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Is 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 youn

Is 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 ago
Looks 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 ago
  No, not even close. Comically uninformed take right here
- civilitty 9y ago
  Selective 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 ago
    You got a link what company offers selective in vitro fertilization (for cosmetic traits, not something like down syndrome)
    - techer 9y ago
      Is gender a cosmetic trait?
  - gwern 9y ago
    PGD 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 ago
      For anyone else who's wondering: https://en.wikipedia.org/wiki/Preimplantation_genetic_diagnosis https://en.wikipedia.org/wiki/Preimplantation_genetic_diagno...
- IntronExon 9y ago
  For 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 ago
You can certainly export the data from 23andme (for yourself) but I couldn't see the code used in the paper.
- kickout 9y ago
  No 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 ago
    Coordinate 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 ago
      That'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 ago
        If 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 ago
    Seems 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 ago
  assuming you want to optimize for height, you'd want to predict it when it's abortable.
  - kridsdale1 9y ago
    As a short person this sounds like genocide.
- hackerman12345 9y ago
  Yes, plenty of evidence shows taller people (up to a point) have more success in many areas.
- patall 9y ago
  My 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 ago
What happens if the results are not favorable?
ig1 9y ago
https://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 ago
The 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/

Is 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 ago

Looks 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 ago
No, not even close. Comically uninformed take right here
civilitty 9y ago
Selective 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 ago
  You got a link what company offers selective in vitro fertilization (for cosmetic traits, not something like down syndrome)
  - techer 9y ago
    Is gender a cosmetic trait?
- gwern 9y ago
  PGD 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 ago
    For anyone else who's wondering: https://en.wikipedia.org/wiki/Preimplantation_genetic_diagnosis https://en.wikipedia.org/wiki/Preimplantation_genetic_diagno...
IntronExon 9y ago
For 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 ago

You can certainly export the data from 23andme (for yourself) but I couldn't see the code used in the paper.

kickout 9y ago
No 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 ago
  Coordinate 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 ago
    That'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 ago
      If 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 ago
  Seems 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 ago
assuming you want to optimize for height, you'd want to predict it when it's abortable.
- kridsdale1 9y ago
  As a short person this sounds like genocide.
hackerman12345 9y ago
Yes, plenty of evidence shows taller people (up to a point) have more success in many areas.
patall 9y ago
My 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 ago

What happens if the results are not favorable?

ig1 9y ago

https://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 ago

The 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/