Wednesday, October 31, 2018

Learning about the elitist opinions of a study's authors through their dubious study

This preprint of an alleged "study, " "GENETIC CONSEQUENCES OF SOCIAL STRATIFICATION IN GREAT BRITAIN", is the kind of filth that has only been suggested in previous studies, but apparently they are feeling puffed up enough to just go full-on eugenic.  I realize that they believe that what they are saying is backed up by genetic evidence, but that's what the phrenologists thought, as well.  Realistically, I can't fully dispute all of the claims, as I am not familiar enough with the geography of England and the socio-economic aspects of their society.  Nonetheless, it's not hard to see what is happening here, if one really wanted to see it, which is that their beliefs about the genetics of superior sorts (i.e.,  people more like them) are causing them to miss the forest through the trees in terms of stratification of a society.  I am quite confident that I can tell you the authors' politics, socioeconomic and geographic backgrounds and opinions about various mental illnesses, without having met any of them.  It is an elitist view of the world, written by elitists, for the pleasure of other elitists.  They should be ashamed.  So, let's go through this, shall we:

Friday, October 19, 2018

More on the idea of "Yoking Stratification"

I posted previously about the idea of "Yoking Stratification," and that post can be viewed here.  In short, the idea is that, GWAS results can be skewed, because individuals with a particular trait often marry/mate with individuals with that same trait. The term for this is assortative mating: i.e., Tall people tend to marry tall people, people with a high BMI, tend to marry other people with a high BMI, and as one study showed, people with a mental illness tend to more frequently marry others with that same mental illness or, to a lesser extent, other mental illnesses.   This is a potential source of population stratification and I think is difficult to control for to any extent.   As I noted in the previous blog post linked above, this could therefore artificially inflate the number of SNP's found to be "significant" for the trait and the polygenic score might just be a reflection of the common genetic markers due to this selective trait mating pattern, but unrelated to the trait itself, in the same way that Ancestry.com determines your racial background via genetic markers that likely have nothing to do with being "Irish" or "Chinese."
This point was driven home recently, when a study came out  with N = 360,000 that failed to find SNP's for "left-handedness." 

Sunday, October 14, 2018

"Minimal Phenotyping" to crank up your GWAS hits creates more problems

This study points out that minimal phenotyping (dumping anyone into your GWAS with a 1 or 2 question screening rather than meeting full diagnostic criteria) for major depression is getting hits that are then tied to CNS enrichment (genes found more commonly in the central nervous system, implying some brain mechanism), but the ones that were "enriched" were actually the extra ones picked up by minimal phenotyping.  This is a problem, because CNS enrichment would be expected to be more prominent for those who met the full criteria for MDD, rather than just answering a couple of questions about depression.  This implies that there are likely false positives, or at the very least, non-specific positives, unrelated to major depression.  Thus, when you try to isolate functional neurological aspects of the disorder, either to understand cause or pursue pharmaceutical options, etc., you are likely barking up the wrong tree.  CNS enrichment is also used as a backdoor method to imply the validity of the genetic variants found in particular GWAS studies related to mental disorders.
So, adding to the fact that there have been no independently replicated, significant genetic variants found for depression, to date, even with minimal phenotyping, we also cannot confirm that these genes have any relation to depression by assessing CNS enrichment.

Thursday, October 11, 2018

New Depression Study Finding 102 Variants. What is Replication?

A new Depression study claiming 102 genetic variants has just come out (pre-publish).  I don't want to do an extended critique, so I will stick to a few main points: