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.

3 comments:

  1. https://www.sciencedaily.com/releases/2014/03/140320173158.htm
    Genetic Variant for Depression? Folks with IBS have significantly more depression than normal folks, and the depression occurs with flareups.

    I'm not saying this is going to be a Red Flag which will characterize all depression.

    (And, of course, this isn't about CNS enrichment).

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  2. Zed, I see you want to believe, I think perhaps there is a correlation/causality issue with your particular example.

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