Armchair Genetics (help for DIY)

Updated April 30, 2019 by MTHFR Living

Thanks to those of you who reached out about our new guest post program. Today we have an excellent piece for those of you trying to figure all of this out on your own. Kiki Kish* will be doing a series of posts about her experiences and knowledge as a MTHFR patient, starting with this guide to genetic testing and what to do with the results.

I remember hearing about the Human Genome Project in the news around the time it was completed in 2003. Did I ever think how it might impact me and that I’d be able to get my whole genome mapped at my fingertips for my personal use to improve my health and that of my family? Of course not.

Well now you can get your whole genome mapped and find out what it means from the comfort of your favorite chair. The fact that lay people can do this and figure out what genetic anomalies we have, how they affect us and what to do about them is really a crazy testament to the modern times we live in, the power of computers and the utility of the internet. We’d prefer to consult with our doctor about it, but the reality is that most are no more up-to-date on it than we are. Practitioners or doctors who know something about genetic problems like MTHFR, the impact of compromised methylation, and how to treat it are hard to find. Thus, some of us choose to self-navigate this very new area of genetics for the common man.

I have been self navigating this kind of thing for two decades. As a self-navigator, nobody is going to spoon feed you; you have to do your homework to learn about it, and decide, perhaps through experiment, what the most effective treatment protocol for you will be.You’re into methylation now. It’s as individualized as you and all your thousands of genes are.  While you may feel that grasping this type of information is beyond your capabilities, remember, knowledge is power. Take what you find and learn about it. Take it to your doctor and ask for her help, but learn about it first. They really should be looking at this anyway because in a few years, they will be dinosaurs if they don’t understand the information that is easily available to their patients. The best use of this information particularly in relation to methylation is in prevention of diseases as well as ameliorating conditions we already have. But it’s also possible to nip in the bud a disease process that has already started. One person used this information to find that a family member had a very high risk of lung cancer, and upon scanning, found three tumors for two different types of lung cancer. My uncle just passed away this year to lung cancer. He never smoked and ate an apple a day.  I suspect he had an MTHFR defect but maybe he was just high risk for lung cancer. Mapping his genome may have shown that.

Back to self-navigating.  How do you get your genome mapped?  By using 23andMe or similar services. 23andMe provides ancestry-related genetic reports and uninterpreted raw genetic data. For our purposes, we want the uninterpreted raw genetic data. It’s a real bargain at $99. There are many other companies that provide interpretation of some small subset of your genetic data charging hundreds or thousands of dollars. To get your own genome mapped, go on the 23andMe website and order their kit. The kit is sent to your house; register it, provide a small saliva sample in a test tube, close it, shake it up, pop it back in their mailer, and in about two to three weeks, they’ll send you an email that your results are available. I don’t think the process could be any easier.

Then what?

There are a number of what I call genetic engines that you can run your DNA genome through to get useful reports that will help make sense of your genetic information and will also help you understand methylation better. Some of them will be able to access your data at 23andMe (with your permission of course) and with some, you will have to enter the data yourself. Here are four that I have found and a bit about them.

Genetic Genie

Genetic Genie is a non-profit site that will access your 23andMe data and produce a short but useful Methylation Profile report customized to the SNPs (single nucleotide polymorphisms or your genes) that they feel are most relevant. Like all the reports, the homozygous mutations are red (two defective genes), the heterozygous are yellow (one defective gene) and those genes that are normal are green. The explanations are good and while an insider told me that their engine is a few years old, it conveys what others say in a brief way that isn’t overwhelming in seven pages. They analyze 26 different genes, those of most concern with regard to methylation and related problems. The report is free with a suggested donation via PayPal of $10. Yet another bargain.

Know Your Genetics

This site is based on the extensive work of Dr. Amy Yasko. Although she didn’t intend to study autism, her work is really leading edge with regard to the treatment of it. I researched autism for my son back in 2000 and found her work extremely helpful. This site will take your manually input genetic information and provide a detailed report on your SNPs to recommend supplements that are categorized as general methylation support and also those that are specific for the individual SNPs that may be problematic. If you run the report from GeneticGenie you will have most of what you need readily available and the rest you can look up in your raw data on 23andMe (login to 23andMe, click on your name in the top right hand corner, and click “browse raw data”). Once you input your 20 SNP results, you can generate a Methylation Profile Analysis. This report is extremely informative, it’s about 56 pages long, and the list of supplement recommendations is extensive, with links to Dr. Amy’s site where the supplements are available. While the supplements listed in the report may seem overwhelming, they are broken down by basic methylation support and then recommendations for the individual problem SNPs so that you can consider the supplements based on the problems you feel are important.

The report contains a useful table that recommends the type of B12 to take based on two SNPs, COMT and VDR Taq.  This is incredibly useful because B12 and the right type of B12 based on your personal genetics is as much of part of your personal methylation therapy protocol as taking MTHF folate. There are four (yes four) types of B12.  More on that in future posts.  But the coolest and most useful thing about Dr. Yasko’s sites is that any questions you have can be answered in their discussion group at www.ch3nutrigenomics.com.  You can ask questions here and there are very knowledgeable people who will answer your questions. You may get seven slightly different answers, but if you are self-navigating, you will have to take the information and disseminate it yourself. Not a problem, you can always ask more questions. Many of the people on this forum put their SNPs of concern in their signatures. I’m sure they were all once newbie self-navigators, but are now further on the learning curve. One woman who answered my questions had 20,000 posts answering other questions. She seemed quite knowledgeable.

MTHFRSupport

This engine will also access your 23andMe results in order to generate a report. This report costs $20, another great deal! Nineteen pages of over 200 SNPs are nicely separated into several categories like thyroid, detox, methylation, clotting factors, celiac, mitochondrial, allergy and others. This report shows you what the risk allele is and which alleles you have. Another nice feature is that you can click on the SNP in the report and go straight to SNPedia (like the Wikipedia of genetic info) where you will find information on the gene as well as many studies on that particular gene related to the condition of concern. So if you observe that you have a number of anomalies affecting one category, you could go and read perhaps a dozen or more research studies on the problem and gain further understanding.

Promethease

Promethease provides very detailed information about your risk factors for many conditions as well as your interaction with about 100 common drugs. They report the good news and the bad news, your likely interaction with about 100 common drugs as well as numerous conditions and other things that have basically not been researched much yet. Warning: knowing your risk for everything under the sun based on current research can be unsettling, but it can also be quite interesting and useful and is only a modest $5 (make sure to download your Promethease data as it will only be on their servers for 45 days). There is a video on their homepage that explains how to download the report, unzip it and navigate it.

As an example of the information Promethease provides, one of my family members (male) has this BAD NEWS: is seven times less likely to respond to certain antidepressants, 6.2 times increased risk of developing prostate cancer, 4.5 times increased myopathy risk (for statin users), but has this GOOD NEWS: reduced risk of male pattern baldness, 10 times to 27 times lower risk of exfoliation glaucoma, greatly increased memory performance, 1.5 times less risk for physical impairment with age, and one copy of the longevity gene.  Promethease ranks the conditions in order of import (a subjective measure), tells you how many references there are (studies that found that same thing), and the frequency with which it appears in the general population. It also tells you which conditions you have a normal risk for, which is comforting.  A description and examples of the report results may be found here.

Other Tools

There are and will continue to be numerous other such genetic engines that can help; they are all different and provide various information and reports based on your genome. Selfdecode.com will recommend supplements and provide reports based on your genome and conditions you have that you input manually. Livewello’s Gene App is another option for your Raw Data. This web application gives results for about 600,000 genes and comes with 8 Learning Resources linked directly to each of the Genes in your Variance Report.. Nutrahacker.com is yet another.It lists gene function, consequences, what to take to compensate, and what to avoid. A limited report is available free, the paid report is comprehensive. And there are probably more and more will continue to pop up.

This kind of information can be overwhelming, but you have to consider again that knowledge is power. If I knew I had a significantly increased risk of something, I would do what I could to prevent that and also make sure I was monitored by a doctor for that condition. In 2007, my husband had an awful treatment for Hepatitis C (Interferon/Ribavirin). This treatment seemed to age him 15 years, and he lost 40lbs that he didn’t need to. It was probably hard on him partly because he is MTHFR heterozygous for both 1298 and 677 and did not tolerate the toxicity of it. Had we known that he had an impaired ability to handle toxins and was unlikely to have a response to this treatment, he would have never undergone it. Promethease actually addressed this treatment noting “ rs12979860 – less likely to respond to Hepatitis C treatment PEG-INF-alpha plus ribavirin”. Before that treatment, he was chopping wood in a manly fashion. After the treatment, he wasn’t chopping wood at all, but he’s progressing quite well on his methylation protocol, so who knows.

The only areas of medicine that I know that seem to be using this genetic information in a useful way is to tailor treatments like chemotherapy and medications such as those for mental conditions (finding who will and won’t respond to certain medications). I’m sure there are other areas, but it really needs to reach the mainstream, our primary care doctors, radiologists, dermatologists, rheumatologists – all of them. All doctors could be using it to help with diagnosis, medications and treatments. Educate yourself, use the information to benefit your family, and try and spread the word to get others on board. Whatever problem you have, improved methylation will help it.

Be informed. Most mainstream doctors have heard about MTHFR but do not take it seriously. As you know by now, methylation is a critical biological process and very important to disease prevention. Good luck.

Always check with your doctor or a qualified practitioner before starting any methylation related protocol.

In 1992, my husband, 24 years my senior, was diagnosed with Hepatitis C. Hep C is a serious liver disease without a cure, so I explored alternative medicine. Now at 75, he is the poster child for transplants and health with Hep C, mostly because I became a self-navigating nutritionist, naturopath and now a budding nutrigenomist. In 2001, my son was diagnosed with Autism. Same thing, no cure, but I used supplements and nutrition; he’s in college making As and Bs. These two situations along with a parent with cancer caused me to do two decades of research on alternative therapies. I was often asked if I was in the medical field probably because I did my research to try and make sure that the doctors were doing a good job. I had problems for which I was prescribed medication, but the doctors, as usual, didn’t discuss what might be causing it. I determined I had a histamine intolerance problem, and in researching that for myself, I found that compromised methylation could be a cause. That led to MTHFR (I’m heterozygous for 677C). Once I did the research on it, as an engineer (M.S), I found the statistical prevalence of the defect and the risk of problems and diseases it causes or contributes to astounding. Everyone in my family as well as those in my extended family who have been tested have the defect and have many related conditions. And that’s how I arrived here. 

* Name has been changed to protect privacy.

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