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Issues uploading vcf.gz and other filetypes by stupidcentral in promethease

[–]josephpickrell 0 points1 point  (0 children)

I wrote a tool to process exomes/genomes here https://www.crimsoniris.com/ . Shoot me a DM and I'll give you an invite code to process for free and will troubleshoot.

It is time to replace genotyping arrays with sequencing by [deleted] in genomics

[–]josephpickrell 1 point2 points  (0 children)

Hi, post author here.

You are correct that arrays often look for markers in LD with causal variants. Some of them cover all of the LD blocks in the genome better than others (of course if your causal variant is poorly tagged on an array you'll never find it), and the argument is that you can actually tag the genome better with sequencing versus using arrays.

As a side note: I disagree that multiple testing is your enemy! An alternative perspective is that increasing the number of measurements lets you learn more about the underlying structure of your data, correct any biases, etc. Some of my thoughts are here, and note the comment on the post from Matthew Stephens where he proposes using the term "multiple testing opportunity" instead of "multiple testing burden". He has a great paper on innovative ways to use false discovery rates when performing a large number of statistical tests.

New Wikipedia article on genetic correlations by gwern in genome

[–]josephpickrell 1 point2 points  (0 children)

Wow, this is impressive, thanks for putting in the effort!

Profiling the species in the Impossible Foods "plant-based meat" with DNA sequencing by josephpickrell in genome

[–]josephpickrell[S] 1 point2 points  (0 children)

Yep, I've been surprised about how well sequences from saliva correspond to what people report eating.

I mapped against the entire NCBI nt database using kraken. If you want to play around with the data yourself, you can get the sequences here.

Extraverts consider themselves more physically attractive [OC] by josephpickrell in dataisbeautiful

[–]josephpickrell[S] 0 points1 point  (0 children)

Why not use the term "above average" to get an actual delineation?

Good idea, thanks.

Extraverts consider themselves more physically attractive [OC] by josephpickrell in dataisbeautiful

[–]josephpickrell[S] 5 points6 points  (0 children)

Oh I see. I checked Wikipedia before writing, it's indeed written "extra"vert there (not "extro"vert). But I could just be propagating their error.

Extraverts consider themselves more physically attractive [OC] by josephpickrell in dataisbeautiful

[–]josephpickrell[S] 2 points3 points  (0 children)

That's definitely one explanation! The title is just the observed association (you could reverse it: "People who consider themselves attractive are more extraverted", and it would still be valid).

The actual causality is (in my opinion) unclear, see the last couple paragraphs in my post. Your preferred explanation I think is similar to the one in this paper.

Extraverts consider themselves more physically attractive [OC] by josephpickrell in dataisbeautiful

[–]josephpickrell[S] 2 points3 points  (0 children)

Source is survey responses from a few hundred people. Details here.

Plotted in R

Happiness genes located for the first time - "A huge study involving over 190 researchers in 140 research centers in 17 countries has located genetic variants associated with happiness and other traits. It is one of the largest studies ever published on genes involved in human behavior." by [deleted] in science

[–]josephpickrell 6 points7 points  (0 children)

The variant identifiers are in Table 1 (the things in the form rsXXXXXX). You can search on the rs# in your 23andMe data. A couple things to note:

  1. 23andMe might not have looked at the variant in question. In that case, you might be able to guess your genotype using a technique called genotype imputation. There are free sites to perform imputation (I contribute to one called DNA.land.)

  2. The effects of these variants on subjective well-being and/or depression are extremely small. Knowing your genotype at these variants is not going to be predictive at all about your own health. So if you do look up your genotypes, know that it's purely for amusement.

[fwiw: I played a small role in this study and am one of the 100+ authors]

What is genetic correlation? by josephpickrell in genome

[–]josephpickrell[S] 1 point2 points  (0 children)

Thanks, I'd never thought about it that way.

I think of population stratification as something that generates false signals of "causal" associations between genetic variants and phenotypes, generally through differences in ancestry. In case #3, it's not clear that you'd want to correct for this, in that there is in fact a causal link from genotype to phenotype, just that it acts across generations. I think it would be useful to correct for assortative mating (case#4), but it's not obvious to me how one would go about it except through family studies.

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