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Abstract We introduce an approach to identify disease-relevant tissues and cell types by analyzing gene expression data together with genome-wide association study (GWAS) summary statistics. Our approach uses stratified linkage disequilibrium (LD) score regression to test whether disease...

Do we also have a thread where members can indicate their willingness to participate in a research project as a patient representative? The willing and available thread is much broader and also asks about roles in charities, the media, and the forum itself. So perhaps we could create a...

I suppose this is the thread where researchers looking for PPI can make a request on S4ME: https://s4me.info/threads/patient-and-public-involvement-opportunities-in-me-cfs-and-other-research.35017/ The call says that "meaningful involvement of patients and/or patient representatives is...

Can anyone explain how people registering their interest would have changed anything? As Jo already argued the committee probably assumed everyone was interested before making a choice. So is it mainly about resumes and official qualifications not being considered?

The paper also focuses on the subgroup comparison of LC patients with or without PEM. Would be more interesting to focus on the LC versus database control comparison. I suspect that Table 2 shows z-values, which indicate how many standard deviations the mean is from the control data. If you...

Big limitation that the controls were from a database: Well spotted; this makes it more likely that they simply didn't do Bonferroni correction at all.

Great that WE&ME is doing this! It says the call is funded entirely by them, and with 7 x €150,000, that would be around one million euros that they put in. It feels like recognition of S4ME, that they are involving multiple members in the jury that decides how this money will be spent. I think...

See a couple of familiar genes from our DecodeME analysis: DCC on chr18 VRK2 on chr2 SOX6 on chr11 The top hit here was on chromosome 1:73,847,802 (chr1:73382119 on GRCh38 coordinates). DecodeME also seems to have a signal there, which we thought might point to NEGR1. I suspect the...

Stigmatization in ME/CFS being worse than in other diseases, including mental diagnoses such as depression, goes against the entire cognitive behavioral model. One of the central ideas of this model is that ME/CFS patients somatize their life problems because they can't deal with the stigma...

A previous proteomics study mostly pointed to the complement system, so while this is potentially related it's not exactly a replication: Proteomic discoveries in hypermobile Ehlers-Danlos syndrome reveal insights into disease pathophysiology - PubMed

Main results in Figure 2:

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...