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Highlighting the gene cards of some of the closest genes that have little competition or that have the top SNP inside it (Forestglip already posted about many of these before). LRRC7 LRRC7 Gene - GeneCards | LRRC7 Protein | LRRC7 Antibody SOX6 SOX6 Gene - GeneCards | SOX6 Protein | SOX6...

Did something similar by looking at SNPs that had a p-value below 5*10^-7 but that didn't appear in 8 regions that DecodeME already highlighted. So they were just below the threshold of 5*10^-8 for statistical significance. But because this threshold is a bit rough and arbitrary, it might be...

The coloc analysis doesn't seem that difficult (there's an R package for it, suspect it's mainly about getting the two GWAS summary data in the right format). But unfortunately, it looks like you have to request access to get the GWAS data on depression. PGC major depressive disorder GWAS |...

Also checked for significant hits in Long Covid such as the FOXP4 gene highlighted by Lammi et al. 2025 (rs9367106) Genome-wide association study of long COVID | Nature Genetics And the 3 SNPs highlighted by Chaudhary et al. but DecodeME didn't have a signal anywhere near these regions...

Coming back to OLMF4 and NEGR1, two genes which had significant SNPs close to them in a big depression GWAS: Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression | Nature Genetics DecodeME also has SNPs close to these genes that were...

More info about it here: https://reporter.nih.gov/search/yRt6xcKZp0uEl3CiqgghbA/project-details/10878255

In this interview with David Tuller, Lipkin seems to suggest that the planned GWAS and collaboration with DecodeME was cancelled. Instead they seem to have set up a different genetics study. They will look at genes of families where more than one person is affected, in collaboration with the...

In the graph above the greater variance in ME/CFS could be due to the decline in strength over the 10 repetitions. If I take only the first 3 repetitions, the variation between groups looks similar.

Was looking at one of the reference in the paper, a review Shechtman 2000 which was highly critical rather than supportive of the measure. It also points out what seems to be the issue here: So I think that's whats happening here: the standard deviations between patients and controls are...

Had a closer look at the raw data, available here: https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-021-02774-w EDIT: posted some other graphs earlier but these were incorrect (they focused on the variation per group rather than per individual). Below is a graph of the...

The difference seems quite large. So apart from the authors interpretation what would be the most likely explanation for this? Is it simply that being ill/having lots of symptoms causes the variation in handgrip strength measurements?

Seems like there is an inflation of the term autonomic dysfunction or dysautonomia. In this paper they report that "38% of the healthy controls had autonomic abnormalities". If it is so common, it's probably not an abnormality anymore? Using the lean test (not tilt table) the study found that...

Probably this study by Peter Novak: https://www.nature.com/articles/s41598-024-52368-x

Not sure if the term 'autonomic symptoms' is a useful category. For at least some of the symptoms it seems that the problem could lie elsewhere than in the autonomic nervous system?

I don't think there's a paradox here. It just shows that the author probably doesn't know anyone with ME/CFS and how a life with severe ME/CFS looks like. Talking to patients and getting to know their life (as Jo has done here and on Phoenix Rising) would help doctors to understand the illness...

They seem to say that they found something similar to the preload failure of Systrom's group: The novel aspect of the paper seems to be that they used O2 pathway analysis, which tries to break down oxygen transport into different aspects. In ME/CFS and Long Covid patients, the problem seems to...

In the DecodeME sample, they did quite some efforts with the questionnaires + self-reported clinical diagnosis to ensure patients had ME/CFS. So I don't think its likely that misdiagnosis would affect the results so much to create spurious relationships of this magnitude. Another option is that...

Social media summary: 1) A new paper found a slight increase of Fibroblast growth factor 21 (FGF-21) in ME/CFS patients compared to controls. FGF-21 is a hormone-like protein that helps to regulate metabolism and has been found to be increased in previous ME/CFS studies. 2) Below is the data...

The intercept of LDSC is often used as a measure of stratification effects or confounding bias. It should be close to 1. If it is substantially higher, it would suggest that population differences between group are inflating the p-values. The good news is that this isn't the case in DecodeME...

With the help of @forestglip, I've finally managed to run linkage disequilibrium score regression (LDSC) on the DecodeME results. The original package is written in the outdated Python 2 which caused all sorts of errors. So I've used the Python package GWASlab which provides a wrapper function...