fdmts

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01:32 pm: Genome, part 1
I just sent a tube of spit to 23 and me.

23 and me are one of three companies already up and running with "personal genomics," and I'm getting what passes for a thousand bucks worth of my genome analyzed. You give them a credit card number, they send a sample collection kit, and in short order you log into their web site to see the results of their analysis. Hopefully, they won't have broken the "download your raw data" feature before I get access. While their web portal is interesting, the potential to use my own data directly is way, way better.

They use a machine from a company named Illumina. The experiment provides a "read" on both strands of my DNA for a single letter at each of more than 600,000 locations in my DNA. These are locations where we have some sort of evidence that a "single nucleotide polymorphism" (SNP) occurs. That is, a one-letter swap that somehow matters in genetics. SNPs are one of the things that count as "genes" these days.

For some of these locations, we have pretty good data on physical traits that are correlated with specific letters. Here is an example entry in snpedia called "Rs1815739". In this case, the evidence suggests that there is a correlation between particular letter pairs (CC, CT, TT) and whether you'll be a better "sprint" or endurance athlete.

For the vast majority of the locations, we know next to nothing. They've been identified as variable locations ... but nobody has a clue what affect (if any) they have. By "vast majority," I mean "more than 99%". Seriously, I'm getting data about myself that will be unwrapped ... project by painstaking project ... over the next couple of hundred years. I plan to crib a couple of scripts from cariaso to email me research summaries of my loci of interest every morning.

For the record, there are a bunch of other things that also count as "genes" which are not measured by this experiment. This is the one that happens to be really easy to measure in bulk right now.

The consent letter in the package is telling:

You should not assume that any information we may be able to provide to you, whether now or as genetic research advances, will be welcome or positive.

So there we go. I'm "getting my genome done," for a few reasons. Primary among them is that I find myself in the role of explaining this technology to friends, family, and customers. If I'm going to form some sort of opinion on it, I'd better be well informed about the whole process. I also have some simple curiosity about the basics of my genetic makeup ... and there are a few "gotchas" out there that would let me adjust my lifestyle in my early thirties to increase the odds of living into my late 90s.

So how does it feel? It feels a bit scary, actually. I wasn't expecting the degree of approach-avoidance that I felt, looking at that little plastic tube ... and then looking at the fedex envelope to ship it off. I know better than most people that "genetics is not destiny," ... and I've been saying for a long time that more accurate information *always* leads to superior decision making. Still ... do I really want to know about Hodgkin's?

Yes. Yes I do.

More pictures of the kit are here.

Current Mood: nervousnervous
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Comments

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From:jrtom
Date:January 18th, 2008 07:50 pm (UTC)
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Interesting. I feel as though I ought to be wishing you luck, but presumably I should have done that about 33 years ago. :)

(Personally, I'm not yet prepared to drop $1000 on getting this information. I'd like to know it...but I'm hoping that the price will drop over the next few years, or even become covered by insurance. Especially because if I find it out for me, I'm going to feel obligated to drop another $4000 on Megan and the kids, too.)

For you it sounds like a good move, though, and I look forward to whatever you choose to disclose about what you find.
[User Picture]
From:fdmts
Date:January 18th, 2008 09:29 pm (UTC)

Bragging rights

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Broadly, I'm most interested because in a few years (less than 25) this information will be as common as having knowledge of your blood type. I plan to be in the business that develops between now and then ... so I sort of need to think deeply about the issues involved.

"No kids" makes things much simpler in a lot of ways, at least for now.
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From:fanw
Date:January 18th, 2008 08:40 pm (UTC)
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This definitely sounds interesting and I'd love to hear more tales of what you get out of this once the results come back. Like jrtom I'm going to wait a little before I try it. It's not just the cost, but that I'm never a first adopter in any technology. I'm sure that in coming years they will discover far more that has a direct genomic link, but I don't currently feel the need to know my "earwax type" [taken from their list of articles]. I'm a little scared by the "compare your genome to your friends" because I can see this become a deathlist. What's that word for when a group of people make a pact and the last person alive gets the goods? Kinda like that. However, I do like the ancestry feature. As someone with O- blood, I'm curious about the connection between the Celts and the Basques. As a person of Northern European blood, I'm curious about the pockets of folks they've found with genetic HIV resistance. All very curious!
[User Picture]
From:fdmts
Date:January 18th, 2008 09:27 pm (UTC)

Raw data

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Yeah, in terms of early adoption, I feel that I probably just paid $1,000 for the privilege of owning one of the first telephones. Pretty soon, they'll be free. On the other hand, I'll get cocktail party bragging rights for a year or so - which is worth it to me.

For me, it's all about the raw data. All three major players are trying to be the portal to your genome. They provide value insofar as they hang on to your information and show you slices of it. I think that this is quite similar to what Yahoo and Amazon did in 1995. They tried to be the one-stop-shop for the web.

I plan to extract all 600,000 data points and do my very own research.
[User Picture]
From:amnesiadust
Date:January 19th, 2008 04:11 am (UTC)

overload!

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</em>I plan to crib a couple of scripts from cariaso to email me research summaries of my loci of interest every morning.</em>

On the one hand... paying $1000 to be inundated with yet more information would be kind of more than I might want to deal with.

On the other hand... cool.
[User Picture]
From:redmed
Date:January 19th, 2008 07:12 am (UTC)

Genographic Project

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In response mostly to fanw, but to others as well:
If you are not sure what you'd do with the info, or are not as sure about flinging $1000 into a tube of spit as my profligate husband ;) you might consider the Genographic Project hosted by National Geographic and IBM. They are looking at how mitochondrial DNA (traded by mom's egg, studies female genetic migration) and Y chromosome haplotyping. Your $$ helps contribute to the testing and mapping of indigenous groups to help fill in the map of migration over time. The map has significantly increased with arrows since fdmts and I did our samples.

What is also good, for mcniadh is that you only need one test for your male and female lineage. So, you and the partner / spouse can do it for your kids, or your parents can do it for you. And it's roughly $100, a factor of 10 cheaper!!
[User Picture]
From:atgatg
Date:January 20th, 2008 01:57 am (UTC)

Neat.

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I totally get it. Or at least it's very appealing to me. I spend all day mining this kind of data, at least half driven by the the possibility of discovering gems hidden in the billions of nucleotides. Maybe it's the same kind of addiction that drove gold prospectors -- except the reward is more intrinsic. Now add the twist that you can look for the secrets in your own DNA: reason to be at least as eager, but a little queasy too.
[User Picture]
From:fdmts
Date:January 20th, 2008 03:02 pm (UTC)

Re: Neat.

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Yeah, it's forcing me to evaluate my genetics in terms of very specific and personal questions. What trends in my family and person do I want to ask about? Which things are more likely environmental, and which are actually predispositions?

This will be food for thought way beyond the price tag.

Question for the master: I want to estimate the number of generations back at which I'm related to some other person. I'm allowed to use SNP data. What's a reasonable model / approach?

My guess is that I start with my siblings: I *expect* 50% identity with them. Cousins, 25%, and so on. So, for the first few generations I've got nice big broad bands of probability. It quickly drops into the noise though.

For each of the markers that I use, I also want to normalize out the population frequency, as well as any selective bias.

For bonus points, don't violate HPPA while you do it.
[User Picture]
From:atgatg
Date:January 21st, 2008 04:04 am (UTC)

Re: Neat.

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I have to say, straight-up, I don't know. I was about to start explaining where the power comes from in the hapmap, but you know that, and that's not what you're asking. Answers to "trait-similarity-across-generations" questions I think end up using pretty complicated bayesian models on deep pedigrees. That math hasn't stuck with me. (Fortunately, plants are prolific enough that we can use homozygous inbred lines and crosses that produce 500 progeny in the first generation).

One point regarding your guess though: you actually will have substantially more than 50% identity with your siblings (at the several hundred thousand measured DNA sites). That is because your mother and father didn't differ at every one of those SNP positions. In fact, they didn't even differ at 50% of those positions ... because they themselves have discernible common ancestry. That's the point (and surprise and power) of the hapmap concept and linkage disequilibrium. We tend to inherit blocks of DNA together. If you have a particular handful of SNPs in a given range of DNA, then you probably know the states of your genes through that whole region. And you know what other populations around the globe share those alleles. That's why 23andme will be able to tell you what groups you have ancestry with.

- Almost enough to propel me to go read some of the primary hapmap literature ...
[User Picture]
From:fdmts
Date:January 21st, 2008 04:08 am (UTC)

Re: Neat.

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Excellent. That's kinda the answer I was hoping for. No simple, direct, "everyone knows it" answer ... but the pieces are there.

Thus, I'm off to read the same primary literature.
[User Picture]
From:_earthshine_
Date:January 20th, 2008 02:37 am (UTC)
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[User Picture]
From:fdmts
Date:January 20th, 2008 03:04 pm (UTC)

No crap

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On the one hand, people who are determined to posit a dystopian future will do so whether you give them electrically powered Zeppelins or genomics. On the other hand, "yes."

That's a decent part of why I'm doing the experiment. I expect (hope) to be shaping some portion of the future in this technology ... and actually doing the thinking for myself is giving me a lot of perspective.
[User Picture]
From:_earthshine_
Date:January 20th, 2008 10:30 pm (UTC)

Re: No crap

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On the one hand, people who are determined to posit a dystopian future will do so ... On the other hand, "yes."

Indeed... I'm a big proponent of not blaming technology for how it's used. That's the main reason why i supported the idea of Napster, for example, despite my vehement support of artists' rights.

The only reason i occasionally come across as technologically reactionary in this regard is because while i do not blame technology for its misuse, i do believe in the possible existence of scenarios wherein a technology should not be developed until we have demonstrated the social maturity to wield it. One of my classic examples of this is my "temporary" stance of being against inter-planetary colonization; i don't think we should be allowed to colonize other planets until we've demonstrated successful management of our conduct on the one we already inhabit.

In my mind, there is this unfortunate misview on the part of many that a civilization's worth can be measured by its technological prowess alone, and this is a dangerous dangerous view that must be checked. It's far too easy for us to fly the banners of human greatness and march ever-masturbatingly toward "Progress" solely technologically, because quite honestly, building better computers and science is a hell of a lot easier than building better people.

That's a decent part of why I'm doing the experiment. ...

You're (as usual) on the point of the thrust to learn about things and understand them as you support them, which i utterly respect.
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