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Phewas The last thing I wanted to check are other GWAS that have signal similar to the one as DecodeME in chromosome 20. I used multiple data sources: - Open Targets offers credible sets so I could check if these overlap with the credible set for DecodeME in this region. This was the case for...

Think it refers to including "Days since last vaccine/infection" and number of Sars-Cov-2 infections in the regression model. I did notice a big effect for recruitment site (being in the LIINC cohort had a bigger effect than having LC or not). That may point to technical artefacts.

Yes, exciting! Ollila said about it: "note also that there is a potential HLA association that is just before HLA-A that we're also going to finemap." Looks like DecodeME also had signal here with a p-value around 5*10^-6. The locus is probably around 29 MB on chromosome 6. The BTN hit in...

I watched the presentation by Hanna M. Ollila titled "The Future of MECFS Genetics". She gave a good impression and presented findings from the big meta-analysis. Here's the direct link to the video: EDIT: I've updated the images to versions with a better resolution. The meta-analysis has...

eQTL Catalogue analysis Had a closer look at eQTL that match the DecodeME signal in this region. This uses data from experiments that measured RNA (gene expression) and linked it to the DNA of the participants. eQTL are the DNA letters that change a gene's expression. Often a GWAS hit cannot be...

I don't think any of the authors have actually done research on ME/CFS, only related conditions such as Long Covid, fatigue or functional disorders. So it's a bit weird to try change medical guidelines on a condition that you haven't actually studied or have expertise in. Their involvement...

Sorry for the late reply. Yes they are all negative values so the deletion is predicted to close chromatin and lower active enhancer marks in the myeloma cell lines.

This reminds me of statements by Elise van De Putte who helped pioneer the FINET treatment in children with CFS. A couple of years ago she stated: Source is this 2023 article: Kinderarts Elise van de Putte: ‘Kinderen worden geweldig onder druk gezet’ - NRC

Thanks for sharing this. The interview is quite interesting. Here's the link to the RCT on ACT Schroder did but which found null results: Acceptance and Commitment group Therapy for patients with multiple functional somatic syndromes: a three-armed trial comparing ACT in a brief and extended...

I had a look at the region using ENCODE data on chromatin openness. I used the SCREEN API which organizes the evidence into candidate regulatory elements (CCREs). I looked at 11 core SNPs for the Decode hit (which have more than 80% of the probability of the signal) and found that 7 were in a...

Here's a self-made graph of the DSQ PEM scores in this study.

Some caution regarding the 25 CFS patients in this study: They also note the following about PEM which was measured with the DSQ-PEM :

This is always very useful to calibrate my own analysis. s-LDSC is quite complex to set up and I certainly could have made a mistake. But I tried to redo their schizophrenia and tiredness analysis and my and their coefficients and p-values correlate at 0.99 so that hopefully means my DecodeME...

Same with tiredness, which looks quite different than ME/CFS in this dataset. The data on tiredness came from the UK biobank using the question: "Over the last two weeks, how often have you felt tired or had little energy?" Source: Deary et al. 2017 Genetic contributions to self-reported...

From the talk around minute 27. Pretty much all autoimmune disorders show a peak and association to HLA, ME/CFS apparently doesn't.

Their data is in supplementary table 26. I only selected a couple of their traits (many used older and underpowered GWAS) but here's the plot with all of them included. The MSN peak is prominent also in substance disorders such as alcohol and tobacco usage.

Did an analysis of the chromatin openness (sc-ATAC-seq) rather than RNA in the brain atlas by Li et al. 2023. The main results look like this: For the full analysis see the thread here: A comparative atlas of single-cell chromatin accessibility in the human brain, Li et al, 2023 | Science for ME

I think this supports the findings of the RNA analyses we did earlier. You can find an overview of these here: Overview of RNA datasets for tissue and cell type enrichment analysis | Science for ME All neuronal traits show peaks at the Intratelencephalic projecting neurons, just like ME/CFS but...

This is similar to the Siletti 2023 brain atlas that we've been analyzing in relation to DecodeME, but instead of gene expression (RNA), the data points to chromatin openness using snATAC-seq. Chromatin is what packages DNA and more open regions suggests more gene transcription and activity. It...

Abstract Recent advances in single-cell transcriptomics have illuminated the diverse neuronal and glial cell types within the human brain. However, the regulatory programs governing cell identity and function remain unclear. Using a single-nucleus assay for transposase-accessible chromatin using...