Should I get genotyped?

post by jsalvatier · 2011-10-24T15:51:56.739Z · score: 7 (10 votes) · LW · GW · Legacy · 12 comments

I've heard several people here mention getting genotyped by 23andme (I assume there are other companies as well). Does genotyping have significant practical benefits or is it mostly for curiosity's sake? If there are significant benefits, what are they?

12 comments

Comments sorted by top scores.

comment by XFrequentist · 2011-10-24T17:50:24.661Z · score: 7 (7 votes) · LW(p) · GW(p)

I signed up because I had studied genomic medicine a bit (pdf), had read Kurzweil's advice about taking advantage of new technologies, and there was a discount!

It's quite a bit of fun to browse, and I've learned a few things that might be useful. I'm a carrier for PKU, which will make me extra vigilant when/if I have children (plus make me encourage my wife to get profiled). Also, gwern pointed me to research on a gene-drug interaction for Modafinil, which indicates that I am not likely to benefit from the drug. Lastly, my grandfather died from Alzheimer's, and it is my absolute most dreaded diagnosis. Finding out that I'm at a substantially decreased risk (Relative Risk=0.69) for the disease was a surprisingly large relief.

PKU is part of prenatal screening in Canada, and I'm not sure how much confidence to put in the Modafinil or Alzheimer's result. It could thus be argued that these examples are of limited benefit, however coupled with the pleasure I've gotten from browsing my genome and the potential for further developments I would say that it is worth the cost.

If you can wait until April, they've had a steep discount around DNA day each of the past few years.

comment by jsalvatier · 2011-10-24T19:29:36.511Z · score: 1 (1 votes) · LW(p) · GW(p)

I'll probably do it around April then.

comment by gwern · 2011-10-24T17:31:21.708Z · score: 6 (6 votes) · LW(p) · GW(p)

I think it's mostly for curiosity's sake, barring rare genetic disorders. I mean, I would like to learn my genotyping so I could check it against various SNPs linked with modafinil and nicotine, but I wouldn't pay $100 for this given the apparent weakness of the links.

comment by buybuydandavis · 2011-10-25T05:36:38.670Z · score: 5 (5 votes) · LW(p) · GW(p)

I doubt that I am alone here in thinking, "of course I want more data". But I'll just respond on how the data is currently actionable.

The main benefit I see right now is in estimating drug response and metabolism. I have a partially functioning variant of CYP2D6 that makes me a poor metabolizer of CYP2D6 substrates. Something like 25% of commonly used drugs are metabolized by the enzyme coded by CYP2D6, and maybe 10% of the population have one of the non or partially functioning variants.

Also, I'm at heightened risk for a particular fairly prevalent condition which strikes aout 10% of the population, while the estimate is that I have a 30% lifetime risk. A real risk in the general population, and significant one for me.

http://www.snpedia.com/index.php/CYP2D6

SNPedia is a wiki compendium of SNP phenotype information. It has an associated software program (Prometheus) that will process your raw SNP data from the genotyping services and correlate it with SNPedia data, giving a printout of "interesting" SNPs, one's related to medical conditions, and one's related to drug metabolism.

There should be better services like this by now. Anyone know of something?

23andme seems rather pitiful in the information it gives. They map SNPs to clinical disease, but not really to gene function or population prevalence. Prevalence is the main value they could provide to their users, but I suspect they mine that value for themselves, and so don't want to share.

About a week ago, someone posted on the potential for smarties to get their full genome scanned for free.

http://lesswrong.com/r/discussion/lw/7wj/get_genotyped_for_free_if_your_iq_is_high_enough/

https://www.cog-genomics.org/volunteer/

comment by James_Miller · 2011-10-24T17:26:15.770Z · score: 5 (7 votes) · LW(p) · GW(p)

For me it's been mostly for fun. But consider if you could handle some very bad news such as finding out you had a much greater than normal chance of getting Alzheimer's disease.

You should definitely do it, however, if you intend to soon have children so you can see your carrier status for lots of diseases. If, for example, you are a carrier for cystic fibrosis then you should check to see if your mate is as well and then use embryo selection to guarantee that your child won't get the disease.

comment by [deleted] · 2011-10-26T10:31:08.112Z · score: 1 (1 votes) · LW(p) · GW(p)

Correction: If either you or your partner are carriers for any genetic diseases, use embryo screening to guarantee that your children won't get the diseases or be carriers.

comment by James_Miller · 2011-10-26T14:30:51.921Z · score: 3 (5 votes) · LW(p) · GW(p)

I disagree. It wouldn't be so horrible if your children were merely carriers especially since by the time your children have children embryo selection tech or its successor will be much more advanced than it is today. True, if you were otherwise indifferent between (1) using an embryo that had one copy of the bad gene and one of the good one and (2) an embryo that had none of the bad genes you should go with (2) but this is extremely unlikely to happen since if you're going to use embryo selection you should look at far more than just that one "bad" gene.

comment by Phocion · 2011-11-01T04:18:49.934Z · score: 0 (2 votes) · LW(p) · GW(p)

With the large number of genetic diseases that exist, it seems improbable that neither you nor your partner would be a carrier for something. So your statement would imply that most couples should use embryo screening, and possibly go through thousands of embryos to find one that is free of any genetic defects. This seems both unnecessarily costly and also unwise- without knowing more about the human genome, we can't be sure that eliminating a defect wouldn't cause worse problems. For example, we know that carriers of sickle-cell anemia are more resistant to malaria. What other correlations would we miss through haphazardly screening out carriers of other diseases?

Of course, in a case like cystic fibrosis, embryo selection is the clear choice.

comment by EvelynM · 2011-10-24T17:13:13.789Z · score: 5 (5 votes) · LW(p) · GW(p)

I got mine done last year. The practical benefit I received was discovering I was not at increased risk of any significant illness, including those which had occurred in my family, which relieved a source of minor worry.

Other than that, mostly curiosity satisfaction, and the opportunity to follow along with SNP research in a more personally significant way.

comment by Antisuji · 2011-10-26T05:08:51.794Z · score: 0 (0 votes) · LW(p) · GW(p)

I got the DNA Day discount a year and a half ago, on the recommendation of a coworker who used to work at 23andme. Probably the most useful thing I learned is that I am a fast caffeine metabolizer and as a result I feel better about drinking coffee regularly.

So, significant benefits? probably not. Amusement value? for sure.

comment by lomonosov · 2011-10-25T05:29:53.080Z · score: 0 (10 votes) · LW(p) · GW(p)

Since my father has early-onset Parkinson's, I have given this question some thought and decided against it.

Being cleared by the genotype does not give you a license to neglect your health. So the generally positive result is for the most part useless, if not slightly detrimental to a healthy lifestyle.

Conversly, your options for prevention are limited were you to find the increased risk of Parkinson's, Alzheimer's, or a similar neurodegenerative disorder. The little you can do to protect yourself against genetically-inherited illness, you should be doing even if your genotype is clear. At the same time, knowing that you are at risk for something unpleasant down the line could be psychologically difficult for the rest of your life, and downright dangerous if you are already predisposed to hypochondria or depression.

There are exceptions to this line of reasoning of course: if you have a history of diabetes in your family for example--diabetes being a disease that responds well to behavioral modification. Or perhaps in the case of an Ashkenazi couple getting tested for Tay-Sachs before conceiving. Outside of these specific exceptions, I don't see any benefit to the test.

comment by [deleted] · 2011-10-26T00:35:01.573Z · score: 4 (8 votes) · LW(p) · GW(p)

"It is no good to try to stop knowledge from going forward. Ignorance is never better than knowledge. " --Enrico Fermi

If you had knowledge of early-onset Parkinson's or Alzheimer's, you could plan for it by making sure to, say, spend much more time with your family than putting in lots of hours at the office with the expectation that you would be promoted later. You would also be able to manage some of them better with early knowledge and expectation of what is coming, and be able to volunteer for drug trials. (It may also affect your planning for cryogenics.)

If you had no knowledge of a neurodegenerative disease, it would be able to kill you anyway, but with no ability for your family to plan for it. You would similarly be unable to make choices about supporting research into that disease with enlightened self-interest. (Obviously, that may make little impact in the short-term, but if you learn in your twenties, then ~five decades of funding with a donation of a percentage of your yearly salary each year may very well lead to advancements in treatment).

Also, suicide is not inherently irrational.