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All really good points, and having prominent people show a path for others to follow could be useful. Having some medical big guns on side could be really useful as you suggest. How it is done is important. Saying we need to improve care, look for treatments, invest in research to build upon...

I’ve been thinking more about this and it would be really useful if we could get hold of that UKB reference data to use with standalone MAGMA and see if it helps align our results. I wonder if it’s worth asking them? It’s not here https://cncr.nl/research/magma/ It’s mentioned here but not...

You’re right it’s something important to be aware of. And the suggestion @Sasha makes of having prominent figures open the door or show a path for others to follow may be useful or perhaps here are other ways they can help or influence things. I’m just far less convinced that there is a...

I hadn’t noticed but then again only just looked into who he was when you flagged it. Looks like a very handy person to have as part of the team! Really interesting, so it’s less a case of the rare variants completely changing the picture or being independent of the common variants found, but...

It's not though. The baseline assumption for the majority of people is that they don't know or even care about ME/CFS. The world we are living in is one in which ME/CFS has been ignored, it is that (and yes for some their positions) which has allowed a small group of people whose minds we will...

It looks from the paper as if the used a tool called coloc described in this paper: Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. Which I think does just compare individual gwas studies via their summary statistics. But one interesting...

There is one result from gene-set analysis I thought may be worth looking into On the group DecodeME_gwas1_infectious_onset the top result was this GSE2770_UNTREATED_VS_TGFB_AND_IL12_TREATED_ACT_CD4_TCELL_48H_UP (link to the MSigDB page for this set) This is a set which comprises "Genes...

Identification of novel genes regulated by IL-12, IL-4, or TGF-beta during the early polarization of CD4+ lymphocytes Riikka Lund, Tero Aittokallio, Olli Nevalainen, Riitta Lahesmaa Abstract Th1 and Th2 cells arise from a common precursor cell in response to triggering through the TCR and...

Some results from running MAGMA locally. Both gene based and gene-set analysis using the above method on each of the DecodeME GWAS subgroups against the full Molecular Signatures Database Human Collections release 2025.1 (MSigDB 2025.1.Hs). Please bear in mind this method differs from the way...

Something I’ve only really started to appreciate going through this process is quite what is being done and quite how clever and meaningful it is… and how those dismissing it are showing their own ignorance and how their ideas about genetics are decades out of date. I’m still pretty ignorant...

Looks interesting! Not sure what sort of computing power it would require… It does use a python library for doing liftover though, which looks interesting! https://pypi.org/project/pyliftover/

I’ve gained a whole new level of appreciation for what you and other people in bioinformatics do.…

Yep, understood. I hoped my earlier comment reflected that and while I have misunderstood in the past, thanks to the explanations you’ve given I think I get your approach now and look forward to whatever you turn up. Same! Friends who are dancers did not appreciate when I’d turn up and copy...

Maybe his is better in the other thread, but I’m yet to get through that one properly! I’m obviously a bit biased as the neurological explanation is something I’ve spoken about before and it just feels more satisfying than a muscular explanation to me and my experiences. That said I really get...

As mentioned above, something @forestglip and I have been working on recently is running MAGMA locally on the DecodeME summary statistics. I wouldn’t necessarily recommend anyone do this or follow these instructions. There may be things wrong with this method and it seems to end up with only...

Severely affected and difficult to say tbh because not very physically active, I’d say no. Maybe if I was more active? Maybe ‘it’s complicated’ would be better as an answer. But it’s not something I’d say is noticeable or limiting currently. There’s can be a sort of pain or tightness perhaps...

Thanks @Chris Ponting I look forward to seeing what more there is to come and echo @Hoopoe in thanking you and the rest of the team, for all you’ve done so far. The more I’m learning the more possibilities and scope there seems to be, exciting times! Really useful answers in general but also in...

Absolutely. The efficiency improvements have been huge. That small local models can do what huge models used to be needed for and that the big players are pushing on efficiency even on their larger models to reduce costs seems far more significant that any imagined progress towards AGI. But the...

I was reading this the other day and it is entertaining in some ways but highlights a number of the ways LLMs struggle. https://www.anthropic.com/research/project-vend-1 A positive read could be that they feel they can fix these issues. But I think it also shows how much the earlier points made...

I thought I made the distinction in my posts and think it’s pretty clear? It also seems most likely that LLMs will stick around in some form but perhaps as the human interface to other forms of AI/ML, that’s what they’re most suited to after all. The scaling stuff for LLMs has always been a...