Acetylcholine/Choline Deficiency in Chronic Illness – The Hunt for the Missing Egg

ucm278430We hear a lot about vitamins and minerals such as B12, folate, magnesium, vitamin C, and so on, but there seems very little talk these days on the importance of dietary lecithin and choline. Are you consuming an adequate amount of acetylcholine, or other phospholipids? The odds are that you are not.

A little bit about choline

The human body produces choline by methylation of phosphatidylethanolamine (from dietary sources such as lecithin and others) to form phosphatidylcholine in the liver by the PEMT enzyme. Phosphatidylcholine may also be consumed in the diet or by supplementation. Choline is oxidized to betaine which acts as an important methyl donor and osmolyte.

For those wanting to see how this relates to the methylation cycle, below is a nice graphic (courtesy of Wikipedia).

Choline metabolism

It is well known that magnesium deficiency is widespread (57% of the population does not meet the U.S. RDA according to the USDA), but the numbers for choline deficiency are even more shocking.
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Clearing up the VDR Taq Confusion

This confusion has been going on for quite a while, and I am writing this blog post to clear things up. Genetic Genie does not have an error when reporting VDR Taq. I used to report the SNP differently, but on January 13, I corrected this SNP to match Dr. Amy Yasko’s Nutrigenomics Panel.

The reason why I think it is important to be consistent between different panels is so that the existing methylation literature makes sense.

To prove that I am indeed reporting results correctly, I’ll show you images of an individual who did both a Nutrigenomics Panel, and ran their 23andMe results through Genetic Genie.

Here is their Nutrigenomics Panel.


Here is their Genetic Genie Panel.


Please notice how VDR Taq matches between the tables. Also, VDR Taq and VDR Bsm are usually inverse of eachother. So if you have VDR Bsm (+/+), you will usually have VDR Taq (-/-). While Dr. Amy Yasko no longer reports VDR Bsm, you can in the Genetic Genie table that this is true.

Here is a quote from Dr. Amy Yasko about this inverse relationship:

Taq and Bsm have inverse results. So it would make sense that Bsm is ++ if Taq is – -.

I hope that clears up the VDR Taq confusion.

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Change Gene Expression and Increase Glutathione with Relaxation Techniques

meditation-pose1Managing stress with relaxation techniques such as meditation, yoga, or biofeedback are things we sometimes ignore when facing a chronic illness. After all, how much can these relaxation techniques really help? I know that question goes through my mind at times. Even though practicing relaxation techniques can feel like a waste of time, practicing them can actually turn genes on and off.

Relaxation techniques change your gene expression

Dr. Herbert Benson did a study comparing 16 people who have regularly evoked “the relaxation response” for an average of 9 years to 19 people that didn’t use these techniques.

The human body has about 30,000 genes. Dr. Benson’s experiment found that roughly 2,000 genes differed in expression between groups. Many genes that triggered inflammation and cell death were turned off in the group that regularly practiced relaxation techniques. However, this deactivation doesn’t appear to be permanent. The daily practice of relaxation techniques such as meditation is necessary to sustain benefits.

When controls were taught techniques to evoke the relaxation response, about 1,500 genes changed their expression within 8 weeks. These were many of the same genes seen in the group that have been practicing these relaxation techniques for years.

Are relaxation techniques really going to fix anything?

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Happy Birthday to Me!

birthday-balloons3Ok, that sounds a bit narcissistic, doesn’t it? And a little bit unrelated to the subject of methylation and detoxification. But in reality, since late 2008, birthdays, holidays, and more were more like an anniversary of how long I have been ill. Negative thoughts would go through my head and tears would come from my eyes for this reason. These weren’t happy days – even if I tried to pretend they were.

This time around, I’m going to try to keep positive.

I created this website several reasons.

  • To help people that don’t have a whole lot of extra cash. Because of how expensive the medical system is, I wanted to make it easy (and free) for people to read their own genetics from less expensive testing.
  • When the medical system can’t step up to the plate, we can and will solve things in creative and collaborative ways. We have power over the medical system, and I think the future of medicine involves direct collaboration of patients, researchers, and doctors.
  • To prove to myself I can do something to benefit the community.

A little more about why I started this project and what’s next

When I started this project, I had no idea so many people would be interested in using it. This wasn’t a project I actually planned. But when I showed a few people a very bare bones website that extracts SNPs, the community urged me to keep the website up. And so I did.

But now I have a purpose. I enjoy working on the site, and it will only evolve into something better over time. I strongly believe that supporting the methylation cycle is important for many. I am still not well, but before I discovered the magic of that first B12 shot, I went through a period that I couldn’t do anything and felt like I was dying all the time. I couldn’t even talk to people most days because of nervous system dysfunction.

Since I want this to be a collaborative effort, I am going to develop tools and graphs to analyze data so the community, researchers, and doctors can all interact on this genetic journey in a dynamic way. I think the idea is unique and is needed. If we can find more patterns, we can find more creative ways to fix these patterns.

I give all thanks the community for urging me to pursue this project. Without you guys, this project wouldn’t exist.

Much love.

-Kyle (aka Genetic Genie)

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Study Confirms CFS Patients Benefit from Folate

19518Folinic acid (a derivative of Folate) was found to be effective according to a study (PDF).

Folinic acid was used at 25 mg a day for 1-2 months. Because there was already an established association between ME/CFS and Folate deficiency, this study did not look at the folate status of their participants. Nevertheless, 81% of patients reported significant improvement in pain and energy level within these one to two months.

This level of improvement is significant for CFS because CFS patients don’t respond favorably to many treatments. Furthermore, contrary to popular belief, CFS patients of a low placebo-response rate at only 19.6% after meta-analysis.

This study also showed immune problems such as marked depletion of their CD19 B-Cell mature B-cell population. This comes as no surprise as this been replicated in many other studies.

This study that I am referencing was done in 2006. Since then, according to what’s indexed in PubMed, nobody has looked at folate in ME/CFS. No, this wasn’t a huge study with a huge number of participants, but the 81% response rate should prompt further research and studies.

You may be wondering: If this data isn’t new, why am I talking about it?

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Methylation Analysis with Automatic Personalized Interpretation Now Here

ggWe’ve been working hard.

Genetic Genie Methylation Analysis with personalized automated interpretation is now available. Some parts of the interpretation are not finished as of this post. We still have some content to change, and we have some custom diagrams to make/add, but it’s here!

You can view an example interpretation here.

If you already have 23andMe, just go to “Methylation Analysis” and upload your file again.

If you want to learn more about the 23andMe genetic testing service, check out 23andMe.com.

Comments, feedback, suggestions, and corrections are more than welcome. Genetic Genie has finished laying the foundation, and now we want this to be a community effort. This should get better and better as we go along if there is participation from the community.

For now, you can leave comments through Feedback or a comment on the blog post. But what would be best for the future? If we made the data an open, editable Wiki, would anybody want to participate in editing and adding content? I think this would be really cool if there are people who are actually interested in taking part in a community effort.

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We Are Hiring Writers that Understand Methylation and Detox SNPs


We are hiring a Medical Writer that understands Methylation and Detoxification SNPs for automated analysis. We prefer someone who has a degree, has helped patients, or has a medical practice.

This is a paid job. Please send me a message through the Feedback form or a message through our Facebook page if you are interested in this position.

Our Facebook page is: http://www.facebook.com/GeneticGenie

Alternatively, you can reach me (Kyle) by phone at:

Please don’t use this number for technical support. If you have technical support questions or any other questions please use the Feedback form.

Further details and compensation will be discussed after you contact me. Furthermore, if you are a practicing physician or health consultant, having your name on Genetic Genie can can you attract patients and/or clients.

We are no longer hiring, but if you are interested in a volunteer position involving writing about SNPs are blog posts, you can still contact us.

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Avoiding Chemicals in Foods on a Budget: The Dirty Dozen

fresh-produceIt’s no secret that our food contains pesticides that are really bad for our body. And it’s also no secret that many patients and families are flat out broke from trying to take care of medical expenses.

But when you are trying to optimize your detox and methylation, the food you eat is important. The U.S. Department of Agriculture found at least 1 pesticide of the 68 samples of conventional produce analyzed.

Pesticides cause brain and nervous system toxicity, cancer, hormone disruption, skin, eye, lung irritation, amongst other things. They are toxic by design.

But there are steps you can take to limit your exposure on a tight budget. The website ewg.com has a guide called EWG’s 2012 Shopper’s Guide to Pesticides in Produce™ that lists the “dirty dozen” conventional fruits and vegetables. Buy these Organic to limit exposure to harmful pesticides.

Here are the fruits and vegetables that made the “dirty dozen” list
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Why support methylation and detoxification? Our ancestors didn’t need to.

024_p3aWe live in a toxic world. We have an epidemic of auto-immune disease. We have an epidemic of Autism. We have more than 80,000 chemicals that are unregulated and have never been assessed for the potential negative impacts on human beings, animals, insects and the environment. And even the chemicals that have been well-studied are often very toxic to the human body. But we still use them. They may impact DNA methylation in a very negative way, cause endocrine disruption, immune dysregulation, alter receptor sites that are necessary for life, and cause cancer. These chemicals may kill animals such as frogs and bees at very low concentrations, but we ingest them, breath them, and let them seep transdermally through our skin.

I won’t even begin to name these chemicals, because there are way too many to name.

So, how do we avoid all these harmful chemicals?
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Think Supporting Methylation is an Alternative Health Fad?

b12vitaminScience goes a process of discovery and de-discovery (when a discovery is proven to be a false discovery). People and physicians also fail to remember that we also go through a process of rediscovery as well.

Independent researchers, doctors, and even patients are researching, writing articles, creating podcasts, and uploading their presentations to YouTube about MTHFR and methylation. But much if not most of their information is unpublished. Many of these people researching don’t even hold a degree in the field. So what happens when you start throwing acronyms such as methylation and MTHFR all over the place while looking at these seemingly overly complex diagrams? People, physicians, and even scientists may be quick to call this activity unscientific and alternative medicine quackery. Something that looks overly complicated (like quantum physics) that seems to have suddenly appear out of nowhere must fall in this category, right?

Welcome to the 21st century. When science doesn’t do their job or is underfunded, independent researchers, doctors, and patients will step up to the plate. Researching isn’t just for those sitting in their Ivory Tower anymore. It’s becoming hugely collaborative.

So let’s get to the point of this post

Think supporting your methylation cycle is some new alternative medicine fad? Think again.

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