Wednesday, May 16, 2012

Methylation SNP's and other 23andme Genetic Results

Since getting my results back from 23andme, I have been digging into my results looking for some clues or some ideas or things to look out for. One of the things that interested me were Dr. Yasko's methylation SNP's. Now that the cost of genetic testing is coming down each year, its popularity is increasing in the chronic illness communities.

Do the answers to our chronic health problems, lie within our genetics? 

To see my results of Dr. Amy Yasko methylation SNP's, check out this google document. At the time of this writing, Dr Amy Yasko was currently testing for 30 SNP's, 25 of those are included in the 23andme test.

I've had about a month or so to study the SNP's. I haven't started on supplements mostly because I don't have the money, but also because my results seem to contradict each other. One mutation says I need this, then another one says I need the complete opposite. Talk about confusing! The one thing that piqued my interest were the homozygous mutations on two COMT SNP's and the homozygous mutation on MAO A. It certainly makes sense why I'm a type A personality. I tend to be on the jittery, anxious side and my norepinephrine levels are elevated upon standing too. It may also explain why I do soo poorly on seemingly innocent supplements like CoQ10, l-Carnitine and other methyl donors. What it does not explain though is why I never had any issues taking methyl B12.

If anyone wants to read up on the complexity of the methylation SNP's, I recommend seeing this website here.

Are the Methylation SNP's As Important As They've Been Made Out To Be?

That's a very good question and one no one knows the answer to yet. After doing more research into all of this, I am quite skeptical of the theory that these methylation SNP's are the reasons why people have autism, CFS or some other chronic illness. I know saying this might upset some people and I do believe having certain combinations of mutations are likely contributing, but I do not see convincing evidence that suggests these are the cause of these conditions. The evidence that really made me question things, was their high frequency numbers in the HapMap populations. "Fixing" these mutations with supplements may only help so much...or maybe not help at all. We really do not know.

It's important to remember that genomics is in its infancy and these methylation SNP's are not the end all, be all. Even completely normal people with no health problems have mutations. I cannot stress that enough! Healthy people do not have -/-'s for all of those methylation SNP's. As I stated above, the genotype frequencies for some of these are actually quite high in the population. If you find out you have one of these, don't panic. Do some fact checking and input the RS ID into the search box at to see how many others share it with you.

In this screenshot, I searched the rs ID for CBS A360A mutation which Dr. Amy Yasko says is the "Trump card". Well 47% of the people listed on here have at least 1 mutation on this SNP, 10% of people have 2 mutations. The scientist in me has to come to the conclusion that it can't be THAT bad if over 50% of the people on OpenSNP carry it. 50% of the US population does not have CFS and Autism...

There's more to the puzzle and I think it's going to be more complicated than just a few Methylation SNP's. I really think it's going to take full genome sequences to figure this out and even still, there's no guarantee any of these illnesses are genetic. Rare variants do not automatically mean a problem and I have nothing but respect for Dr. Yasko, but I question some of the SNP choices she's made with her testing. If a 1% frequency variant is meaningless to protein changes, then how can be say something with nearly 60% frequency is causing debilitating, life changing chronic illnesses?

A Small List of My Rare Variants

Over the past few weeks, I've spent just about every waking hour (sad pathetic life, I know) digging through my 23andme results. I have found some really weird things, so weird I can't find any information on it. I've been copying/pasting my interesting variants into a document and moving on to find new things. 

Perhaps it will all make sense eventually. :)  Within the past few days, I found out I have some very peculiar genotypes on my CYP3A5 and CYP3A43 genes. These are the enzyme pathways in your body responsible for breaking down medicines, toxins, lipids, cholesterol, estrogen and much much more. The ones I have listed below are less than 1% frequency in CEU populations. Some of them are so rare, no one on even has them, unless you want to count the 41,000 year old Denisova Hominin...haha

Hopefully as more people add themselves to this website, I won't end up being the only person with these genotypes!

In my unprofessional opinion, it's these rare genotypes that are interesting and likely meaningful. I figure whatever is wrong with me (us) can't be THAT common or more people would be suffering from it. Here's a list of the very low frequency genotypes I have on the CYP genes. I'm sure there are more, but these are the ones I found by hand.

Do any of you have these? If so, please contact me. My contact info is at the top of my blog. 
rs1081004 is TT 

rs28371764 is AA Currently no one is reporting this genotype on

rs545400 is AA 
rs667660 is GG 
rs585071 is GG
rs688926 is AA
rs501275 is GG
rs549061 is AA

If you also decided to go with 23andme instead of Dr. Yasko's test, in my next post, I'm going to show you how to locate your results to Dr. Amy Yasko's Methylation SNP's. I created a spreadsheet that will take all of the guess work out of it!

Quick Links:
Determining Your Yasko Methylation SNP's with 23andme Data
How to Get the Most Out of Your 23andme Data Part 1
How to Get the Most Out of Your 23andme Data Part 2
How to Get the Most Out of Your 23andme Data Part 3 (Coming Soon)
How to Get the Most Out of Your 23andme Data Part 4 (Coming Soon)

1 comment:

Musicchick581 said...

Were your 23 and me results conflicting with Yaskos at all?