Estimating Neanderthal ancestry from 23andme data

Angela

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See:

Mathiesen et al
http://mathii.github.io/2018/10/05/estimating-archaic-ancestry-from-23andme-data

"[FONT=&quot]23andMe don’t actually report Neanderthal ancestry proportions - rather, they report the number of Neanderthal-derived variants you carry out of a set of around 1400 ascertained in [/FONT]Sankararam et al 2017[FONT=&quot]. The procedure is described [/FONT]here[FONT=&quot]. They also report which quantile you are in, in terms of these variants, and how you rank relative to people you know. Unfortunately these estimates don’t correspond very well to Neanderthal ancestry proportions."

"[/FONT]
[h=3]An indirect estimate of Neanderthal ancestry[/h][FONT=&quot]Among people with the same genome-wide ancestry, there is likely very little variation in Neanderthal ancestry. So an indirect way of estimating Neanderthal ancestry would be to just assume that Neanderthal ancestry proportion is just a function of genome-wide ancestry, and estimate that function. To do this, we first estimate Neanderthal ancestry in the SGDP, as in Pruefer et al. Then, we restrict the SGDP data to SNPs that are found on the 23andMe genotyping array and compute its principal components. Next, we can project our 23andMe results onto the PCs defined by the SGDP. Finally, we fit a model to the SGDP data that expresses Neanderthal ancestry as a function of the first few PCs. So when we project our 23andMe data onto the SGDP PCs, this model gives us an estimate Neanderthal ancestry. The kind of model we need to fit is called a generalised additive model and can be fit using the R package mgcv.[/FONT]
[h=3]Indirect, but not that intersting.[/h][FONT=&quot]I computed the statistics described above and wrote an R script to project 23andMe genotype data. The figure below shows the first two principal components of the SGDP, and the contour lines show the corresponding proportions of Neanderthal ancestry. You can generate this figure and project your own 23andMe data onto the PCs using the scripts here. It’s not that interesting though, because Neanderthal ancestry is just a function of genome-wide ancestry so two people with similar ancestry will always have the same genome-wide ancestry.[/FONT]
[h=3]Other approaches.[/h][FONT=&quot]If you wanted to get a fully personalized estimate, you could combine this with an [FONT=MathJax_Math-italic]f[/FONT][FONT=MathJax_Main]4[/FONT]f4 ratio on the data itself - e.g. you could use this estimate as a prior, and use the [FONT=MathJax_Math-italic]f[/FONT][FONT=MathJax_Main]4[/FONT]f4 ratio and error to compute a posterior. I’m not sure that this would actually help very much, since the uncertainties are so high. But you might be able to identify people (if there are any) who have particularly extreme Neanderthal ancestry proportions. With large datasets you could recompute [FONT=MathJax_Math-italic]f[/FONT][FONT=MathJax_Main]4[/FONT]f4 ratio proportions and principal components on that dataset itself and get more accurate estimates, as well as individual level estimates."[/FONT]
 
23andme Neanderthal traits:

Hoarders, they kept getting lost and then argued for directions, no fear of heights, better sprinters than distance runners, no hitchhiker’s thumb, they sweated a lot, less likely to blush easily :)

uDbCVID.jpg
 
Not very high in number of variants: 238

More than 48% of testees.

[h=1]You have more Neanderthal DNA than 48% of other customers.[/h][h=1]You have more Neanderthal DNA than 48% of other customers.[/h]
[FONT=&quot]You have 2 variants associated withhaving difficulty discarding rarely-used possessions.
[/FONT]

[FONT=&quot]
hangry.93988b1196e1.svg
You have 1 variant associated withgenerally not feeling angry when hungry (hangry). (And vice versa)
[/FONT]

[FONT=&quot]
fear_heights.80693e4b33e5.svg
You have 2 variants associated withbeing less likely to have a fear of heights.
[/FONT]

[FONT=&quot]
sprint_vs_distance.acb9ece49fc0.svg
You have 1 variant associated withbeing a better sprinter than distance runner.
[/FONT]
 
Not very high in number of variants: 238

More than 48% of testees.

You have more Neanderthal DNA than 48% of other customers.

You have more Neanderthal DNA than 48% of other customers.


You have 2 variants associated withhaving difficulty discarding rarely-used possessions.

hangry.93988b1196e1.svg
You have 1 variant associated withgenerally not feeling angry when hungry (hangry). (And vice versa)

fear_heights.80693e4b33e5.svg
You have 2 variants associated withbeing less likely to have a fear of heights.

sprint_vs_distance.acb9ece49fc0.svg
You have 1 variant associated withbeing a better sprinter than distance runner.

Well, here's a surprise, my husband has only more Neanderthal than 11% of testees. That's a shock.

[FONT=&quot]You have 1 variant associated with [/FONT][FONT=&quot]having a worse sense of direction.

[/FONT]
(I can personally attest to that. He will NOT admit it, and becomes angry if I mention that perhaps I should give the directions, so I resigned myself early to taking detours that are longer than a direct route, or going around in circles for a while until he admits failure and lets me guide him. Probably has contributed to my blood pressure spikes! :) Patience comes hard for me.)

I would have thought muscle composition would have something to do with it, yet for him in the new traits section it says:

[h=2]your genetic muscle composition is common in elite power athletes.[/h]
Why do some people get reports on some traits which others don't.
 

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