Wednesday, March 06, 2013

23 and Me

This is the century in which personal DNA sequencing became affordable. And so it was unavoidable that curiosity would finally have me sign up at 23andMe, spit in a plastic tube, and see what's in my genes. Primarily, I just wanted to know how it works. So here's how it works for those of you who share my curiosity and are thinking of having a look at their genetic information too.

How does it work?

First thing you do is order a spit kit. It contains a plastic tube with some preservative and exact instructions how to send it back to the lab. 23andMe is located in California. They ship outside the US, but not to all countries; you can find a full list here. Cost for the spit kit is presently at US$ 99. To this you have to add the shipping and customs cost for a "human sample" which comes at US$ 79,95.

I ordered the spit kit on January 4th. It was shipped January 10th and arrived in Germany within a few days. They ask for quite some amount of saliva, so it's not really done with "just spitting." It took me half an hour or so to fill the tube up to the mark.

There's a number on the spit kit that you have to register on the website. For this you have to set up an account if you haven't already done that anyway. Then close the tube and seal it into a plastic bag with a biohazard logo which goes into a padded envelope. The spit kit comes with customs forms that have to be filled in. (If you live in the US, the procedure is easier). To send it back  to the lab, you have to drop off the envelope at a DHL Express station. So if you think of doing this, you might want to check where you find the closest one to your place.

On January 18, I received an email saying the sample arrived in the lab.  They tell you the analysis takes on average 6 weeks. On March 4th, after exactly two months, I got the results. It should be said that that they don't actually sequence the whole DNA. They look for about a million SNPs that are known or suspected to be interesting for one or the other reason.

What do you get?

First thing you see when you log in to view your results is the question whether you want to opt out of receiving health information. If you do, you only get information about your genetic ancestry.

Once logged in, you can browse the raw data if you like, this will give you a long list with names of SNPs, their position, and your genotype. For the average user like me, who doesn't know a terrible lot about genetics, this isn't very useful though. What's more useful is the summary you get that tells you what's known about your genotypes, what this means, and how reliable this information is.

In the "Health" menu, you have the categories "Disease Risk," "Carrier Status," "Drug Response" and "Traits." Disease risk and drug responce is self-explanatory. Carrier status tells you if you carry any known mutations responsible for heritable genetic diseases (which you might not necessarily get yourself but just pass on to your kids). Disease risks come in percentage of likelihood to develop some disease, and they tell you whether your risk is higher or lower than average. In addition the results are labelled by stars telling you roughly how reliable the conclusion from existing research is. Drug response gives you a list of drugs you are likely to respond to more or less than average, which is valuable medical information.

The first three categories in the "Health" menu contain more details than I'm comfortable sharing publicly, so let me instead show you a screenshot of the "Traits" list, which you could summarize as fun facts


Blue eyes, curly hair, and, no, I don't use deodorant. I've always assumed the rest of the world is just somewhat weird when it comes to their arm pits.

Now let's look at the ancestry, which you see in the screenshot in the left menu. The "relative finder" isn't working yet, it says they're still processing my data. For all I know I haven't lost any relatives, so I'm not expecting to find many. The ancestry composition tells you where your genes came from 50 years ago, it looks like this:



So, I'm European, but then you already knew that. From what I know of my family, I'd have expected more East European and less North European though; I'm somewhat surprised about this. Who knows what my ancestors have been up to.

And then you can trace your maternal and paternal line. The maternal line comes down through mitochondrial DNA which is exclusively inherited from the mother. Allegedly, if you look back long enough, we all go back to the same woman, referred to as Mitochondrial Eve. But there have been a few mutations since and the line has split, which allows some localization. 23andMe lists your haplogroup and shows its estimated distribution about 500 years ago:
Again, it looks more nordic than I'd have expected.

The paternal line is traced via the Y-chromosome. So I'll have to convince a male relative to spit for this information. I think I know what my younger brother will get as a birthday present ;o)

The website

The website is very functional, readable, and works well. What I appreciate very much is that they don't just give you a likely correlation between your genotype and some trait, but, if you click on an item, you get a list of scientific papers and a short summary of the research status. So you don't have to believe what they tell you but can make up your own mind.

You can also, if you find the time, fill out some dozens of surveys that they use to find cross-correlations between what you report and your genetic information. The participation is entirely voluntary. They've found some links in this way, eg the "curly hair" SNP that you see in the first image (the one that appears with the 23andMe logo) is such a case. So you can actively contribute to research in the area, which I find a nice twist.

Taken together I'd say it's worth the money. I had previously toyed with the idea to sign up with 23and Me, but before January 2013 you had to get a subscription for the webpage in addition to the cost for the sequencing and the shipment.

It is btw entirely coincidental that my favicon looks pretty much like the 23andMe logo. I've used this icon since 1997 I believe, it's supposed to be a mixture of an x and a lightcone.

22 comments:

Paul Andreas said...

It should be noted that in some countries (for example Germany) you might be obliged to declare health risks you learn about through genetic testing to insurances (in Germany it is insurance against working inability and life insurances above a certain value).

I wanted to get tested recently but refrained from doing so because I want to keep open the possibility to get insurance. The cutoff amount for working inability insurance where you have to declare in Germany is not very high when you compare it to normal salaries of academics.

CapitalistImperialistPig said...

But are you Neandertal? My friend was very proud of his Neandertal percentage.

Phil Warnell said...
This comment has been removed by the author.
Phil Warnell said...
This comment has been removed by the author.
Phil Warnell said...

Hi Bee,


Obviously better then tea leave, palm, head lump and tarot card reading. Looks like something that has some value. What CapitalistImperialistPig said about the Neandertal content would also be interesting to know, but as I've learned they’re not looking for that. With the relative minimal cost I’m surprised family doctors don’t make such a thing part of a standard work up so at least they know what they should perhaps be looking for. It might make things not only more efficient and also perhaps at less cost if some of their patients are at less risk in respect to some things.


Best,

Phil

Giotis said...

Southern, Eastern, Northern Europeans or Balkan, French, German. Genetically it doesn't make sense. A tribe based categorization I would understand:

i.e. Slavic, Germanic, Anglo Saxons, Nordic, Celtic etc.

Peter Shor said...

@Giotis: I have read that when the Anglo-Saxons came in and took over England, they didn't exterminate the current inhabitants, but just ruled them and, to some degree, enslaved them. So most English people have a large fraction of Celtic (and pre-Celtic) genes. I assume this is why there is one category for "British and Irish" rather than two for Anglo-Saxon and Celtic, as you expect. My guess is that the same kind of thing happened in the other areas of Europe, and these are the best actual fits for genetic categories.

Uncle Al said...

http://www.nature.com/jid/journal/vaop/ncurrent/full/jid2012480a.html
http://pubs.acs.org/iapps/wld/cen/results.html?line3=armpit
C&EN 91(8) 48 2013 [25 February]. Recessive gene for lacking a transporter protein. ~98% of non-Asians are armpit-challenged. Asians are mostly double-recessive (broadcasting trimethylamine rather than trans-3-methyl-2-hexenoic acid and butyric acid).

"They ask for quite some amount of saliva," Think of pickled herring or jalapeƱos. GeneTree contrasts with much more powerful 23andMe. The Mormons say I am 11% East Asian: (40 yr)(365.2422 d/yr)(3/7 d walking)(5 hr/d)(1 mph) = 31,000 miles or 50,000 km. Moses went out for Chinese? 23andMe says "94% Ashkenazic Jew." The Huns came to us, and shared.

Phillip Helbig said...

"I have read that when the Anglo-Saxons came in and took over England, they didn't exterminate the current inhabitants, but just ruled them and, to some degree, enslaved them. So most English people have a large fraction of Celtic (and pre-Celtic) genes."

Right. This is obvious: Most English people look English and not like the current inhabitants of Angeln (in the state of Schleswig-Holstein in Germany, just below Denmark but on the Baltic coast) and the various Saxonies in Germany (who are largely descended from the people who lived there when the Anglo-Saxons invaded England). This is especially true of English children. England has been invaded many times, and no-one thinks that the Romans, or the Vikings, or the Normans substantially displaced the native population, rather than just gaining control of the government.

Sabine Hossenfelder said...

Hi Phil,

There's some interesting info about how many docs use genetic tests and why here. The prime reason, it seems, not to use it is that they don't feel competent. My doc here would probably think I'm totally nuts. Actually, she probably already thinks I'm nuts ;o) Best,

Sabine

Phil Warnell said...
This comment has been removed by the author.
Phil Warnell said...

Hi Bee,

So why it’s not being used is instead of having hammers looking for nails, we could have plenty of nails and yet a shortage of hammers :-) Still seems to me if a genetic predisposition or the opposite is so easily identifiable it’s something our primary diagnosticians need to know about and utilize.

Best,

Phil

Peter Shor said...

You post may answer a question I've had about deodorants. I react badly to anti-perspirant, so I can only use deodorants which don't contain it. Many of these smell good, but don't seem to stop me from smelling bad, and I was wondering who bought these products. Now maybe I know.

peteratsal said...

Good stuff...I'm curious, did you find any actionable advice that changed your behavior? For example, diseases you didn't know you were predisposed to? The snippets you show are interesting, but I feel that it's nothing I wouldn't know about myself already, right?

peteratsal said...

What diseases does the report show you whether you have a predisposition or not? I can't find this on 23andme.com! I am toying with the idea of ordering a spit kit, but I'd rather not pay 100 dollars to find out "you have slightly curly hair/ blue eyes" - ya know? Good article.

Sabine Hossenfelder said...

Peteratsal,

You can find a list of diseases for which you get a risk assessment here

https://www.23andme.com/health/all/

As to me, some of them come out higher than average, some lower, but by and large nothing very far off the average. The ones that came out with a higher than average risk are diseases that for all I know nobody in my family ever developed, so I don't really see the need to do anything about it. Best,

B.

Sabine Hossenfelder said...

Oh, and regarding your other question, yes, I did learn some things that I found very interesting. Besides the anchestry which, as I mentioned looks more North European than I expected, I had never heard of the ABCC11 gene variant before. I had heard of the ACTN3, and I always assumed I probably don't have any working copy. Turns out I have one though.

Besides this, I didn't know there's a genetic predisposition for pain tolerance. This gave me something to think about because one of my daughters has a noticeably smaller response to pain than the other, so I am guessing it's not that one of them seeks more attention, but that I passed my "higher than average pain tolerance" on to the other.

There's some other things that I found interesting, but I'll stop here. I think it gives you an impression. Best,

B.

Arun said...

Inspired by your example, I sent my sample in weeks ago. Not having heard from 23andme, I checked by logging in there, this is what they said: :(

Arun, our laboratory attempted to isolate DNA from your saliva sample. Unfortunately, the sample did not yield sufficient quantities of DNA.

Your sample is going through a second round of DNA isolation.

Arun said...

Got my results!
I'm more Neanderthal than most :)
http://arunsmusings.blogspot.com/2013/06/23-and-me.html

mgarner said...

I'm mixed race Latino, so I'm very curious to find out my heritage. Thanks for great artocle, maybe I'll do this for my birthday!

Alwayscurious said...

I'm thinking of getting this done but I am curious about the insurance question that Paul Andreas posted. Does anyone know if you have to disclose such a thing in the US?

Ashton said...

I'm half English (Yorkshire, Durham, and Lancashire backgrounds) and in my 23andMe results, I have a small amount of "British/Irish", a bigger amount of "French/German", and a bigger amount of "Unidentified Northern European". I believe, that the "British/Irish" reading is indicative of Celtic Britonic origins, given that to be scored as such, they must be specific to the British Isles, and that the "French/German", and perhaps "Unidentified Northern European" also, is picking up on Germanic Anglo-Saxon origins. My Y Chromosome Haplogroup, from my Yorkshire Patrilineal lineage, is I2a, which is very rare there, and is believed to be a residual of the Pre-Celtic times in Britain, i.e., the Doggerland era.