Tuesday, October 22, 2019

When You Don't Realize You Are a Eugenicist

This study related to geographic stratification of genetic variants had a lot of promise and is actually quite a good source of information, in my view, on the inherent problem with the UK BioBank and population stratification issues that confound GWAS. Unfortunately, the authors take it in a very different direction, exemplified by this quote in a promotion piece written by the lead author:
With this paper, we ended up showing how social stratification in a modern meritocracy makes it increasingly less likely that someone close by shares recent ancestors with you and more likely that they share a genetic talent for socio-economic success. 
This is, to put it bluntly, eugenics. The paper in question shows nothing of the kind. In my view, in fact, it shows the opposite; that this is not a "modern meritocracy," and I think that holding such a belief is a sure tip-off of the biases of the authors in their rather misguided and disturbing conclusions.
Let's take a look at the study with a starting point of assuming that all of the genetic variation seen in "Educational Attainment" is related to population stratification and assortative mating that confounds GWAS (particularly in the UK BioBank).

Thursday, October 10, 2019

PTSD and the GWAS Hype Machine

A new PTSD GWAS makes a few bold claims.  I think it's a good example of the kind of hype that these studies, which show next to nothing, crank out to hype their results. In this puff piece related to the study, they start with:
Large study reveals PTSD has strong genetic component like other psychiatric disorders
Which 1. It does not and 2. Is not really shown to be true of other psychiatric disorders, either, except in the same hyped fashion as this study. Now let's look at this from the same puff piece:
The study team also reports that, like other psychiatric disorders and many other human traits, PTSD is highly polygenic, meaning it is associated with thousands of genetic variants throughout the genome, each making a small contribution to the disorder. Six genomic regions called loci harbor variants that were strongly associated with disease risk, providing some clues about the biological pathways involved in PTSD.
 If it is highly polygenic, on what basis are they saying this if only 6 loci were strongly associated with disease risk (this is not even accurate, as I'll discuss in moment)? "Genome-wide, a substantial number of variants had some level of association with PTSD, showing the disorder to be highly polygenic," What this is saying is that there are other loci (presumed genetic variants) that did not reach significance, but they include through the subterfuge of "polygenic scores." There is no basis, other than the hopefulness of those doing these studies, that these below significant findings are anything more than non-significant findings. I'll  also note that none of these 6 loci were found in previous studies. Thus, this is an entirely unreplicated study. Now, let's take a look at the loci they did claim to find: