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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.

Digital Biometric Measures in Long COVID: A Secondary Analysis of the STOP-PASC Randomized Clinical Trial Fatma Gunturkun, Haley Hedlin, Bren Botzheim [Line breaks added] Key Points Question What are longitudinal digital wearable biometric measures and trajectory patterns in participants with...

I'd be really interested in a follow up of the brain enrichment by looking at enrichment in specific brain cell types. The brain finding is interesting, but hard to know what to do with it since the brain is a big place. The following studies show examples of looking at specific cell-type...

It looks like they're just making sure it's safe, since they refer to it as a "test", not a "treatment", at least in the abstract. I'm just concerned that: 1. Their symptom scale may not be well-suited enough to capture symptom exacerbation. 2. It may be the case that for most people with TBI...

Contents: 1 The history of chronic fatigue syndromes including ME/CFS and Long Covid 2 When to suspect ME/CFS or Long Covid 3 The diagnosis of ME/CFS and Long Covid 4 Primary ME/CFS or Long Covid versus secondary chronic fatigue 5 Theories of causation 6 What do you tell a patient? 7...

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...