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ME/CFS and Long Covid: Diagnosis and management of chronic fatigue syndromes Gavin Spickett [Line breaks added] Abstract This book covers the history and characteristic symptoms of ME/CFS and Long Covid in adults. Children are not discussed in detail. It discusses the extensive differential...

Exercise-Induced Symptom Exacerbation and Adverse Events in Moderate-to-Severe Traumatic Brain Injury Gallow, Sara BPhysio; McGinley, Jennifer PhD; Olver, John MD, FAFRM; McKenzie, Dean PhD; Williams, Gavin PhD Objective To determine the incidence of exercise-induced symptom exacerbation and...

@Chris Ponting, as arnoble says, can you clarify, was the tissue enrichment based on putting those 13 genes into a discrete gene set and seeing if those 13 genes specifically, without regard for their actual p-values/z-scores, were enriched among all genes expressed in a tissue? Or was every...

MAGMA manual if anyone wants to look. DecodeME says (bolding added): "These genes" does seem to imply that they looked at expression of specifically those 13 genes. Maybe it's just the wording. The bits I understand in the MAGMA papers seem to indicate that the gene-property analysis has a...

They're just different methods of predicting the important genes, so the results won't be exactly the same. (Again, keep in mind those 13 genes aren't necessarily related to the brain enrichment.) The candidate genes were determined based on genes known to be differentially expressed due to a...

Hmm. I think on its face that does make sense (though not sure how much confidence this actually allows us to have in selecting genes based on expression). I wonder if any of the papers I linked above that did MAGMA tissue analyses did anything similar. I didn't read any yet, just grabbed the...

Chris said in the webinar: That's a great benefit to those individuals of course if they could be notified that they have these rare diseases. But on top of that, I feel like this could be valuable for identifying common mechanisms of ME/CFS, if you don't take the position that these...

Yes, that's how I understand it. For each gene, they look at all the many SNPs that are in or around that area of the DNA where the gene's code is located to give that gene a score based on how significant those nearby SNPs were in the GWAS (how high they are in the manhattan plot). They account...

I thought it'd be interesting to compare the DecodeME result for the tissue analysis to other papers. I searched for "MAGMA tissue" in Google Images, DuckDuckGo Images, and searched in Google Scholar to find other papers that included plots like the one here. Panic disorder: Brain regions are...

I don't think that's what's happening though. I'm pretty sure the following is right, but it's hard to find good explanations. MAGMA is fully separate from the part where they selected candidate genes based on things like eQTLs and nearness. Instead they take every gene and assign it a score...

wigglethemouse posted them a few posts back. These are in order of significance, with most significant at the top.

Thanks for pushing back on their paper Hutan. The grouping looks even tighter in chillier's random data.

I think the rsids that have a "P" (for proxy) refer to another variant in LD with the DecodeME SNP that they tested in the other cohorts if the other cohorts didn't have the variant in question. The ones you named: 1. GRCh38 variant 13:53194927-GT-G rs35306732 2. GRCh37 variant 13:53750354:A:G...

I'm just learning about this, but I think technically these 13 genes weren't necessarily enriched in brain tissue. I'm having ChatGPT explain MAGMA to me, and it says it's basically two different analyses. The 13 highest scoring genes from the first part are likely to play a role in the brain...

On the topic of the brain expression, I don't remember much discussion about this yet. While all 13 brain tissues had enrichment of ME/CFS genes, there is an ordering of most to least significant that might give some clues. Written out and grouped: I added pituitary gland even though it...

On the topic of "what does DecodeME" show, my feeling is that it's really early for anyone to be saying with much confidence that the genes they found point to any specific pathway. From the DecodeME blog and paper respectively: Here are the candidate genes suggested by DecodeME: Is it...

Just adding the context from Wikipedia for why they say candidate gene studies don't replicate:

TLDR: They didn't do the replication with a second cohort properly, and the significant SNPs don't replicate in DecodeME. Fukuda criteria. They found significantly more participants had the T allele in the TNF-857 SNP. Also fewer had the A allele in the IFN-γ-874 SNP, but this was much less...

A first study of cytokine genomic polymorphisms in CFS: Positive association of TNF-857 and IFNgamma 874 rare alleles N Carlo-Stella, C Badulli, A De Silvestri, L Bazzichi, M Martinetti, L Lorusso, S Bombardieri, L Salvaneschi, M Cuccia Published: 2006 [Line breaks added] Objective In the...

Clinically Meaningful Improvements in Long COVID Symptoms Following Ketogenic Metabolic Therapy Combined with Lifestyle Interventions—A Clinical Case Report and Review of the Literature Dana Dharmakaya Colgan, Diane D. Stadler, Aluko A. Hope, Heather Zwickey, Todd E. Davenport, Thomas Weimbs...