intro and genetic testing 8-2015

[phoenix76]

Hi, I am new to the forums. I just recently received my results from 23andme.com, ran my results through genetic genie and now mthfrsupport, and am looking for a good guide on how to interpret all of these figures. I am sure that a lot of you have tremendous amounts of knowledge from each other and your experiences. I would not mind tapping into that if that is what the forums are about. However, I still would like to find some good resources to read and come to my own conclusions as well. Kindly let me know if I would need to upload data and what is possible on the site. Thanks and have a great night!
-Jen

 

[pogoman]

seeketh out @caledonia and peruse her links.

 

[phoenix76]

I would like to post information--but there are a lot of homozygotic and heterozygotic results. Which are most important to report? Would I benefit from uploading my MTHFR results? If so, how to I erase my personal details from the report before sending it out?

@calendonia--what would you recommend?

Thanks!

 

[ppodhajski]

What I am about to write might sound overwhelming, but it is only overwhelming because it is new, so just be patient, you will learn!

The most important report you can run is from http://promethease.com/

While it does not hold your hand as much as MTHFRSupport and Genetic Genie, which are both great, It provides much more searchable information.

And instead of just doing a Google search for these genes, learn how to use Google Scholar. https://scholar.google.com/
This will tie you into the research instead of the speculation and exploitation that seems rampant lately. DO NOT TRUST ANYONE. AND TRUST THEM LESS IF THEY ASK YOU FOR MONEY.

Understand the importance of cofactors and how they effect genetic expression:
https://en.wikibooks.org/wiki/Structural_Biochemistry/Enzyme/Cofactors

(It is my opinion and experience that these are the only things we should supplement with. Anything else is just a drug to me.)

You can find the cofactor for a gene, if it has one, by looking the gene up in Uniprot:
http://www.uniprot.org/

For example MAO-A uses FAD as a cofactor, which is a reduced form of Vitamin B2 (Riboflavin)
http://www.uniprot.org/uniprot/P21397

And you can also get some clues by finding out where a gene is expressed by looking it up in the Human Tissue Atlas:
http://www.proteinatlas.org/

For example MAO-A
http://www.proteinatlas.org/ENSG00000189221-MAOA/tissue
The left side shows what tissue the RNA is expressed, which is most important in my mind.

https://en.wikipedia.org/wiki/Gene_expression

It seems to me that when I have a bad SNP in a gene I can trace symptoms back to the organ when the RNA of the gene is expressed. I have bad MAOA SNPs and I used to have terrible digestive issues.

Lastly, understand that a single gene is just a traffic light in a metabolic process so you need to look at all the genes in a metabolci process to get an idea what to eat and what supplements to take. For example MAOA:

https://goo.gl/photos/onwJTJNGtZSkqowF7

This is also a great site that has a bunch of pathways.
http://smpdb.ca/

Lastly I want to say, there is great hope in knowing you genetics. I am proof. I was sick for 25 years, disabled for 15. I am now on no medications and am working to get off disability.

 

[juniemarie]

This is such valuable info and links. This stuff is so overwhelming for most of us and to have guidelines on ways we can further our understanding and treatment helps tremendously.

 

[phoenix76]

Thank you ppodhajski for all the information provided--it is overwhelming but I am taking it one step at a time--and it will probably take a long time to learn all of this information and it seems worth it.

I notice that some people have certain gene mutations in their signature line. How do you know which ones to pick? I have A LOT!

I am glad that you are feeling better and are working toward getting off of disability...that must have been hard but you sound like a strong person. Keep it up!

 

[juniemarie]

@phoenix76 I just picked the ones I was +/+ for and put them together in red, and the ones I was +/- for and put them together in blue. Those are the only ones I knew about from info I got after uploading my 23&me raw data onto Genetic Gene

 

[phoenix76]

Well here are my stats in my signature from genetic genie...not sure how to write in a different color though. There are many more of these gene mutations that I have not listed that came out of mthfr and now promethease. I attempted to look up a few genes in uniprot @ppodhajski --for example cyp1b1 looks like it has a cofactor of iron (heme)--do I have this right or am I looking in the wrong place? It looks like it has to do with estrogen, what does that mean?

Any suggestions on which are the most important gene mutations to focus on would be great. It seems like a lot of information to look at and try to figure out. My detoxing issues were pretty evident after taking birth control years ago--where that one trial was enough to say no in the future and then SSRIs around that same time and after my son was born 3 years ago--another bad reaction. Do not do well with caffeine nor sulfa drugs or really most antibiotics. I have tried to be as holistic as I can but sometimes things like ashwaghanda were a bit much--but I have been on a low dose of thyroid medication for several years so that could have been too much of a combo for me. I really took a downward spiral after my son was born--had all the "fixings" for delivery and beyond (pitocin, epidural, anesthethic -- which I take hard as well, morphine drip--did not know they gave it to me, Norco afterwards) with a C/S when I thought I would go as natural as possible. I must of crashed hormonally so of course my docor told me that I should take SSRIs made it worse...then went off of them after 8 months, then probably looking back had strange withdrawal effects 3 months later, and then went back on them not knowing better and felt even worse--merry go round of meds--then finally got off of everything psychiatric--it was horrific at the time. That is why I am searching for answers as to the story of my genes and what it appears I can handle if I need medication in the future.

So I like my vitamins/minerals, homeopathy, and use spices--sort of an ayurvedic approach to life without many of the herbs--I can be at times too sensitive to these things. I would like to optimize my health to feel better--not as irritable, reduce PMS, have more energy, better digestion--may have leaky gut and IBS, and not worry about my health so much! Sad to say I was on a lot of antibiotics growing up because of sinus problems and my doctor and mom thought this was the way to treat it and not really look at anything else--diet, allergies, etc. But that was over 20 years ago--lots of probiotics since but I wonder how much of a hit my immune system took and how much it still may need to be fully healed.

That's the short story. Thanks for any assistance....I appreciate your time. Have a great day!

 

[ppodhajski]

Well here are my stats in my signature from genetic genie...not sure how to write in a different color though. There are many more of these gene mutations that I have not listed that came out of mthfr and now promethease. I attempted to look up a few genes in uniprot @ppodhajski --for example cyp1b1 looks like it has a cofactor of iron (heme)--do I have this right or am I looking in the wrong place? It looks like it has to do with estrogen, what does that mean?

You are right, iron is a cofactor. That CYP gene does a lot of stuff!

Any suggestions on which are the most important gene mutations to focus on would be great. It seems like a lot of information to look at and try to figure out.

Do you have a promethease report?

Do not do well with caffeine nor sulfa drugs or really most antibiotics. I have tried to be as holistic as I can but sometimes things like ashwaghanda were a bit much--but I have been on a low dose of thyroid medication for several years so that could have been too much of a combo for me. I really took a downward spiral after my son was born--had all the "fixings" for delivery and beyond (pitocin, epidural, anesthethic -- which I take hard as well, morphine drip--did not know they gave it to me, Norco afterwards) with a C/S when I thought I would go as natural as possible. I must of crashed hormonally so of course my docor told me that I should take SSRIs made it worse...then went off of them after 8 months, then probably looking back had strange withdrawal effects 3 months later, and then went back on them not knowing better and felt even worse--merry go round of meds--then finally got off of everything psychiatric--it was horrific at the time. That is why I am searching for answers as to the story of my genes and what it appears I can handle if I need medication in the future.

If you have trouble metabolizing medications because of CYP (Cytochrome 450P) genes it could make you feel bad when taking these medications. When you get a promethease report do a search just for CYP, sort by frequency and see what you see. They all use iron as a cofactor so maybe get your iron levels checked?

The three month SSRI withdrawl..you much have been on prozac, it has a long half life. I was on prozac and the same thing happened.

So I like my vitamins/minerals, homeopathy, and use spices--sort of an ayurvedic approach to life without many of the herbs--I can be at times too sensitive to these things. I would like to optimize my health to feel better--not as irritable, reduce PMS, have more energy, better digestion--may have leaky gut and IBS, and not worry about my health so much! Sad to say I was on a lot of antibiotics growing up because of sinus problems and my doctor and mom thought this was the way to treat it and not really look at anything else--diet, allergies, etc. But that was over 20 years ago--lots of probiotics since but I wonder how much of a hit my immune system took and how much it still may need to be fully healed. !

Based on what you are saying here I would check MAOA, MAOB, COMT, FADS1, FADS2, SUOX, BTD, MCM6. I think we will see your COMT, MAOA and MAOB genes being the slow ones.

You sound a lot like I was.

 

[caledonia]

Hi Phoenix76,

Wow, if your SNPs are written down correctly, you have a very rare triple mutation for MTHFR. I've only seen 3 people with a triple online.

I'll make some comments on your symptoms, but in general go to my signature at the bottom for my methylation documents and other helpful links.

Any suggestions on which are the most important gene mutations to focus on would be great. It seems like a lot of information to look at and try to figure out. My detoxing issues were pretty evident after taking birth control years ago--where that one trial was enough to say no in the future

Birth control pills are notorious for depleting folate. With three MTHFR mutations, no you wonder had issues. Depression is commonly reported.

and then SSRIs around that same time

You have some CYP (detox) SNPs which off the top of my head would make metabolizing SSRI's difficult.

and after my son was born 3 years ago--another bad reaction.

Assuming you had some kind of painkillers or anesthesia or something - same deal - bad detox SNPs, not to mention MTHFR.

Do not do well with caffeine

Your CYP1A2, which metabolizes caffeine, is somewhat slow. Adrenal fatigue can also affect this. I have no mutations and have trouble with caffeine, but the better my adrenals get, the better I can tolerate it.

nor sulfa drugs

Your CBS mutations + possibly mercury toxicity could be culprits here. (causes trouble with sulfur)

or really most antibiotics.

Check the CYP SNPs for which ones metabolize antibiotics. Fluoroquinolones are especially bad for those with MTHFR.

I have tried to be as holistic as I can but sometimes things like ashwaghanda were a bit much--but I have been on a low dose of thyroid medication for several years so that could have been too much of a combo for me.

Thyroid issues are common for both MTHFR and mercury toxicity.

I really took a downward spiral after my son was born--had all the "fixings" for delivery and beyond (pitocin, epidural, anesthethic -- which I take hard as well, morphine drip--did not know they gave it to me, Norco afterwards) with a C/S when I thought I would go as natural as possible.

Yeah - hold the fixins please! :-( CYP SNPs and MTHFR are suspects here. If you need anesthetic in the future, google "anesthetic and CFS" to find a list of ones which you should tolerate better. The nitrous oxide in the anesthetic depletes folate.

I must of crashed hormonally so of course my docor told me that I should take SSRIs made it worse...then went off of them after 8 months, then probably looking back had strange withdrawal effects 3 months later, and then went back on them not knowing better and felt even worse--merry go round of meds--then finally got off of everything psychiatric--it was horrific at the time. That is why I am searching for answers as to the story of my genes and what it appears I can handle if I need medication in the future.

SSRIs - see CYP SNPs for which ones detoxify SSRIs. I have many of the same CYPs as you and also had trouble with SSRI withdrawal syndrome many months after I got off. Definitely horrific.

A double MTHFR A1298C mutation, as well as COMT and MAO A mutations are also associated with mental health issues.

So I like my vitamins/minerals, homeopathy, and use spices--sort of an ayurvedic approach to life without many of the herbs--I can be at times too sensitive to these things. I would like to optimize my health to feel better--not as irritable, reduce PMS, have more energy, better digestion--may have leaky gut and IBS, and not worry about my health so much! Sad to say I was on a lot of antibiotics growing up because of sinus problems and my doctor and mom thought this was the way to treat it and not really look at anything else--diet, allergies, etc. But that was over 20 years ago--lots of probiotics since but I wonder how much of a hit my immune system took and how much it still may need to be fully healed.

I would suggest starting with the gut (4R Gut Rebuilding Program). You have to specifically kill off candida or other gut bugs. Taking probiotics is probably not enough to crowd them out. Also consider mercury toxicity as an exacerbator of gut issues.

 

[ppodhajski]

On MTHFR and MAOA, they are both FAD (Riboflavin) dependent enzymes.

http://www.uniprot.org/uniprot/P42898
http://www.uniprot.org/uniprot/P21397

COMT is Magnessium dependent, but be careful because I found I had way less a need for magnesium when I was supplementing with riboflavin.

http://www.uniprot.org/uniprot/P21964

In my opinion and experience, "gut rebuilding" is a dead end. Getting enough riboflavin fixed my gut on its own. And I thought for years I had some bacteria or fungus.

 

[phoenix76]

Thanks to both @ppodhajski and @caledonia. Food for thought....I had been on Paxil years ago after birth control problems and had just gotten on thyroid meds a couple months before that---had a bad bout of mono, then after son was born Prozac for a few days then a switch to Zoloft for 8 months...off for 5 months (misquoted myself earlier)...then not so good merry go round of meds when trying to reintroduce Zoloft. The nightly brain zaps jolting me awake and lots of anxiety before I reintroduced the Zoloft after the 5 month hiatus was what really scared me into going back on the drugs not knowing that it was a withdrawal effect. Then on merry go round of meds with psychiatrist (first and last time I will see one) was even worse--more anxiety like I wanted to hide from everything--so unlike me--ended me up in the hospital (not suicidal) on my own--I do not think I slept well or really at all for almost a week before I said enough was enough--you people figure it out because I do not want to go nuts from that much sleep deprivation--adrenals were probably so worked up at that point from the drugs that I could not sleep. I know it was medication induced because I have never felt that freaked out before or wanting to crawl out of my skin without medication--it was always when I introduced something that did not agree (birth control, SSRIs ,and the merry go round of so many drugs I cannot mention them all). I do not think anyone thinks they will be in the hospital over medications until you either experience it yourself first hand or you are with someone experiencing it.

Now with the information I have and the past history of medication problems, I will be very carefully what I take in the future. I want my son tested for his genetic makeup too. I wish I would have known these things--could have prevented a lot of problems--but at least I can do something about it now, for my family, and possibly for others (when I get around to figuring this out!).

You are right on many of the conditions present especially on my mom's side of the family for emotional problems--depression not as bad as anxiety for me--wonder how much the chocolate I would eat on a regularly basis was fueling this. Yoga has helped me tremendously--not always asanas (poses) but really the daily meditation, deep breathing, the outlook on life. If I do not work out though at least 3 times per week though--cardio/weights/stretching, I do feel "depressed" but not a true depression. More achy and irritable. But irritable is the mainstay here for as long as I can remember. Do my scores look estrogen dominant and does use of progesterone cream help in your opinion? I am on the fence about its utility for me--it is okay and helps me to have a better period--not as much PMS--but I wonder about its detoxing out of the body. I like the book What Your Doctor Doesn't Tell You About Perimenopause.

So I will check out mercury toxicity in the body along with other heavy metals. Would you like me to share the promethease report? Not sure how to do it without personal details.

Gut--it is difficult to say if I have candida--no smells, discharge, or itching characteristic of it but my tongue is slightly coated white but I have a lot of allergies too. No bacteria noted on GI doctor tests--I looked as clean as a whistle! I keep up with my probiotics--that is for sure. I usually do a no sweets Lenten time and feel great--sugar is inflammatory but it is not as if I am craving it as much as muffins/breads at times. It is addictive though.

On another note, how do you know how much riboflavin to take...and I would suppose it should be activated. And how do I check on (not sure how to requoute)
"Based on what you are saying here I would check MAOA, MAOB, COMT, FADS1, FADS2, SUOX, BTD, MCM6. I think we will see your COMT, MAOA and MAOB genes being the slow ones." Is it further testing to see what is slow versus better functioning?

Thanks again...if you want pointers on yoga or guided imagery (not certified in hypnosis yet), just let me know! I would like to help others too with the knowledge I have to offer =o) Take care.

 

[ppodhajski]

@phoeniz76 Meditation helped me tremendously as well. I was a practicing Theravada Buddhist for years. But I will say it will not cure anything. Diet, lifestyle, and cofactor vitamins are the combo that make me feel better than I did in 30 years. I was hospitalized twice with anxiety and once suicidal.

The next report you should get is from http://promethease.org/ It is only $5 and will help you find the SNPs we are talking about. I can ask you to look up certain ones once you get that.

 

[phoenix76]

That's great that you meditated for years. Do you still? It has helped me with emotional concerns--but in the midst of the medications issues, it can only do so much. And I understand it does not fix the overall health issues--just helps t ground and calm.

The whole package of lifestyle you mention is the key. I can see the validity about gut issues too but everyone is different. There definitely feels there is something off in the gut--IBS perhaps so I have been on a FODMAP diet trial but do not see this amazing improvement but some. I look forward to figuring out how much of these cofactors to take to help myself and not have them cancel each other out.

I do have the report from promethease.
This is an interesting report and vary detailed--almost too much until I understand where to look for things.

 

[ppodhajski]

Great. I will post a series of SNPs you can look up. I used to have IBS-D. No more unless I eat a lot of dietary amines. I tried every gut health thing under the sun but I based on your other symptoms I am guessing it is a neurotransmitter issue at the root.

 

[phoenix76]

Thank you...I will see what comes out fixing things with cofactors. I have heard of neurotransmitters in the gut especially serotonin and how an imbalance can effect the gut but am not well versed on it. More things to research...I am glad I like research!

I found this on dietary amines http://aminerecipes.com/low-amine-grocery-list/. Is this a good resource or is there something better out there? There is a food list you can click on to open another page as well.

 

[ppodhajski]

Thank you...I will see what comes out fixing things with cofactors. I have heard of neurotransmitters in the gut especially serotonin and how an imbalance can effect the gut but am not well versed on it. More things to research...I am glad I like research!

I found this on dietary amines http://aminerecipes.com/low-amine-grocery-list/. Is this a good resource or is there something better out there? There is a food list you can click on to open another page as well.

That amine list is the best around. Note that there is only very sketchy info on the amount of dietary amines in foods and that list was made by a citizen scientist, but when I matched my known sensitivities to that list it was pretty much spot on.
Keep researching amines, monoamine oxidase, and COMT and you should start to see a pattern.

 

[phoenix76]

Great. I look forward to setting some time aside for this and seeing where I need to look on the promethease report. Off to work now... Have a wonderful afternoon!

 

[ppodhajski]

Finally got home. Here is the first list of SNPs I look at: The allele next to the SNP number is the allele that makes the enzyme work more slowly, leaving more catecholamines (like serotonin) around. Also, the alleles are those listed in promethease. The 23andme alleles might be reversed (different).

MAOA
rs909525 A (Will be T in 23andme)

MAOB
rs2283729 A
rs1799836 G (Will be C in 23andme)

COMT
rs4633 T
rs4680 A
rs165722 T

I am homozygous for all of them.

 

[caledonia]

I want my son tested for his genetic makeup too.

Good idea. Hopefully, he got more SNPs from his dad and they aren't as bad as yours.

Do my scores look estrogen dominant and does use of progesterone cream help in your opinion? I am on the fence about its utility for me--it is okay and helps me to have a better period--not as much PMS--but I wonder about its detoxing out of the body. I like the book What Your Doctor Doesn't Tell You About Perimenopause.

CYP1B1, and COMT are associated with estrogen. Try pharmaceutical grade fish oil for PMS - could be an EFA deficiency issue. Works for me anyway. If you need to lower estrogen, do cruciferous veggies or DIM or IC3 which are components of said veggies or calcium D glucarate if CBS is an issue.

So I will check out mercury toxicity in the body along with other heavy metals.

Check out Andrew Cutler frequent low dose chelation. Do a hair metals and minerals test interpreted with Cutler's counting rules. Other styles of chelation may make you worse.

Gut--it is difficult to say if I have candida--no smells, discharge, or itching characteristic of it but my tongue is slightly coated white but I have a lot of allergies too. No bacteria noted on GI doctor tests--I looked as clean as a whistle!

Which GI tests?