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You mean like the causal factor might be a specific type of neuron found in many regions of the brain, and the order just relates to what proportion of each tissue is made up of that neuron type?

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:

Since I previously ran AlphaGenome with all the significant variants, all the brain-expression protein-coding scores can be found in the spreadsheet in this post. And scores for expression in all tissues and with all types of genes can be found in the much larger file at this GitHub repo...

I no longer have access to mapMECFS, the platform for sharing raw data for the deep phenotyping study. But I previously posted about doing statistical tests on all 435 CSF metabolites, and cortisol was in fact one of the chemicals that was in the data. And in another post where I posted the...

Good catch. They've published a correction. Corrigendum to “Beyond COVID-19 in people with HIV: Specific miRNA expression profile persist after SARS-CoV-2 clearance” [J Infect Public Health 19 (3) (2026) 103108] Web | PDF

I'm not sure if this is what you mean, but I was initially also thinking that it was basically outputting the same things you'd find in GTEx. But I don't think it's that. I'm pretty sure it doesn't "know" where in the genome the strand of nucleotides you give it is, or where any genes are. I...

Africa Africa (excluding South Africa and MENA countries) South Africa Asia China India Israel Japan Korea Middle East, North Africa (the MENA countries) and Turkey Russia South Asia South-East Asia Europe Austria and Switzerland Baltic States (Estonia, Latvia, and Lithuania) Belgium...

The plot for cortisol levels in cerebrospinal fluid looks similarly striking to the CRH finding. I would think that this would have already been tested in people who are alive, though I can't immediately find a study looking at CSF cortisol in ME/CFS. I don't see any mentions of CSF on the...

Interestingly, the top four significantly enriched tissues based on MAGMA are the same four tissues as DecodeME, in the same order: Frontal Cortex, Cortex, Anterior Cingulate Cortex BA24, Nucleus Accumbens. From DecodeMe: Edit: Looking at the MAGMA plots I previously compiled from several...

Large sample size is very important in GWAS, and that was their rationale for combining. Even though they're not the same disorders, I think it's reasonable to suspect that they may have some factors in common, which a shared GWAS would uncover. Another benefit is that any such findings would...

NEGR1 was almost significant in DecodeME, and has had significant associations in depression GWASs. It's mentioned here for anxiety:

Both technically right, but just to prevent confusion, the position given by jnmaciuch and in the anxiety paper, is using GRCh37 assembly coordinates, while the one I gave is in GRCh38 coordinates, which is the assembly used by the DecodeME summary stats and LocusZoom above. (Though it's close...

The BTN2A2 SNP is given as rs58825580, which is chr6:26365451:T:G. In DecodeME, that SNP had a -log10p=1.60642, or p=0.025.