, welcome to the forum and….
Great Name! :)
Title: Re: Genetic profile results
Post by: berlin1984 on August 04, 2021, 04:13:58 AM
Yes please. If you have any fancy tools from your university to find commonalities I'd happily donate my 23andme SNP txt file.
Title: Re: Genetic profile results
Post by: Quantum on August 04, 2021, 09:14:07 AM
Is there any effort ongoing to organize a compilation of genetic profiles (SNP-array, whole ex/gen-ome seq, etc.)? If there are sufficient number of profiles (along with some demographics information), it should be possible to analyze the data together using a case-control design in order to detect potential genetic loci involved in POIS. I'm currently doing my PhD in genetics and would be willing to spend some time on this if the data can be put together.

Edit: By genetic profiles, what I want is the raw genotype calls of all the SNPs tested, not just a summary.
Interesting project, begonePOIS.   I do not think we know exactly how many members here have their genetic profile done.  I, for one, just received my results this month.  I can easily transfer an SNP VCF file or another type of file. 

How many profiles would you need, as a minimum, for this project to be feasible?

Title: Re: Genetic profile results
Post by: Muon on August 06, 2021, 03:00:03 PM
Is there any effort ongoing to organize a compilation of genetic profiles (SNP-array, whole ex/gen-ome seq, etc.)? If there are sufficient number of profiles (along with some demographics information), it should be possible to analyze the data together using a case-control design in order to detect potential genetic loci involved in POIS. I'm currently doing my PhD in genetics and would be willing to spend some time on this if the data can be put together.

Edit: By genetic profiles, what I want is the raw genotype calls of all the SNPs tested, not just a summary.

1) How do I know you are not a random data farmer from the internet?
2) My knowledge is severly limited about this subject. What test needs to be done, where can one do such thing?
3) Someone could list labs across the world offering these tests.
Title: Re: Genetic profile results
Post by: Quantum on August 06, 2021, 07:34:39 PM
Is there any effort ongoing to organize a compilation of genetic profiles (SNP-array, whole ex/gen-ome seq, etc.)? If there are sufficient number of profiles (along with some demographics information), it should be possible to analyze the data together using a case-control design in order to detect potential genetic loci involved in POIS. I'm currently doing my PhD in genetics and would be willing to spend some time on this if the data can be put together.

Edit: By genetic profiles, what I want is the raw genotype calls of all the SNPs tested, not just a summary.

1) How do I know you are not a random data farmer from the internet?
2) My knowledge is severely limited about this subject. What test needs to be done, where can one do such thing?
3) Someone could list labs across the world offering these tests.

No short answer to explain what genomics is and what it is useful for, so below are some key points to consider.

Since the cost of having your own genome sequenced is going down rapidly, more and more companies, on the web, offer the service.  Typically, you are sent a little box with a swab and instruction to take a sample in your mouth ( inner cheek), that will hopefully contain enough of your own, personal cells, and send that back to the lab.  After a delay, if the sample was ok, and the lab was not too backlogged, you will receive online your genomic data, which you can usually download in different file formats ( it took me about 5 months to get my results... Covid backlogging...)

The use of all this is to compare your own DNA sequence, in your own genes and in all of your DNA, to what is considered the reference human genome in its latest version.  Because, for any locus in any gene, you can have what is called a SNP ( Single Nucleotide Permutation) .  Those are like small mutations on one pair of nucleotides in your DNA ( you do not have the most current one).  Some SNPs have no consequence, some others happen to be on a critical coding section of your DNA, so, for example, the little change can lead to one amino acid being changed in the protein, and, if this protein is an enzyme, it can be non-functional, or be like 60% active compared to the "normal" reference, enzyme.

Many kind of sequencing is available, but currently, since the prices are down big time, the best bargain is to go for a Whole Genome Sequencing (WGS), where you will have 100% of your DNA mapped.  The most popular tests from a few years ago, like 23andMe, and Ancestry,com, typically map about only 1% of your DNA.  It includes most of what is known right now about genomics.  But since the price for a WGS is now the same as a partial sequencing, the near future is WGS, in my opinion, because you will not need to re-do another sequencing in the future for sections you did not have mapped the first time.

I had my WGS done this year.  I have chosen a deep, 30X, mapping.  This means that, on average, for every base pair, you have around 30 samplings done.  I say in average, because for some positions, when quality was not optimal for the testing results, you may get only 12 samples to determine your real base pairs at that specific locus ( those techniques are still rather new).  You have WGS at 10X for 99$, but I feel that 10X mapping will sometimes fall short on a specific locus, so you will not be sure what is your real data at that position. You cannot rely on only 2 or 3 samples on a specific position to determine your own data there, better have a couple of dozens at least, because there are still some discrepancies in the results.  But if you have 26 results on 28 for a locus that says G-A as the pair of nucleotides you have there, you know it is really G-A, and that you are homozygote there ( two identical alleles from both parents). 

There is now 100X WGS available, but too expensive for my taste ( around $1000), and not obvious that it is clearly a plus-value over the 30X.  My 30X was at $299 with Nebula Genomics.  But there are many other companies now offering WGS, and still more offering partial genome sequencing.  For WGS, you have Nebula Genomics, sequencing.com ( $399 for WGS 30X, currently), Invitae, Dante Labs, Veritas Genetics, and so on. Do some research, and compare plans.  Apart from the quality of the sequencing, look for the file formats you will be able to download your data in.  The usefulness of that is that you can then upload your data to other sites offering you both free or paid apps to analyze your data ( However, take a look at the privacy policy of a site before uploading your data there)

Once you have your data, you can use databases to compare your genome with the reference genome, and also to look for which SNPs you have that are already know to probably cause you a problem.  But the analysis is something you have to get used to, it is not simple, and too complex for me to explain it all here.  However, you can just pay to have your data run into a program that will give you a report of what has been found in your genome, considering the current knowledge on genomics.

Special analysis can be done with a specific population having a specific problem, and run the program against a database of "normal" subjects, to see what SNPs the affected subject may have in common that the general population does not have.  This may lead to finding some genetic causes to some specific health problems.  This is what is offered for POIS by begonePOIS.

Genomics is a science on its own, so when you are interested, take the time to learn about it.  The most valuable outcome is that you can find tips and supplements, and a diet that is really adapted to your own genome. One well-studied example is for the gene MTHFR, coding for an enzyme that is important in the methylation pathway - if you have certain known SNPs there, you can adapt your lifestyle, diet, and supplements, and be more healthy.


Title: Re: Genetic profile results
Post by: berlin1984 on August 21, 2021, 02:29:56 PM
There is a lot of genetics discussion also from here ongoing: https://poiscenter.com/forums/index.php?topic=2373.msg19924#msg19924
Title: Re: Genetic profile results
Post by: demografx on August 21, 2021, 11:04:20 PM

…What I find very interesting…that a lot of people in the forum are engineer/science/nerd type of guys…

Could be a coincidence that people like us are more likely to visit this kind of forum, but could also be a genetic clue for something.


I was a large-database statistical-modeling entrepreneur with an advertising business clientele. For many years.

Nerdy!

:)
Title: Genetic testing analysis
Post by: rollercoaster on August 22, 2021, 12:45:50 PM
I have my raw data from 23andMe and also my geneticGenie profile.

My hypothesis is that my POIS is caused by a hyperactive immune system which is in-turn caused by genetic mutations.

Why do I think so?

All this leads me to believe that the root cause of my POIS is related to an overactive immune response.
How can I get to know if I have any genetic variation that causes this hyperactive immunity? I cannot interpret the results of genetic genie profile.
Is there any company / website out there that can help me figure this out from my raw data?
Thanks

Methylation report from Genetic Genie attached.
Title: Re: Genetic profile results
Post by: Clues on August 22, 2021, 03:25:50 PM
Rollercoaster, in my case it also very much seems like my immune system (and nervous system?) is overly sensitive. However based on my limited understanding, the cause isn't necessarily genetic. I've read in various places that it's possible for the immune system to become overly sensitised to various triggers. For example, see the very recent post somebody made about the cause of IBS.

Maybe it's possible for the immune system to be desensitised somehow. This is my biggest hope at the moment. I'm trying out the Wim Hof method with this in mind, but the results are inconclusive so far. I'm less sensitive to cold, and to light exercise, but orgasm triggers the same symptoms as before.
Title: Re: Genetic profile results
Post by: Iwillbeatthis on August 28, 2021, 05:03:11 AM
Why getting your whole genome sequenced can be unhelpful by Dr Amy Yasko - one of the pioneers of the methyl cycle:

"There is one final critical point that needs to be reiterated with respect to SNP testing. There are approximately 25,000 genes in the human genome. Dr.Yasko personally believes in only looking at SNPs that are in well defined pathways where it is clear how to add nutritional support to bypass imbalances. Having a laundry list of SNPs without a way to use nutritional support is not consistent with the way she approaches health. So, whether you have a test that gives you 1000 or 5000 SNPs this is still only a fraction of the total number of genes in your body and frankly having more SNPs is not the issue. The real question is whether the SNPs you have are in a pathway that has been characterized so you know what to do to help restore your body to health. The reason Dr.Yasko focuses on the methylation cycle is that it is a well defined pathway, it is very clear where nutritional support can bypass mutations and the pathway we look at IS the system the body uses to edit and correct problems with other genes. So regardless of how many other SNPs there are in the 25,000 or so other genes in the body, IF those genes are regulated by methylation, then having your methylation cycle in balance gives you the tools you need to help to turn on or off those other genes that are NOT part of the 30 SNP methylation panel. This is called epigenetics, and Dr.Yasko has given entire talks just on this topic. Having the methylation cycle function optimally and bypassing SNPs in this pathway allows the global editing function in your body to help to correct issues with any number of other genes in the system. THIS is why this pathway is so critical for health and wellness."

"Recall that every cell in your body contains identical DNA, which is why blood, saliva, hair, fingernails can be used to evaluate your personal DNA. There are approximately 25,000 genes in the human body that code for proteins, but it is not practical to look at all 25,000 genes. While every cell in the body contains the information about your total genetic profile, tests that look at genetics choose specific genes to evaluate and look for changes or mutations. I personally believe in only looking for changes in the DNA in well-defined nutritional pathways where it is clear how to add natural supplements to bypass imbalances. I feel that whether you have a test that gives you 30 or 1000 or 5000 markers this is still only a fraction of the total number of genes in your body and frankly having more markers is not the issue. The real question is whether the information that you have is in a pathway that has been characterized so you know what to do to help restore your body to health. The nutritional pathway that this program focuses on is something I call “The Methylation Cycle”. The methylation cycle is a well-defined nutritional pathway in the body. When you look at the suggested nutritional support, you are working to increase the ability of the entire Methylation Cycle to run properly, keeping in mind that it has been functioning to some degree in spite of any mutations in particular genes. Nutrigenomics is just one aspect of the factors that determine your health. I see complex health conditions as multifactorial in nature. That means that while your nutrigenomics are a piece of the puzzle they are not the whole picture. The environmental burden of toxins you are exposed to, along with infectious agents (viruses, bacteria, fungal infections, yeast) and the stress on your system all impact your overall health."
Title: Re: Genetic profile results
Post by: Quantum on August 28, 2021, 08:04:40 AM
Hi IWBT,
What I understand from this comment from Dr Yasko is that having  lot of data is not helpful if we do not have the knowledge to know what to do with this data in order to improve our health.

However, the science of genomics is rapidly evolving and new data is adding each month.  Considering that a Whole Genome Sequencing (WGS) is now about the same price as partial sequencing, paying for example $299 for a whole sequencing is a good choice.  Once you have all of your data, you can analyze only the parts you want - only the methylation-related SNPs if you want.  As the science of genomics is improving, you still have all of your genes data to do whatever new panel is available.

I guess her comment dates back a few years when a methylation panel could cost 100$, and a whole genome sequencing was around $1000 or $2000.  Now that a WGS is almost the same price as a very partial ( less than 1%) sequencing, it is a very interesting option.

I sure hope that, in some years, there will be many pathways that have been researched as much as the methylation pathway, and that we will have far more complete databases on the many SNPs.  For now, many SNPs are called 'VUS' or Variant of Uncertain Significance, meaning that we do not know yet what is their significance to the function or health of our body  ( see https://en.wikipedia.org/wiki/Variant_of_uncertain_significance (https://en.wikipedia.org/wiki/Variant_of_uncertain_significance) ).   

Title: Re: Genetic profile results
Post by: Quantum on August 28, 2021, 08:47:29 AM
For those who have their genome sequencing done, I have discovered this week a free and interesting site where you can use tools to analyze your genome results:  https://geneticgenie.org/ (https://geneticgenie.org/)

They offer an overall analysis of your SNPs, with their GenVue Discovery application, at https://genvue.geneticgenie.org/ (https://genvue.geneticgenie.org/)

They also offer two panels, for now:  Methylation, and Detox.  The Methylation Panel contains information on every SNP tested in the panel.  The Detox panel is less developed in terms of interpretation info, only listing your results, but with a minimum of research, you will know what it means.


It is free to use but you can make a donation if you want.
The max size of the file you can upload there is 1 GB.  If you have a Whole Genome Sequencing, which is about 40 GB in size, the best file to upload there instead is a file with your SNPs only, that is, only the positions where your alleles are different from the reference genome ( that reference may be hg19/GRCh37 or hg38/GRCh38).  For example, my VCF file containing my SNPs is about 225 MB in size.  The VCF file format ( Variant Call Format) is only one kind of format, there are others that you may have your data in, and most are accepted by this website ( 23andMe, AncestryDNA, ...)

The general report ( Variant Report) is very interesting.  In the first tab, 'Genetic Conditions', it shows your SNPs for which there are expert reviews, meaning that the potential effects of those SNPs are better known. However, the fact of having such a variant does not necessarily mean one has or carries a condition or disease - it only means that you have a predisposition of developing this condition.  Since we have about 25 000 genes, you may have other genes that have blocked or compensate for the effect of a particular SNP, so you do not have this condition at all.
In the Variant Report, you also have a tab for SNPs about potential unusual drug responses to specific drugs.  You also have tabs where are listed your rare mutations of less than 1% frequency listed in ClinVar ( having a rare mutation may be more significant than having a common variant).  Being listed in ClinVar means that some information is known about these SNPs. There is also a tab for uncommon mutation of between 1% and 5% frequency, that are reported in ClinVar ( more frequent, but still relatively rare).
For each SNP list in your report, you have an abstract concerning this SNP, tags concerning its degree of pathogenicity and clinical significance, and links to many databases  ( LitVar, SNPedia, OMIM, dbSNP) having a specific page for this SNP, so you save a lot of time and easily find information on this on this specific SNP.

Doing the same report next year will produce a different report, with more data, and updated information.  In 5 years, it would be a quite different report, far more complete and descriptive ( information on more SNPs, more complete information on already known mutations, and so on).  I am very enthusiastic about this new developing science!

Let me know if you try the tools geneticgenie.org !
P.S.  I saw that Rollercoaster used this website for the reports he posted in this thread :)
Title: Re: Genetic profile results
Post by: Prospero on August 28, 2021, 01:06:56 PM
Rollercoaster, thank you for your reports, I have added the data in the first page.
Quantum, would you like to share your GeneticGenie reports with us?
Title: Re: Genetic profile results
Post by: berlin1984 on August 28, 2021, 01:48:03 PM
They offer an overall analysis of your SNPs, with their GenVue Discovery application, at https://genvue.geneticgenie.org/ (https://genvue.geneticgenie.org/)

Wow nice. Thanks. I knew the panels and I had posted my results in the test result thread last year but I did not know GenVue, maybe it did not exist yet. Looks like a curated and nicer version of Promethease.

I found this for myself, very interesting:

Gene: BTD
Variant: c.1336G>C
(p.Asp446His)
rsID: rs13078881
Ref Allele: G
Alt Allele: C
Freq: 1.857% uncommon
Biotinidase deficiency, Autosomal recessive
Low clinical importance, pathogenic
I guess I need to buy a biotin supplement and see what it does. Note that I only have reduced activity, the full mutation is apparantly screened at birth even(?)
https://en.wikipedia.org/wiki/Biotinidase_deficiency
https://www.geneticlifehacks.com/genetics-of-biotin-deficiency/

The other one is:
Gene: AMPD1
Variant: c.133C>T
(p.Gln45Ter)
rsID: rs17602729
Ref Allele: G
Alt Allele: A
Freq: 3.8139% uncommon
Muscle AMP deaminase deficiency, Autosomal recessive
Low clinical importance, Likely pathogenic — Causes Adenosine Deaminase Deficiency in a recessive manner. Most of the time individuals do not report symptoms, but when symptoms do exist they to be post-exercise symptoms of muscle weakness, muscle pain, and getting tired more quickly.
https://www.geneticlifehacks.com/ampd1-deficiency/ says A/G: 50% reduction in AMP Deaminase function and recommends Creatine or Ribose.


Maybe more in other tabs, let's see :-)
Title: Re: Genetic profile results
Post by: Quantum on August 28, 2021, 02:39:17 PM
Rollercoaster, thank you for your reports, I have added the data in the first page.
Quantum, would you like to share your GeneticGenie reports with us?
Sure Prospero.
I will join the Methylation and Detox report with this post.
I have to figure out how to join the HTML report like Rollercoaster did, with a few hundred KB in size... when I try to upload it, the file is 4 MB , so there must be another way to upload it.
Title: Re: Genetic profile results
Post by: Quantum on August 28, 2021, 03:16:05 PM
Ok, I have found a way to reduce the Variant Reports files size. I use the 'print" function of the browser and save it as a PDF.  It keeps the links clickable but the report loses a little color in the process.   


Here is my 'Genetic Conditions' report, which is a small file.  Also, my 'Rare Mutations' report, which is quite large, at 2 MB, because it is done from a WGS ( Whole Genome Sequencing).  I have over 180 rare mutations listed, compared to about 20 in rollercoaster's report ( Done from a partial sequencing, so less SNP listed).

Take note that I do not have all of these diseases ;)  You have to get use to read gene reports as 'potential' to have certain conditions or not having them. We have around 25000 genes, and it is a very complex machinery, so even if I have a homozygous rare mutation for a terrible syndrome that could have caused me mental retardation, short stature, infertility, and so on, it was only a potential phenotype.  This 'bad gene' may have been blocked by another gene or a combination of other genes I have.  So, before we can find what causes POIS symptoms, a lot of work will have to be done.  We have to see what mutation is really manifesting as a phenotype in our body.  All mutations are not clinically significant, and not all clinically significant mutations manifest as an actual clinical problem.  The genome data analysis will progress in the years and decades to come, but for now, caution is advised in interpreting genetic results.


An interesting way to find what genes are linked to POIS would be to do a GWAS ( Genome-Wide Association Study).  This means you run the genome of a group of POIS sufferers against the genome of a reference population without POIS, and find what mutations and SNPs the POIS sufferers have in common that the general population does not have.

This is the kind of test that was proposed by BegonePOIS, earlier in this thread.  However, he did not answer yet my question about how many genome files from POIS sufferers he would need to run this kind of test and have significant results. But clearly, the more genome sequencing files we have from more different POIS sufferers, the better it would be.


 
Title: Re: Genetic profile results
Post by: Quantum on August 28, 2021, 03:41:38 PM
They offer an overall analysis of your SNPs, with their GenVue Discovery application, at https://genvue.geneticgenie.org/ (https://genvue.geneticgenie.org/)

Wow nice. Thanks. I knew the panels and I had posted my results in the test result thread last year but I did not know GenVue, maybe it did not exist yet. Looks like a curated and nicer version of Promethease.

I found this for myself, very interesting:

Gene: BTD
Variant: c.1336G>C
(p.Asp446His)
rsID: rs13078881
Ref Allele: G
Alt Allele: C
Freq: 1.857% uncommon
Biotinidase deficiency, Autosomal recessive
Low clinical importance, pathogenic
I guess I need to buy a biotin supplement and see what it does. Note that I only have reduced activity, the full mutation is apparantly screened at birth even(?)
https://en.wikipedia.org/wiki/Biotinidase_deficiency (https://en.wikipedia.org/wiki/Biotinidase_deficiency)
https://www.geneticlifehacks.com/genetics-of-biotin-deficiency/ (https://www.geneticlifehacks.com/genetics-of-biotin-deficiency/)

The other one is:
Gene: AMPD1
Variant: c.133C>T
(p.Gln45Ter)
rsID: rs17602729
Ref Allele: G
Alt Allele: A
Freq: 3.8139% uncommon
Muscle AMP deaminase deficiency, Autosomal recessive
Low clinical importance, Likely pathogenic — Causes Adenosine Deaminase Deficiency in a recessive manner. Most of the time individuals do not report symptoms, but when symptoms do exist they to be post-exercise symptoms of muscle weakness, muscle pain, and getting tired more quickly.
https://www.geneticlifehacks.com/ampd1-deficiency/ (https://www.geneticlifehacks.com/ampd1-deficiency/) says A/G: 50% reduction in AMP Deaminase function and recommends Creatine or Ribose.


Maybe more in other tabs, let's see :-)

Very interesting.  Be sure to update us about these 'genomic supplements' and their effect on your health.
In my case, I already knew about Vitamin D and have taken 2000 ui daily for over a year now, and my blood level are ok now ( it sure help me get some more energy and resistance to infections and inflammation).
In my data, I also found SNPs suggesting I should take more B12, more vitamin A, and more choline. Since last month, I have taken what I call my 'genomic vitamins' daily, and I looks like it gave me maybe 5% to 10% more energy, which is significant..  As a bonus, my ever-present canker sores seem to heal faster and be far less painful.  It is too soon to conclude, but so far it is positive.   

 
Title: Re: Genetic profile results
Post by: drop247 on August 28, 2021, 09:26:10 PM
Berlin,
I have the same mutations as you. What are the odds of us both having two uncommon mutations I wonder? It could be a lead to investigate further.

Gene: BTD
Variant: c.1336G>C
(p.Asp446His)
rsID: rs13078881
Ref Allele: G
Alt Allele: C
Freq: 1.857%uncommon
CADD: 23.3

ClinVar Submissions (15)

    Biotinidase deficiency, Autosomal recessive

Hetero
CG

Gene: AMPD1
Variant: c.133C>T
(p.Gln45Ter)
rsID: rs17602729
Ref Allele: G
Alt Allele: A
Freq: 3.8139%uncommon
CADD: 36

ClinVar Submissions (6)

    Muscle AMP deaminase deficiency, Autosomal recessive










Title: Re: Genetic profile results
Post by: berlin1984 on August 29, 2021, 04:52:57 AM
Berlin,
I have the same mutations as you. What are the odds of us both having two uncommon mutations I wonder? It could be a lead to investigate further.

Nice!  ;D

Although they might not be so uncommon in white/caucasian (assuming you are, sorry if this is incorrect)

Did you also see my mutations here: https://poiscenter.com/forums/index.php?topic=2684.msg42120#msg42120 ?
Title: Re: Genetic profile results
Post by: Progecitor on August 29, 2021, 06:38:22 AM
They offer an overall analysis of your SNPs, with their GenVue Discovery application, at https://genvue.geneticgenie.org/ (https://genvue.geneticgenie.org/)

Wow nice. Thanks. I knew the panels and I had posted my results in the test result thread last year but I did not know GenVue, maybe it did not exist yet. Looks like a curated and nicer version of Promethease.

I found this for myself, very interesting:

Gene: BTD
Variant: c.1336G>C
(p.Asp446His)
rsID: rs13078881
Ref Allele: G
Alt Allele: C
Freq: 1.857% uncommon
Biotinidase deficiency, Autosomal recessive
Low clinical importance, pathogenic
I guess I need to buy a biotin supplement and see what it does. Note that I only have reduced activity, the full mutation is apparantly screened at birth even(?)
https://en.wikipedia.org/wiki/Biotinidase_deficiency
https://www.geneticlifehacks.com/genetics-of-biotin-deficiency/

The other one is:
Gene: AMPD1
Variant: c.133C>T
(p.Gln45Ter)
rsID: rs17602729
Ref Allele: G
Alt Allele: A
Freq: 3.8139% uncommon
Muscle AMP deaminase deficiency, Autosomal recessive
Low clinical importance, Likely pathogenic — Causes Adenosine Deaminase Deficiency in a recessive manner. Most of the time individuals do not report symptoms, but when symptoms do exist they to be post-exercise symptoms of muscle weakness, muscle pain, and getting tired more quickly.
https://www.geneticlifehacks.com/ampd1-deficiency/ says A/G: 50% reduction in AMP Deaminase function and recommends Creatine or Ribose.


Maybe more in other tabs, let's see :-)

I currently don't have the funds to do genetic profiling, but I have tried biotin before. As I mentioned it induced an acute POIS attack for about 1-2 days as if I actually had an O event. That is why I wanted to know if others had a similar experience. So if you take biotin be prepared for the worst even though a biotinidase deficiency would suggest that biotin supplementation could help you a lot. The amount I had taken couldn't be considered much as it was only a 300 mcg capsule. As I remember one to two hours after consumption I developed quite severe bloodshot eyes and felt generally unwell. Be sure to keep some saffron at hand if this happens as it helped me reduce the effect.
When I first took biotin I was at the beginning of acute POIS and the result was quite severe, however at another time I took it at the beginning of the chronic phase and it hit me less severely then. I planned to do some more tinkering with biotin as I think I noticed that the urine completely lost its burning quality at the time and my theory was that biotin only shifts POIS from the urine to the blood by preventing the excretion of the causative compound. Given your genetic results now I am not so sure if it is only a modifier of POIS, but be sure to report if you experience something similar. At best it may really help in your case, however our medication profile seems to align a lot and it has to be more than coincidence.
Title: Re: Genetic profile results
Post by: drop247 on August 29, 2021, 10:53:05 AM

Nice!  ;D

Although they might not be so uncommon in white/caucasian (assuming you are, sorry if this is incorrect)

Did you also see my mutations here: https://poiscenter.com/forums/index.php?topic=2684.msg42120#msg42120 ?

Yes, I'm Caucasian. I checked my histamine degradation mutations and I do have the same reduced HNMT mutation as you. I do not have the reduced DAO production though. How are your methylation cycle genes? I'm heterozygous on one of them that says results in a 40% reduction in methylation.

So in summary on top of the Biotin and AMP deficiency genes I also have the following histamine degradation deficiency genes:

HNMT:
rs1050891 A/A: reduced breakdown of histamine compared to G/G

Methylation:
rs1801133 A/G: one copy of MTHFR C677T allele (heterozygous), decreased by 40%
Title: Re: Genetic profile results
Post by: Prospero on August 29, 2021, 10:57:18 AM
My data doesn't include the two mutations mentioned by berlin and drop.
Under the "genetic conditions" category, there are mainly my MTHFR variants, a SERPINA1 variant (may induce alpha1 antitrypsin deficiency), the same CCDC170 variant as Quantum (estrogen resistance) and LCT;MCM6 double mutation (lactase persistence).
"Other risks" include variants for MT-ND1, BCKDHA, UGT1A1, ACTN3, PCSK9, DHCR7, DGUOK, HEXA, COL5A1, HTT, SLC6A20, EHBP1, DCAF17, FGFR4 and CCL2.

@ Quantum, thank you for your reports, I'll add the data soon.
Title: Re: Genetic profile results
Post by: drop247 on August 29, 2021, 11:38:16 AM
the same CCDC170 variant as Quantum (estrogen resistance) and LCT;MCM6 double mutation (lactase persistence).


I have these too. Though they seem like very common variants.
Title: Re: Genetic profile results
Post by: berlin1984 on August 30, 2021, 10:14:27 AM
Berlin,
I have the same mutations as you. What are the odds of us both having two uncommon mutations I wonder? It could be a lead to investigate further.
Gene: AMPD1
Variant: c.133C>T
(p.Gln45Ter)
rsID: rs17602729
Ref Allele: G
Alt Allele: A
Freq: 3.8139%uncommon
CADD: 36
Muscle AMP deaminase deficiency, Autosomal recessive

Found a great blog post explaining how this can lead to daytime sleepiness.
https://medium.com/@atomoton/mutants-among-us-the-unexpected-effects-of-a-mutation-in-ampd1-b4f99c911377
Title: Re: Genetic profile results
Post by: drop247 on August 30, 2021, 11:53:20 AM
Berlin,
I have the same mutations as you. What are the odds of us both having two uncommon mutations I wonder? It could be a lead to investigate further.
Gene: AMPD1
Variant: c.133C>T
(p.Gln45Ter)
rsID: rs17602729
Ref Allele: G
Alt Allele: A
Freq: 3.8139%uncommon
CADD: 36
Muscle AMP deaminase deficiency, Autosomal recessive

Found a great blog post explaining how this can lead to daytime sleepiness.
https://medium.com/@atomoton/mutants-among-us-the-unexpected-effects-of-a-mutation-in-ampd1-b4f99c911377

Thanks for the link. I will experiment with caffeine like it suggests. I don't tolerate coffee probably because of the histamine but I have caffeine pills. I've also read Ribose is used to treat AMPD1 so I've ordered that and will let you know if I have any positive results with it or caffeine pills.
Title: Re: Genetic profile results
Post by: berlin1984 on August 30, 2021, 01:42:25 PM
Are you sure you have coffee problen because of histamine?
Because we have the same genes there, maybe your problem is somewhere else with coffee, e.g. this slow/fast metabolizer of caffeeine?
(But: you might have more histamine load because of "wrong" gut bacteria or diet)

I'm trying creatine again, used to take it before but stopped. It's supposed to help too.

Title: Re: Genetic profile results
Post by: drop247 on August 31, 2021, 05:58:19 AM
Nope I'm not sure at all. I go back and forth on whether my issues are histamine related or not.