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I don't think the chromatin data gives answers to this question but I'll analyse further using phewas and eQTL and will try to get back to this.

I did the same analysis as for the chr20 region. Finemapping with Susie gave a credible set with 64 SNPs that is hard to reduce to a smaller number: the probability is spread out across these SNPs. CA10 is the only protein-coding gene nearby but a lncRNA called ENSG00000310017 falls inside our...

Interesting presentation during the PRIME symposium by Matthias Wielscher. He only talked about this briefly but it looks like his team did a n analysis of rare variants (so similar to the Astrazeneca data that highlighted BTN2A1) using All of US and the UKBiobank cohorts. The All of us Cohort...

Thanks, sounds interesting although I didn't come across strong signals to T-cells in the chromatin data so am a bit skeptical about this line of thinking. Would like to get more detail about the graphs shown during the presentation. Chris Ponting also presented a T-cell theory based on the...

Yes I think that's the case for this locus on chromosome 20. It's all still speculative. But I plan to do similar analyses on the other signals and then see if any patterns or links emerge. If we test gene categories across all the DecodeME results then they point to the CNS and neuronal...

ARFGEF2 could be the gene for this link because mutations have reported "preferential damage to the basal ganglia" and "hyperintensity of the putamen" which was associated with movement disorders. Some references: Movement disorder and neuronal migration disorder due to ARFGEF2 mutation - PMC...

Made a summary of this paper here:

Regarding the direction of effect, it seems that the ME/CFS risk alleles are associated with lower cortical volume, increased risk of schizophrenia but decreased risk of bipolar disorder. That study thought that CSE1L is the most likely candidate gene based on eQTL data. Genomic Dissection of...

I noticed that in the Astrazeneca analysis of rare variants, multiple ME/CFS categories have PREX1 (a candidate gene in this region), around p = 10^-4. Not really close to significance, but perhaps it's a valuable signal. AstraZeneca PheWAS Portal

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.