Thanks for this piece. Really great! I will definitely come back to this more than once, whenever I've forgotten what had been talked about. What I didn't quite catch in the text is why some of your dots in the graphs are grey and why some are black? I might have missed it in the piece, but if not, I think it could be useful to be included somewhere.Blog: DecodeME: the biggest ME/CFS study ever
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DecodeME: the biggest ME/CFS study ever - ME/CFS Science
The first results of DecodeME are in, the largest research project ever undertaken on myalgicContinue readingDecodeME: the biggest ME/CFS study evermecfsscience.org
@ME/CFS Science Blog , spotted a typo, "Rare SNPs might show langer and clearer effects"
I would think there's a tremendous amount of different analyis that can be done to see how closely related ME/CFS is to a different illness in some sense. My impression is that whilst LDSC gives an indication on the genetic correlation between illnesses the reason to not necessarily take these data too seriously is not necessarily related to how diagnosis was recorded can alter the results (which is sort of how I understood what the text said) but probably rather that to compare the genetic basis of two illnesses in such a way can or may not be appropriate depending on the context. I would imagine that there are illnesses that are entirely different in symptoms and presentation but that share variants in the same region (or as you mentioned in the text that it matters where the genes is expressed) and illnesses that are similar in symptoms and presentation and are similar in terms of the underlying biology but that don't share variants in the same region. In short your results may reflect the following: Pleiotropy (shared genes), Shared risk factors, or correlated measurement artifacts without reflecting anything genuinely connecting the mechanisms of illnesses. Of course you know these things much better than me, I just thought the justification to not take the LDSC too serious was maybe a bit too short for my taste in the text?
I haven't had a closer look but I've understood LDSC estimates global correlation, rather than anything else. Now it seems to me that this possible error in finding an HLA-association that doesn't exist suggests that there is room for imputation error in lots of different places (presumably only the significant findings where triple checked to hold water?). I find it possible that this additionally means that LDSC can from time to time identify common noise not signal as long as there is something systematically causing such issues?
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