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Here are the results of my brief analysis of this locus (there's more about my methods and approach in the chr20 locus). Credible set This region also had one credible set of 86 SNPs over a 180 kb. It’s in a gene desert, far removed from protein coding genes but lies in a long non-coding RNA...

Made a brief summary of the results here:

New breakthroughs on: Local smoothing and the Kakeya conjecture The Exponential Time Hypothesis is talse Existence of quantum chromodynamics and completions of the Standard Model Working with academic communities to build scientific understanding | OpenAI Would be interesting in hearing...

I had a closer look at this locus using the methods I previously applied to chr20 and other loci. No breakthrough unfortunately, but I’m sharing my results in case they are useful to others. Finemapping Finemapping the locus with SUSIE gave one credible set with 92 SNPs. But ca. 80% of the...

I agree that there's a lot of uncertainty in the chromatin and histone mark data (the databases are still too small and don't cover enough situations and context), but genetics mostly point to risk factors. So it's about how you get ill when you don't have ME/CFS yet. And these genetic hits all...

I think the gut diseases like IBS are interesting because CA10 isn’t expressed in the gastrointestinal tract. So that likely points to the specific neurons linked to the stomach and gut being involved in these diseases through CA10 (over?)expression. On the other hand, it’s interesting that...

Predictions The AlphaGenome gave no valuable results or insights. eQTL Also, no real matches in the eQTL datasets. The best I found for CA10 was a weak signal in serotonergic neurons (PP.H4 = 0.365, lowest p = 1.7e-3). It does give some info about the direction of effect. If this signal is to...

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...