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Thank you, I'm working through adding relevant quotes. This is such blatant manipulation of statistics, it's amazing: - https://lp-fortellinger.no/en/2022/02/24/venke-midtlien-2/ - https://lp-fortellinger.no/en/2022/02/24/kristin-stolen-2/

Would you count sickness response during infections as an illness? As far as I know, that's largely thought to be symptoms produced by the brain. There are some similarities with the symptoms of ME/CFS, so it might be worth looking into the biology of the sickness response. For example, first...

Previously on Qeios with two comments: Orexinergic and Hypothalamic Dysfunction in CFS/ME: An Integrative Review with a Focus on Precision Medicine

An integrative review on the orexin system and hypothalamic dysfunction in myalgic encephalomyelitis/chronic fatigue syndrome: implications for precision medicine Noé López-Amador [Line breaks added] Abstract Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating...

I've come across the claim that the Lightning Process (LP) intervention, at least in some cases, includes coaches teaching patients to misrepresent or lie about their symptoms to others. If this were true, any trials of the LP which rely on subjective outcomes would be completely unreliable as...

The example locus you gave might be one of the harder ones to do this with because there are so many genes around the locus. There's a good chance the causal variant isn't the top hit, so one of the other variants near another gene might be causal.

From the link: Somewhat brilliant way to make money.

Yes, I think it could be worded better. I haven't seen anything that makes me think they limited follow-up tests to only those 13 genes.

See here (different letters used but same idea): The tissue gene-property analysis is a linear regression of all genes. Z is a gene's score from the GWAS and Et is a gene's expression in a tissue. Both of which are continuous, not binary. For the gene-set analysis (the ubiquitin, synapse gene...

Radio New Zealand: 'Genetic links found in ME/CFS patients' "New research has found myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is partly caused by genetics, related to the immune and nervous system. The study - the world's largest into the condition - identifies DNA...

Yes, combined with Zhang's synapse findings, it seems more and more likely to me that the brain is part of the picture. I can't remember if we have other reason to think about synapses specifically. Maybe your earlier suggestion of thinking about which of the genes from the top loci have an...

Let me know if you run into issues. There were a few annoying roadbumps in the process. Maybe. I imagine the eight main loci might be related to brain, might not. Maybe 6 are, and 2 are related to the immune system. But MAGMA is more like, if you average out all of the genetic signal, what does...

How the actual math works, I don't know. But somehow it returns SNPs that are a different significance from the actual measured SNPs.

The actual machine that reads the participants' DNA, to make it more afforadable and practical, only actually physically observes a subset of locations on the DNA. In DecodeME, that's 800,000 locations where the output could tell you the actual letter that all the participants' had at these...

Oh, last thing for now. Like the DecodeME study, FUMA ran a MAGMA gene-set analysis on various curated gene sets. And like the study, it didn't return any significant gene sets after Bonferroni correction. But it might be interesting to look at the gene sets that had the lowest p-values: I...

FUMA also has exactly the MAGMA cell type enrichment I was hoping for. There are hundreds of different cell-type expression datasets to choose from to do analyses like the tissue enrichment above. I don't really know how to choose from them, or even to examine which cell-types are included...

Filtered for only the SNPs in the qced file.

I figured out how to upload the summary statistics to FUMA, which also does MAGMA analyses, so I tried to see if I could replicate the brain enrichment. There are a lot of customizable options, so I was not able to get the same exact results. I also had to convert all the SNPs from GRCh38 to...

I think the plot shows the data from only the sequenced SNPs and the main imputed SNPs (imputed everywhere but HLA). They did HLA imputation separately, and I'm guessing they didn't add that to the summary statistics or the plot yet because they aren't sure that part is quite right.

Figure 3, tissues that significant genes are enriched in, in terms of gene expression (based on GTEx expression data). EBV-transformed lymphocytes were not a significant tissue, just one of the few lowest p-value non-significant tissues, but probably nothing very exciting.