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Abstract Background Hypermobile Ehlers-Danlos syndrome (hEDS) and hypermobility spectrum disorders (HSD) are prevalent conditions characterized by symptomatic joint hypermobility and a substantial public health burden, for which no causal treatment is currently available. In the absence of a...

One very minor thing: could it be that you used MAGMA v.1.08 rather than v1.10? Because 1.08 is what the FUMA SNP2GENE website uses when I try it. When I used MAGMA v.1.10 on my laptop without the FUMA website, I got slightly different results.

Good musing, thanks. Regarding proteins: I suspect these databases are less comprehensive and an extra step removed from actual DNA SNPs, but it would still be interesting to try this. I think we have to fit DecodeME into the many genetic analyses that have already been done, especially for...

MAGMA connects SNP associations with the disease (ME/CFS) to genes. If a couple of SNPs are located inside the gene, their p-values are combined into a gene signal. The window option lets you include SNPs into the gene signal that are not in but just next to the gene. I thought that allowing a...

I was able to replicate Paolo's meta-analysis (MVP + DME_1) using MungeSumstats R package (takes a while to load!) and METAL as the paper describes. I got the same number of SNPs (8,859,361) and top hits. Sometimes the z-sign is flipped but don't think that matters much. I noticed, however...

Oh apologies, I didn't realize he did a sensitivity analysis. If I understand correctly, the primary analysis is with the full gene set and the average of the dataset as a covariate, while the sensitivity analysis is only with the top 10% of genes by specificity score for each cell type, hence...

From Supplementary Table 4, data for the full DecodeME-chort. EDIT: This is from a sensitivity analysis. See the full results in forestglip's post below. Cell TypeRaw p-valueFDR-p-value SATB2_LRRC7_positive_cells0.00136070.04380017 Purkinje_neurons0.00146420.04380017...

They also did cell-type analysis and found the strongest connection with inhibitory neurons. These are slightly different cells from what we previously saw with the Siletti et al. brain atlas. The data source they used is the Descartes Human single-cell atlas, which is fetal-derived (77 cell...

Looks like a useful analysis, with similar findings to what we previously discussed. The genetic correlation with ME/CFS and depression was substantial (around 0.6, as we posted before using tools such as LDSC and BIGA GWAS). But when they looked for strong signals for both ME/CFS and...

Abstract Allodynia (perceiving touch as painful) is an enduring symptom of neuropathic pain. While acute pain is initiated by afferent signaling from the periphery to spinal cord, pain chronification recruits ongoing activity in supraspinal sites. One such site that has been proposed to be...

Noticed that SPATA25 appears a couple of times in the AstraZeneca analysis of rare mutations. AstraZeneca PheWAS Portal Not sure if there's a relation but it's mainly involved in the development of mature sperm cells.

I noticed that SMCHD1 was one of the genes below the significance threshold that was associated with ME/CFS in DecodeME. it seems to play a role in X-chromosome inactivation SmcHD1, containing a structural-maintenance-of-chromosomes hinge domain, has a critical role in X inactivation - PubMed

Looks like they don't have a letter to the editor format and that a critique would fall under 'General commentary.' https://www.frontiersin.org/journals/immunology/sections/systems-immunology/for-authors/article-types I don't like that they mention "Authors are required to pay a fee (B-type...

Yeah agree here are some other studies pointing to this problem: https://www.nature.com/articles/6604491 https://pmc.ncbi.nlm.nih.gov/articles/PMC4577098/ The mean concentration in patients was more than 7 times higher (126 versus 17 ng/ml) than in controls, suggesting this is likely a...

I think the reason is that since that the dbSNP, which provides a database of rsID for SNPs, no longer provides a file for common variants since version 151. So for their latest release, 157, you have to download and query a massive file vcf file that also includes rare variants and likely...

This 2020 paper on the H-MAGMA method also includes a list of 1,841 pleiotropic genes that were found in 4 or more out of 5 tested neuropsychiatric conditions such as ADHD, autism, schizophrenia, bipolar disorder and depression. I checked the FLAMES list from above to see of any appear in it...

With covariate I meant a data column with the average gene expression in the dataset that you can choose to condition on or not. From what I remember, the Duncan et al. file only gives the relative gene expression in the dataset per cluster, so not the absolute gene expression for each cluster...

Perhaps the file provided by Duncan et al. 2025 paper might be useful? it gives a specificity score matrix file for Siletti et al 2023 atlas. EDIT: so it's each cluster's gene expression relative to the total gene expression of the dataset. It doesn't work with a covariate...

I noticed that the 2019 Watanabe paper on cell type analysis using MAGMA has a supplementary note where they explain their choice of using the average gene expression per dataset as a covariate, rather than just the absolute gene expression per cell type. It's basically what we already saw...

Ah apologies if I misunderstood!