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The data is available on https://www.macromapqtl.org.uk

If you consider that the prevalence of ME/CFS is far lower than depression, then most people in the depression studies wouldn't have ME/CFS. My sense is that it'd be difficult to get such high correlations based on people in the depression studies having ME/CFS if only a small portion of the...

Yes, just to confirm, the BIGAGWAS website says "9999 represents NA for numerical data".

"Great, maybe people with ME/CFS have a genetic predisposition to unhelpful beliefs. Unfortunately, none of the treatments you have suggested have worked, so lets examine the specific mechanisms through which these genes cause ME/CFS. The genetics seem to be pointing to people with ME/CFS having...

Yes, just sorted by p-value. (And that enormously significant correlation with depression does come from comparing to a study with an enormous sample size: 371,184 depression cases) Good idea to look at top correlations. I wonder what that milk one is about. Just under your significance...

The only result I see of these from a search of the words is multiple sclerosis in UK BioBank and it doesn't look to be significant. (Also all results from all tested traits are in the attached files if you want to explore.) From UK BioBank: Multiple Sclerosis: Diagnoses - main ICD10: G35...

I've now run this tool on a few different datasets using LDSC to find genetic correlations between ME/CFS and other traits. I'll attach all results for download and just mention some specific correlations. Wikipedia: First I ran it on the dataset "PGC (Psychiatric Genomics Consortium) and...

The above was the 10th most significant locus in the main GWAS (though its p-value of 1.19e-7 didn't pass the genome-wide threshold). NEGR1 appears to be the closest gene. Lead variant: 1:73,126,414:C:CA There appears to be evidence linking NEGR1 to depression. Link to PubMed search for...

Which part of the conclusion goes beyond the evidence? It seems fairly reserved to me. They saw many studies that found reduced CBF in ME/CFS. They said CBF is reduced in ME/CFS. The reason for the CBF reduction (deconditioning, medications, ME/CFS pathophysiology, etc) is a different...

Awesome! I'm not yet positive I understand it right, but I've been trying to find if there's any tool to find the best correlations based on raw genetic data from thousands of other traits, and this might be it? And you don't even have to convert to grch37 or rsids.

Some posts about sleep disturbance in ME/CFS have been moved to: Sleep problems in ME/CFS - discussion thread

Favorable responses to upadacitinib, a JAK1 inhibitor, in long COVID patients with predominant neuropsychiatric symptoms: case reports in 2 autistic patients and one typically developing patient Harumi Jyonouchi, Jeffery Kornitzer, Lee Geng [Line breaks added] Abstract The long-term impact of...

I see a few reasons: - Different reference panel (1000G vs UK BioBank). - Liftover to another assembly only loses 0.3% of variants, while our mapping to SNP method lost 6% (though it's unclear how many more are lost later in both methods when MAGMA refers to the LD reference panels) - I don't...

Just a guess, but I think the UK BioBank data might not be open access like 1000 Genomes is. Maybe worth checking though.

I get a print subscription to Science. I've been excitedly waiting for this issue, and it finally came:

Yeah, I don't know where to start to find the right files. It's all so interesting. It feels like there's so much hidden treasure in this data file of DNA, and all these free tools across the internet to analyze it. I'm just very lacking in the experience and energy departments, so most of it...

Looks interesting. I tried to see if I could do anything, but it's too much stuff I don't know how to do, like the part about creating credible set files. In other news, based on a suggestion by @hotblack, I tried to use the UK BioBank reference panel for FUMA instead of the 1000 Genomes...

Hmm, the veterans affairs website says: The file it links to is a 2011 document, but the above study (which appears to be commissioned by the VA) is from 2015. Edit: See appendix A for the literature review from the VA in 2009 that found the evidence was not sufficiently strong to connect PB...

Note that the script hotblack posted includes a lot of extras for convenience, like remembering settings for future runs. These are the only required steps we used: FUMA does make MAGMA much easier (though requires converting to GRCh37). I've been looking for other online tools for analyzing...

Information from Veterans Affairs: Bateman Horne Center says this for dosages for orthostatic intolerance: Interestingly, potentially lower dosage for military than for OI patients.