Saturday, January 30, 2016

SSC SNP picks

er, ... no ... .

I mentioned in my previous post that you could link a SNP (eg rs4570625) to your own 23andMe results using a link like this:
Scott Alexander at the almost-always-reliable* Slate Star Codex wrote (November 2014) this amusing post "How To Use 23andMe Irresponsibly" describing his favourite SNPs.

Well, now they're my favourites too and I copy his (lightly edited) thoughts below, but with the SNP references switched from his choice - SNPedia - to my choice, 23andMe.

Quick reminder: most traits in life are quantitative, they come in degree, not kind. In the human genome they are polygenic - many SNPs are involved (and other genetic mechanisms too) .. so one SNP is hardly going to be decisive. In most cases.

--- How To Use 23andMe Irresponsibly - (from SSC)  ---
"rs909525 is linked to the so-called “warrior gene” which I blogged about in the last links roundup. People with the normal four or five repeat version of these gene are less violent than people with the three-repeat version, and people with the two-repeat version are massively overrepresented among violent criminals. ... Although this SNP isn’t the warrior gene itself, it’s linked to it closely enough to be a good predictor.

"This is on the X chromosome, so men will only have one copy (I wonder how much of the increased propensity to violence in men this explains). It’s also one of the minus strand ones, so it’ll be the reverse of what SNPedia is telling you. If you’ve got T, you’re normal. If you’ve got C, you’re a “warrior”. I’ve got C, which gives a pretty good upper limit on how much you should trust these SNPs, since I’m about the least violent person you’ll ever meet. But who knows? Maybe I’m just waiting to snap. Post something dumb about race or gender in the open thread one more time, I dare you…"

I'm T and my mother, Beryl Seel was (T;T), both .. normally unwarlike.

"rs53576 in the OXTR gene is related to the oxytocin receptor, which frequently gets good press as “the cuddle hormone” and “the trust hormone”. Unsurprisingly, the polymorphism is related to emotional warmth, gregariousness versus loneliness, and (intriguingly) ability to pick out conversations in noisy areas.

"23andMe reads this one off the plus strand, so your results should directly correspond to SNPedia’s – (G;G) means more empathy and sociability and is present in 50% of the population, anything else means less. I’m (A;G), which I guess explains my generally hateful and misanthropic outlook on life, plus why I can never hear anyone in crowded bars."

We're both (G;G) which makes us kind and empathic ... .

"rs4680 is in the COMT gene, which codes for catechol-o-methyltransferase, an enzyme that degrades various chemicals including dopamine. Riffing on the more famous “warrior gene”, somebody with a terrible sense of humor named this one the “worrier gene”.

"One version seems to produce more anxiety but slightly better memory and attention; the other version seems to produce calm and resiliency but with a little bit worse memory and attention. (A;A) is smart and anxious, (G;G) is dumb and calm, (A;G) is in between. if you check the SNPedia page, you can also find ten zillion studies on which drugs you are slightly more likely to become addicted to. ..."

Both of us are (A;G) which makes us average and average.

"rs7632287, also in the oxytocin receptor, has been completely proportionally and without any hype declared by the media to be “the divorce gene”. To be fair, this is based on some pretty good Swedish studies finding that women with a certain allele were more often to have reported “marital crisis with the threat of divorce” in the past year (p = 0.003, but the absolute numbers were only 11% of women with one allele vs. 16% of women with the other). This actually sort of checks out, since oxytocin is related to pair bonding. If I’m reading the article right (G;G) is lower divorce risk, (A;A) and (A;G) are higher – but this may only apply to women."

Both my mother and I are (A;G) which makes her a bit .. flighty?

"rs11174811 is in the AVPR1A gene, part of a receptor for a chemical called vasopressin which is very similar to oxytocin. In case you expected men to get away without a divorce gene, this site has been associated with spousal satisfaction in men. Although the paper is extremely cryptic, I think (A;A) or (A;C) means higher spousal satisfaction than (C;C). But if I’m wrong, no problem – another study got the opposite results."

I'm (C;C) as was my mother, Beryl Seel, which means .. probably nothing.

"rs25531 is on the serotonin transporter. It's Overhyped Media Name is “the orchid gene”, on the basis of a theory that children with one allele have higher variance – that is, if they have nice, happy childhoods with plenty of care and support they will bloom to become beautiful orchids, but if they have bad childhoods they will be completely screwed up. The other allele will do moderately well regardless. (T;T) is orchid, (C;C) is moderately fine no matter what. There are rumors going around that 23andMe screwed this one up and nearly everybody is listed as (C;C)."

For my mother and myself, 23andMe did not report on this one.

"rs1800955 is in DRD4, a dopamine receptor gene. It's overhyped media name is The Adventure Gene, and supposedly one allele means you’re much more attracted to novelty and adventure. And by “novelty and adventure”, they mean lots and lots of recreational drugs. This one has survived a meta-analytic review. (T;T) is normal, (C;C) is slightly more novelty seeking and prone to drug addiction."

I was not genotyped at this location and my mother, Beryl Seel was (C;T) which made her a little bit adventurous with lots of use of recreational sherry.

"rs2760118, in a gene producing an obscure enzyme called succinate semialdehyde dehydrogenase, is a nice polymorphism to have. According to this article, it makes you smarter and can be associated with up to fifteen years longer life (warning: impressive result means almost certain failure to replicate). (C;C) or (C;T) means you’re smarter and can expect to live longer; (T;T) better start looking at coffins sooner rather than later."

I'm (T;T) and my mother, Beryl Seel was (C;T) which makes me resigned to an early grave. She lived to 92.

"rs6311 is not going to let me blame the media for its particular form of hype. The official published scientific paper on it is called “The Secret Ingredient for Social Success of Young Males: A Functional Polymorphism in the 5HT2A Serotonin Receptor Gene”.

"Boys with (A;A) are less popular than those with (G;G), with (A;G) in between – the effect seems to be partly mediated by rule-breaking behavior, aggression, and number of female friends. Now it kind of looks to me like they’re just taking proxies for popularity here, but maybe that’s just what an (A;A) nerd like me would say. Anyway, at least I have some compensation – the popular (G;G) guys are 3.6x more likely to experience sexual side effects when taking SSRI antidepressants."

I'm (G;G) and my mother, Beryl Seel was (G;A) which makes me out to be some kind of bad boy!? I must remember to keep off those SSRI tablets.

"rs6265, known as Val66Met to its friends, is part of the important depression-linked BDNF system. It’s a bit depressing itself, in that it is linked to an ability not to become depressed when subjected to “persistent social defeat”. The majority of whites have (G;G) – the minority with (A;A) or (A;G) are harder to depress, but more introverted and worse at motor skills."

I predicted I would be (A;A) based on poor motor skills and in fact I'm (A;G). My mother, Beryl Seel was the normal (G;G) which is consistent with her not-bad motor skills (except at driving).

"rs41310927 is so cutting-edge it’s not even in SNPedia yet. But these people noticed that a certain version was heavily selected for in certain ethnic groups, especially Chinese, and tried to figure out what those ethnic groups had in common.

"The answer they came up with was “tonal languages”, so they tested to see if the gene improved ability to detect tones, and sure enough they claimed that in experiments people with a certain allele were better able to distinguish and understand them. Usual caveats apply, but if you want to believe, (G;G) is highest ability to differentiate tones, (A;A) is lowest ability to differentiate tones. (A;G) is in between.

Sure enough, I’m (A;A). All you people who tried to teach me Chinese tonology, I FRICKIN’ TOLD YOU ALL OF THE WORDS YOU WERE TELLING ME SOUNDED ALIKE."

Both of us test (A;G) so I'm sure we would have struggled with Mandarin, a daily requirement in Bristol.
So, just to reiterate, if you have a 23andMe account, click on the rs... links and see how you scored.


* If you care, I don't share his worries about the existential threat of the 'new AI'.

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