Thursday, May 19, 2016

Genetic Testing

If you have read my post on Hereditary Hemochromatosis (HH) you will know that I ordered some genetic testing from 23andMe to verify I had the mutated genes related to HH and to confirm that was the cause of my iron overload.  I mentioned then that instead of getting a doctor ordered HFE gene test to verify I decided to pay out of pocket $200 for the 23andMe test because I was interested in some of the other data.  So what do you get when you order one of these tests and what can you do with it.

The process is pretty simple you order the kit, spit in a tube, send it back in the box they provide and then wait.  The website says 12 weeks.  Mine took around 10.

2/5/16 Registered 
2/10/16 Transit 2/10/16 Receiving and Quality Inspection 
2/17/16 DNA Extraction finished 
2/25/16 DNA Analysis completed 
4/10/16 Quality Review Completed 
4/10/16 Initial raw data
4/12/16 computation and report generation

So what do you get.  You get a number of reports in different categories.

Carrier Status Reports - These are optional you don't have to get them if you think its going to be something that maybe will weigh on your mind.  I got them and honestly for me there wasn't really anything in here that stood out for me.  

Ancestry Reports - What you would expect, reports on where I came from.  Shocking I know but I'm 99.9% likely to be European.  

Wellness Reports - Some more mildly interesting information.  I metabolize caffeine pretty well, I'm a deep sleeper, lactose tolerant and a sprinter.  Again nothing earth shattering.  

Traits Reports - physical trait information

If you drill down to the view reports.  For Facial Features it looks like this.

If I then drill to eye color, you get this

Again, its all mildly interesting but nothing that is too earth shattering.  For the most part, that's about it.  You used to get more than this but in all its wisdom the FDA cracked down on the site.  You used to get health reports that showed if you were genetically susceptible to certain things.  However the FDA saw this as a service providing disease diagnoses which made the service a medical device and that they were subject to explicit FDA approval.  23andMe worked out an agreement with the FDA to continue selling the test, but only providing raw genetic data and ancestry information not health reports.

However, you can still get this information by using other services.  Since you can dowload the raw gene data from 23andMe you can use that data to feed into other services and get more information.

Screen shot of the raw file

First I ran it though Rhonda Patrick's new free tool.

This report has most of the common single nucleotide polymorphisms that I often like to talk about in podcasts and during presentations. Including polymorphisms that affect the absorption or utilization of nutrients like omega-3 ALA, vitamin B12, vitamin D, vitamin E, as well as polymorphisms that affect the interaction between our bodies and other dietary components like to saturated fat or heterocyclic amines which are formed when meat is cooked at high temperatures (among other things).
Here are my results

If you click to read more you get something like the following.

This is definitely more like it and produces some actionable results.  For example I learnt that supplemental vitamin E is probably not good for me.  And that I should avoid over cooking meat.  As of this writing this is the first version of this tool and Rhonda has said that she plans to add additional polymorphisms that she thinks are important.  So I'll probably want to come back in the future to see if there are any updates at some point.

As you know if you read my post on Hereditary Hemochromatosis I also pulled my data into a tool called Promethease.  It costs $5 and gives you a ton of information.  First off it immediately confirmed I had the gene for Hereditary Hemochromatosis.  It color codes the bad ones in red and gives them a magnitude number.  You can see it was a Magnitude of 4 below.

You have a bunch of filter options as I have 19872 gene values of which 349 are bad.

By default it will sort by magnitude descending but you can customize your search many different ways.

If I just show the bad and sort by magnitude Hereditary Hemochromatosis is the second entry.  I actually have something above it and I've now found out I'm an APOE e4 double carrier.  Wow, I really nailed the genetic lottery.

It means I'm at a very high risk for Alzheimer's.  I basically have a 1 in 2 shot to get Alzheimer's by the age of 80.  It also means I'm a slow recycler of cholesterol so my lipid panel is going to be higher regardless of what I eat.  Not the greatest news in the world but I'm a firm believer that it is better to know and act accordingly.  I can now try to stay on top of the latest Alzheimer's research and obviously I'm looking at everything to improve brain function.  More info on APOE e4 and what I'm doing about it is too much for this post but I'll cover this more in the future.  However based on this finding and some of the other findings from Rhonda's gene report I have reduced my saturated fat intake a bit and switched it over to more poly and mono fats.  So Olive oil instead of butter in some spots.

Talking of fat intake you can also use your data to plug into this flowchart from this article and see what kind of diet and exercise is best for your body.

rs4994 8 37823798 AA
rs1042713 5 148206440 GG
rs1799883 - don't have that one
rs1801282 3 12393125 CC

Interestingly it says I will lose more weight on a low fat diet.  This is the opposite to how I eat as I eat a high fat diet.   Of course I don't need to lose weight either so you have that, still interesting anyway and the price is right (free).

So I then took this concept to the next level and had DNAFit analyze my 23andMe data.  DNAFit is a site based in the UK a bit like 23andMe but they gear specific Diet and Exercise strategies for you based on your genes.  They also accept the 23andMe data feed. There are a number of options between Diet and Exercise and how much data you want.  It can cost anywhere from $79 to $400 if you already have the 23andMe data.  I went with the basic info for Diet and Exercise and it cost $149.  If you had to get the gene test as well you're looking at $400.  In of itself its probably too expensive for most people but if you do already have the 23andMe data it has some pretty interesting info.  I got back 3 reports, one on diet, one on fitness and a nice one page infographic you can see below.

If you want to view the full report pdf's for me you can get them here.

Power/Endurance Profile

So I'm more of a power responder and I would agree I'm a better sprinter than an endurance athlete.  But I also have the body of an endurance athlete and am a hard gainer in the gym.

Aerobic Potential (VO2 Max)


Based on this they do make post exercise nutrition recommendations.

Its pretty basic because personally I can't take Vitamin C because that increases my iron absorption which isn't good with HH and as we saw on Rhonda Patrick's  report Vitamin E can be harmful for me.  So I'll ignore these, but the concept is interesting.

Injury Risk


Carbohydrate Sensitivity

This seems to line up with what I'm seeing from taking frequent blood glucose readings.  Something I still struggle with but I'll expand on that another time.  I do eat low carb high fat.  Also most of the carbs I do take in are from potatoes, white rice, starchy veg and a minuscule amount of fruit.

Fat Sensitivity

They also go over the following, if you're interested check out the whole report for me here.

Anti Oxidant Need
Omega 3 Need
Vitamin B Needs
Vitamin D Needs
Salt Sensitivity
Alcohol Response
Caffeine Sensitivity
Lactose Intolerance
Coeliac Predisposition

So overall there is some pretty interesting info.  I would take some of it with a grain of salt but I found it at least more informative than just the plain 23andme and in some cases it supports ideas that I already had in particular my carb tolerance.

Finally you can compare some of your stats to olympic athletes, unsurprisingly all from the UK. As of this writing: Craig Pickering (Sprinter, Bobsleigh), Greg Rutherford (Long Jump) and Andrew Steele (400 M).  Nothing useful here but a bit of fun.  I choose Craig as he is a Sprinter.

I'm on the left you would think his power response would be higher as a sprinter.

Finally the closet Libertarian in me should probably point out the potential privacy issue with getting your DNA data.  There have been cases of the police requesting data from 23andMe and making people suspects based on this.  Read this Wired article.  That's kinda scary and also the idea of your data getting handed over to a health insurance company and your rates being adjusted based on your genetic makeup are not out of the realm of possibility.  However you can delete your data from 23andMe by written request

Account Deletion: You have the right to delete your genetic information from our systems. Within thirty (30) days of receiving your written request, we will delete your account, and your information will not be included in any future research, including future research by other organizations. Any research conducted prior to the end of the thirty (30) day period following receipt of your request will not be altered or halted. Once your account is deleted it will not be retrievable. For purposes of clarity, any user-generated content you contribute will not be deleted and your genetic information associated only by barcode may be retained at the laboratory. Click here for more information.
This is not something I've done yet but will probably make that request at some point.  It also means you should probably be fairly careful in what other tools use your data.  So just keep that in mind if genetic testing is something you want to try.


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