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Accurate Genomic Prediction of Human Height
- guiambros 9y agoIs there any way to export data from 23andme, and find the SNPs and calculate on your own? Would be nice if you could predict the height of your kids at a young age.
- gwern 9y ago> Is there any way to export data from 23andme Yes. > and find the SNPs and calculate on your own? No. I'm not sure Lello et al have released the polygenic score in question. > Would be nice if you could predict the height of your kids at a young age. You can already do that with Galton's midpoint regression method (indeed, he invented the entire method of regression based on predicting children's heights from their parents!). What you could do is predict which sibling will be taller, though.
- scardine 9y agoLooks like we are not that far from the dystopian future depicted in the movie Gattaca[1]. [1] https://en.wikipedia.org/wiki/Gattaca https://en.wikipedia.org/wiki/Gattaca
- kickout 9y agoNo, not even close. Comically uninformed take right here
- civilitty 9y agoSelective in vitro fertilization has been around for at least a decade now, where you select fertilized eggs based on genetic markers. It's not direct genetic engineering yet, but we're pretty much already in Gattaca.
- kickout 9y agoYou got a link what company offers selective in vitro fertilization (for cosmetic traits, not something like down syndrome)
- techer 9y agoIs gender a cosmetic trait?
- gwern 9y agoPGD has been in use to a very limited extent, testing on just 1 or a bare handful of specific genetic diseases, along with basic checks for gross abnormalities like microscope examination. Use of full SNP arrays is still very new and no one has ever used them to select based on complex traits like height.
- Footkerchief 9y agoFor anyone else who's wondering: https://en.wikipedia.org/wiki/Preimplantation_genetic_diagnosis https://en.wikipedia.org/wiki/Preimplantation_genetic_diagno...
- IntronExon 9y agoFor tall, muscular people with certain superficial features? Probably. For intelligence and deeper features, all while controlling for undesirable adverse effects (like early cancers, epilepsy, and so forth) hell no. What we don’t know about the brain alone is staggering, nevermind how tweaking it with ensembles of genes will impact the whole human. So relax, we have plenty of dystopia without designer babies.
- Y_Y 9y agoYou can certainly export the data from 23andme (for yourself) but I couldn't see the code used in the paper.
- kickout 9y agoNo code in paper, correct. Very easy to implement via R or python. One of the authors (Gustavo de los Campos) has alot of code that could probably be coped/pasted with little editing from his website. Algorithm is actually painfully simple. Just relying on massive data (500K individuals)
- gwern 9y agoCoordinate descent is simple but the resource requirements may complicate your implementation running over n=500k with tens of thousands of markers each; as it was described to me, they were using a workstation with like 128GB RAM... (Plus of course you need access to the UKBB dataset in the first place.)
- moyix 9y agoThat's to replicate the study; presumably if the authors released their trained model it would be much less computationally expensive to run it on your own data?
- gwern 9y agoIf by trained model you mean PGS, yes, it would be trivial. While the fitting of the optimal weights may be computationally intensive, it's still just a simple little linear model: look up the SNP value, add or subtract a small coefficient for each of the 30k or whatever 'activated' SNPs, and get the net total.
- nextos 9y agoSeems code is derived from this Julia package written by the authors: https://github.com/gdlc/BGLR.jl https://github.com/gdlc/BGLR.jl
- linkmotif 9y ago> Would be nice if you could predict the height of your kids at a young age. Would it?
- gruez 9y agoassuming you want to optimize for height, you'd want to predict it when it's abortable.
- kridsdale1 9y agoAs a short person this sounds like genocide.
- hackerman12345 9y agoYes, plenty of evidence shows taller people (up to a point) have more success in many areas.
- patall 9y agoMy sister turned out 6'3, my parents would have given a lot to predict that height some years before (as they feared she might end up even taller). Same is probably true for very small people that give their kids growth hormones. And If you are looking for a sport your child is good at it might also help. Sure you can construct very adversial uses of such a technology here but that does not mean that the tech itself is bad.
- siruncledrew 9y agoWhat happens if the results are not favorable?
- ig1 9y agohttps://dna.land/ https://dna.land/ (New York Genome Center/Columbia University) has a height-model based upon genome data which you can just plug your 23andme data into. (You can also give them your actual height so they can improve their data set)
- monkeypizza 9y agoThe people at promethease monitor new studies for information on new variants & results of studies. You upload your dna from 23andme to them and they give you a full report without government interference. https://promethease.com/ https://promethease.com/
- amelius 9y agoI didn't read the article, but isn't this like predicting country of birth? I.e. how well is the prediction if you take someone from the US and let them grow up in Africa?
- kickout 9y ago(redacted). But still disagree this is not what the underlying study is concluding
- moyix 9y agoLike many traits, height is a mix of genetic and environmental factors. Based on things like twin studies, we know that 60-80% of the variation in height is due to genetic factors [1]. This paper shows that you can predict height from genetic information with an accuracy that is in line with that heritability estimate. It doesn't mean that it will be 100% accurate all the time, since environmental factors (e.g. nutrition) will account the remaining 20-40%. [1] https://www.scientificamerican.com/article/how-much-of-human-height/ https://www.scientificamerican.com/article/how-much-of-human... "The short answer to this question is that about 60 to 80 percent of the difference in height between individuals is determined by genetic factors, whereas 20 to 40 percent can be attributed to environmental effects, mainly nutrition."
- beefman 9y agoThis result is explained by Hsu in a recent talk at the Allen Institute.[1] [1] https://news.ycombinator.com/item?id=16386749 https://news.ycombinator.com/item?id=16386749
- kickout 9y agoGood post/paper in general. Predicting traits in humans has been more challenging than most geneticist want to admit. The good news is that most high heritable traits will become "solved" as we enter a new order of magnitude of data availability (i.e 5 million people instead of 500k). Much work left to do though, and there are interesting methods being developed in this space
- jonmc12 9y ago> there are interesting methods being developed in this space Would you mind posting any relevant links? Is there general agreement in the field that more data is the solution?
- petra 9y ago"Replication tests show that these predictors capture, respectively, ~40, 20, and 9 percent of total variance for the three traits. ". This seems very low, almost like saying genes don't have any practical predictive power, right ?
- deleted 9y ago[deleted]
- joe_the_user 9y agoWell, it would be pretty astounding if genes (edit: genes by themselves) were a strong predictor of height. We've seen average height go up tremendously in places like Japan based on improved nutrition.
- bobcostas55 9y agoGenes are a strong predictor of height (in certain populations), AND it has gone up tremendously in places like Japan. Both are true. To speak of the influence of genes also assumes a certain environment. If we look at western populations for example, the heritability of height in adulthood is something like 0.8. But this is predicated on that western environment where ~nobody has nutritional deficiencies. A uniform, high-quality environment means that there is little besides genes that can influence height. If something happened and a large portion of the population had such deficiencies, the influence of genes would be diminished.
- gwern 9y agoWhat criterion are you using in which 40% of variance is zero practical predictive power?
- jamesmishra 9y agoIn his book Behave[1], biologist Robert Sapolosky explains the issue as follows: > Heritability scores are relevant only to the environments in which the traits have been studied. The more environments you study a trait in, the lower the heritability is likely to be. He goes on for several pages, describing the ways the surrounding environment can change an organism's gene expression, and I think this quote best summarizes his point: > Here’s a rule of thumb for recognizing gene/environment interactions, translated into English: You are studying the behavioral effects of a gene in two environments. Someone asks, “What are the effects of the gene on some behavior?” You answer, “It depends on the environment.” Then they ask, “What are the effects of environment on this behavior?” And you answer, “It depends on the version of the gene.” “It depends” = a gene/environment interaction. [1]: https://www.amazon.com/Behave-Biology-Humans-Best-Worst/dp/1594205078 https://www.amazon.com/Behave-Biology-Humans-Best-Worst/dp/1...
- gumby 9y agoThis looks pretty good: digging into the supplement it appears they controlled for age, which is how the controlled for things like improved nutrition, elimination of smoking while pregnant etc
- michaelhoffman 9y agoUpdated version at https://doi.org/10.1101/190124 https://doi.org/10.1101/190124
- jpalomaki 9y agoStep towards designer babies? Check the genes after fertilization, reject embryous if the genes are not ”right”.
- sszz 9y agoThe models are predicted off of "~20k activated SNPs" - 20,000 separate mutations, most of which have really small effects on height. "Designer babies" are pretty far off (IVF is awesome and great, but not trivial, so it would be risky to do this just to make sure a baby will be...probably somewhere near average height). Engineering the right mutations with CRISPR/Cas9-based gene editing would be astronomically expensive (and is realistically impossible); filtering embryos for the right genetic background would also be incredibly expensive and probably impossible, as you'd be relying on the natural, stochastic arrangement of those 20,000 mutations to be in sync with the vision you have for your baby.
- gwern 9y agoHaving small mutations is irrelevant; it could be dozens of large effects or thousands of small effects, it doesn't matter, you get a normal distribution anyway. The question is how much variance there is and how much of it you can predict. Or let me put it this way: how much do siblings (ie embryos) vary in height? It's by quite a bit, often several inches. Most of this is due to genetics. And this PGS is able to predict half of the genetic contribution. So... (If you're curious, my best estimate is that embryo selection could boost height by about an inch on average.) > filtering embryos for the right genetic background would also be incredibly expensive and probably impossible It would cost about $2000 for the biopsies and SNP arrays of the usual ~5 embryos, and can be done either now or in the next few years and could have been done years ago if any real effort was put into it.
- sszz 9y agoYou would only be able to select from those 5 backgrounds, however, and the predicted heights for those embryos will be drawn from a normal distribution; you can only "design" from what you've sampled. On the other hand, if you sampled millions of embryos, you could find the rare few predicted to grow to be 6'5" person -- but this would be very expensive and basically impossible without synthetic embryos.