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It wasn't done in the DecodeME paper, though it was attempted by me. It seemed to point to neurons all over the brain (excitatory, "GABAergic", and just "neurons"). I'm hoping they do something like this in the final paper. Edit: Cell types from this study: Edit: Note that the analysis I did...

Yeah, it's possible. It's more meant as one piece of evidence. If the GWAS points to a gene's expression in one specific tissue, and other evidence implicates the same tissue, it adds to the evidence. Though, it could be that a hypothalamus association might just exist due to similarity of...

Considering that this GWAS has many different anxiety phenotypes combined together, and considering the overlap with DecodeME in MAGMA, my suspicion is that this may be getting to a "root" specific component that all these diseases, including ME/CFS might have in common. Maybe further very...

To add to the above post, they are looking for how well SNP associations match with gene expression in specific tissues. Like DecodeME did using a different method, where they found, for example, that ME/CFS SNPs matched up with expression of RABGAP1L expression in several specific tissues.

A transcriptome-wide assocation study (TWAS), used here, does something like trains a machine learning model to predict expression of a given gene based on SNP patterns (using existing expression databases like GTEx), then uses some method (that I don't really understand) on GWAS summary...

2021 study, but I was interested in it because it's so large (>350,000 cases), and to see how the MAGMA tissue enrichment might compare with DecodeME or a large anxiety GWAS, which seem to have similar MAGMA results. Here is the MAGMA tissue enrichment from this study: In order of...

Bi-ancestral depression GWAS in the Million Veteran Program and meta-analysis in >1.2 million individuals highlight new therapeutic directions Abstract Major depressive disorder is the most common neuropsychiatric disorder, affecting 11% of veterans. We report results of a large meta-analysis...

This is Scientific Reports, which is not as prestigious as the main Nature journals, like Nature and Nature Medicine. This journal apparently has the largest number of articles/year of any journal, which suggests to me that they probably allow many less rigorous articles.

Email from IACFS/ME (original bolding): Some of you may recall that IACFS/ME previously published a Newsletter several times a year, edited by the amazing Dr. Rosamund Vallings of New Zealand. Given the many developments in ME/CFS, Long COVID, and related conditions, we felt this is the perfect...

I don't know anything about these proteins, but if you want to see how they're related, you should be able to click the lines between proteins on the STRING plot, and it'll give you all the evidence it based the relationships on.

I was waiting to get a reply from someone at mapMECFS to see if it would be okay for me to still post the data I previously analyzed, and I was told I could. I see it's already been mostly discussed at length, but they also suggested I note that there may be reasons for the differences, such as...

68 statistical tests and no multiple test correction. We should expect around 5% of these, or 3.4 tests, to be p<.05 by chance. 5 tests had p<.05. So I think likely most or all of these findings are due to chance.

Interesting that the sex bias is opposite of typically seen.

Some general discussion about AlphaGenome has been moved to: Advancing regulatory variant effect prediction with AlphaGenome 2026 Avsec et al

Oh, nice. I learned something new. Here's what the plot of DecodeME looks like with non-coding RNA:

Yeah, every score returned by AlphaGenome. The predictions are limited to the same length as the strand of DNA sent for inference, with the limit for that being 1MB. The interval it scored genes on can be seen in the scored_interval column, which for this variant is chr6:25714888-26763464. When...

I think it's likely that it's not actually all these brain regions affected in these disorders. Similar genes are expressed in different parts of the brain, so if only one brain region is actually causal (say, frontal cortex) and thus is significant in MAGMA, then I think it's possible that...

I suppose it's possible there are actually two loci in DecodeME. I guess we'll need a larger GWAS or multi-ancestry to see them separated out more clearly. @ME/CFS Science Blog also previously looked at where the depression NEGR1 lead SNP sits, relative to DecodeME. It looks like the anxiety...

I posted in another thread, but I think this is notable enough to mention here. In a large GWAS (122,341 European ancestry cases and 729,881 controls) of anxiety-related traits (GAD, panic disorder, social phobia, agoraphobia or specific phobias), MAGMA tissue enrichment was tested. The four...

Not quite. The top NEGR1 variant from this paper is highlighted, overlaid on DecodeME's results: