Preprint Initial findings from the DecodeME genome-wide association study of myalgic encephalomyelitis/chronic fatigue syndrome, 2025, DecodeMe Collaboration

Obviosuly, I hope that's not the case, but I think its a question that still needs to be asked.
I think it's very unlikely.

The ancestry was controlled for by first choosing similar European ethnicity as the UK Biobank controls and then by adding the first 20 principal components as covariates in the regression analysis. These PCs showed no clear pattern anymore between patients and controls as seen in Supplementary fig 1.
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There was also no strong sign of inflation in the QQ-plot. If there was some systematic difference between patients and controls we would expect p-values to deviate from a uniform distribution across the board except only the very low ones as we see now. This suggests the GWAS is picking up a more subtle signal than selection bias or ancestry differences.

Next there are the hits found. Two loci had only 1 protein coding gene so we have strong reasons to suspect these are involved: CA10 for chromosome 17 and OLFM4 for chromosome 13.

CA10 has been found in a chronic pain GWAS
This gene encodes a protein that belongs to the carbonic anhydrase family of zinc metalloenzymes, which catalyze the reversible hydration of carbon dioxide in various biological processes. The protein encoded by this gene is an acatalytic member of the alpha-carbonic anhydrase subgroup, and it is thought to play a role in the central nervous system, especially in brain development. Multiple transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]
CA10 Gene - GeneCards | CAH10 Protein | CAH10 Antibody

OLFM4 has been found to be a biomarker for the severity of Infectious Diseases
This gene was originally cloned from human myeloblasts and found to be selectively expressed in inflammed colonic epithelium. This gene encodes a member of the olfactomedin family. The encoded protein is an antiapoptotic factor that promotes tumor growth and is an extracellular matrix glycoprotein that facilitates cell adhesion. [provided by RefSeq, Mar 2011]
OLFM4 Gene - GeneCards | OLFM4 Protein | OLFM4 Antibody

These hits seem to point to the underlying pathology of ME/CFS and not some confounding factor.

The MAGMA analysis (which takes all SNP-influenced genes into account) strongly points to the brain, more so than many other GWAS that forestglip posted here.

I think it's quite unlikely that this is all a coincidence or driven by something else than ME/CFS.
 
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Much as I may feel the same sometimes I don't think we should be making this into a campaign of 'we're right you were wrong'. It is not the most effective way to make friends and influence people. We should be laser focused on improving care and finding treatments. And we've shown good research is the path to that.

I agree, but I still have concerns that a shadow remains over ME/CFS that could negatively impact chances of getting funding. I really hope the DecodeME results are enough to make a solid case for SequenceME & Long Covid—it seems crucial we get that info—but I don't know.

There are other arguments in its favour, including that it's a pioneer study that has implications for other conditions, but DecodeME will probably need to supply most of the weight.
 
I think it's very unlikely.

As do I, but in a sense I think that is icing on the cake. The first step is showing that ME/CFS is a biologically meaningful diagnostic grouping - which was the point originally referred back to.

The BPS people have pointed out that we have had genetic studies reporting risk-associated alleles in the past so this is nothing new. But these were studies of small samples that would need replication and as far as I am aware none of them have replicated. There may still be replication issues with DecodeME but my reading is that it is much harder to argue that data from a large, well documented study is due to chance.

Nevertheless, I am interested in the fact that previous studies have picked out HLA-DQ and HLA-C (I don't recall anything else much) and I am still unclear as to whether all these results are in fact compatible, even if confusing at present.
 
I agree, but I still have concerns that a shadow remains over ME/CFS that could negatively impact chances of getting funding.
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 universal or strongly held belief that ME/CFS is in the mind or that we should focus efforts on that. I was ignorant when I got it and I expect many were. And that is why we were so vulnerable.
 
In other news, based on a suggestion by @hotblack, I tried to use the UK BioBank reference panel for FUMA instead of the 1000 Genomes reference as I did before. It looks like that was the main reason my results were somewhat different from the paper's results.
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
It’s mentioned here but not available
There is a MAGMA ‘all’ here but it’s huge and no mention of UKB
 
I’m just far less convinced that there is a universal or strongly held belief that ME/CFS is in the mind

I think what many people have in their minds, much the same as what medics have in their mind, is there isn't clear biological explanation then it is all in the mind. So ME/CFS is captured by the default assumption, not that they have a specific opinion on it.

But if that's the default position, then if a prominent medical or establishment figure says it's all in the mind, then they would accept that is the case.

That is what we're up against.

But was struck by Andy's comment at the webinar about the press conference they held. Andy said that this was his first conference, so he didn't have much experience. But he hadexpected pushback with journalist probing psychosocial explanations.

But it turned out, presented with strong biological evidence from a big study that appear to them to be done very soberly , they were happy to go with that.

That the guardian lead science correspondent (Ian Sample ) who had been very pro psychosocial exclamations, then with a biomedical story illustrates that point (or it does if I have my facts straight .
 
I’m just far less convinced that there is a universal or strongly held belief that ME/CFS is in the mind or that we should focus efforts on that. I was ignorant when I got it and I expect many were. And that is why we were so vulnerable.
It's hard to know how widely held the belief is but my idea of getting some big medical guns to make a statement is primarily to convince people in the medical profession, since they're the ones likely to read it and the ones who don't listen to anyone else. ME/CFS has been swept into the MUS/FND bucket and stories from PwME about how they're gaslit and dismissed by medical professionals are rife. We have case after case of PwME in hospitals who have difficulty feeding being starved because of how their illness is viewed.

As with the general public, there's surely a mix of views among the medical profession but even if as few as 10% of doctors and nurses think that ME/CFS is all in the head, they're in a position to cause catastrophic damage to the lives of vulnerable PwME.

And it would be hugely helpful for many PwME to have such a letter to show sceptical family members and friends. In the last few days, one of the forum members has posted about appalling treatment from family members due to their belief that his illness isn't real.

The MEA was criticised here some time back about it's 'It's real!' messaging about ME/CFS, and I would agree that our charities shouting 'It's real!' is likely to be counterproductive - because they're representing patients, and if it's all in our heads, of course we think it's real, even if it's not. But it's a different thing entirely if highly respected people in the medical profession are saying so - and are doing so off the back of this new kind of solid evidence, if it really is that solid (which is my point of doubt here - I don't understand enough about this to know how solid it is).
 
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It's hard to know how widely held the belief is but my idea of getting some big medical guns to make a statement is primarily to convince people in the medical profession, since they're the ones likely to read it and the ones who don't listen to anyone else. ME/CFS has been swept into the MUS/FND bucket and stories from PwME about how they're gaslit and dismissed by medical professionals is rife. We have case after case of PwME in hospitals who have difficulty feeding being starved because of how their illness is viewed.

As with the general public, there's surely a mix of views among the medical profession but even if as few as 10% of doctors and nurses think that ME/CFS is all in the head, they're in a position to cause catastrophic damage to the lives of vulnerable PwME.

And it would be hugely helpful for many PwME to have such a letter to show sceptical family members and friends. In the last few days, one of the forum members has posted about appalling treatment from family members due to their belief that his illness isn't real.

The MEA was criticised here some time back about it's 'It's real!' messaging about ME/CFS, and I would agree that our charities shouting 'It's real!' is likely to be counterproductive - because they're representing patients, and if it's all in our heads, of course we think it's real, even if it's not. But it's a different thing entirely if highly respected people in the medical profession are saying so - and are doing so off the back of this new kind of solid evidence, if it really is that solid (which is my point of doubt here - I don't understand enough about this to know how solid it is).
indeed. If you have it long enough or badly enough then you eventually come across the 'moments of truth' where people's walking the line of hiding it as not being quite as insidious underneath as it really is comes out. The same people who keep up the facade of 'I just think stress doesn't help' or 'I don't think that it is just that there aren't any treatments yet' which are exactly the same things that those who do get it would say slowly do let slip that sadly they aren't very nice and actually are using that to hide a really not very nice version of it.

But you have to be there when it happens and we have all probably had years at a time where we have wanted to 'think the best' of those same people who then eventually consistently enough do things that let slip how clear their orthodoxy really is.

I also had the same thing whilst I was stuck in the 'looking for the pat on the head' stage and 'playing nice' where I'd fall for the 'those who have seen it are just looking for the worst in people' rather than it being the case where they guy who is the lovely old gentleman who is always friendly and kindly suddenly finds out you have ME and realises they can say snide outright obviously grim things to you and that label means that unless you are recording them on video (and you won't know when the hit and run will come even if you could whip said video out) everyone will go into that misogynistic presumption that the person with ME must has 'misheard or been sensitive or it wsan't intended'. People like that count on that.

Once my ME/CFS became 'not invisible' even if I still avoided telling people whose business it wasn't what it actually was as a diagnosis, it was astounding the level of this behaviour I had coming at me. I remember relating to a friend who people you thought were good people now knew noone would believe me if I reported their 'seemingly out of character, but now what I get because they can get away with it' and was shocked that she got it when I explained.

That's what I mean I think by getting severe enough ME/CFS is like having a truth potion on who other people are. Because they start acting towards you how they've clearly always wanted to act outright knowing they don't even need to veil it because heck who is going to believe or care when it is someone who looks as ill (and therefore mad, not help by many HCPs are too stupid/been taught wrongly about a decade ago that cognitive fatigue is 'mental health' rather than exhaustion - and that one gets right up my nose as someone who did a lot of cognitive psychology, so yes it is stupid) as me reporting them.

Some of us get to see the veil come off. And strangely at the stage where it does there is obviously soemthing 'universal in what signals I'm giving out' because then it becomes a very common pattern ie all those who are that way all seem to start doing it just at a point where I got x ill and was suddenly more cast out of the bits of society I'd been in before than I had been, like leaving job etc.


And yes I know that most pwme who are less ill than I am and who are still in the phase where they have jobs or people who respect them etc so aren't vulnerable yet are just as bad as those who don't have ME on not just doubting the very honest pwme who are reporting it but gaslighting them. ANd it has been designed to be that way by the divisive messaging trying to divide us up in that way so that the more severe are really abandoned ironically by those who will many of them end up there themselves. Because it now probably happens to me most from pwme that they either outright minimise what I've just said precisely and accurately or say some justifying thing like 'must have had a bad day' as if it isn't a regular enough pattern, or 'really unusual because I (as if they are exactly the same as me so that's an experiment) didn't get that' as if that's another way of them side-stepping saying they choose to not believe me.


It isn't all of them that are like this, but put it this way I put some effort into finding those who aren't and I can at least guess at that maybe I can half-delude myself I can trust, and that wasn't easy. I had the same issue with 'friends' mind you of course. Some pretty shocking realities of who I'd been hanging round with for over a decade not realising what a bunch of idiot bigots they were until I kept pushing at them and refusing to 'drop being ill in their face' and do the smalltalk acting like I wasn't exhausted and pretend positive nonsense. And you get a sudden flip and reveal. The whole idiots who believe the placebo stuff from pop-psych seems to be one rabbit hole some of them were hiding in. And there is like this coercion that you are required to lie and only be positive about your life to certain people's faces which leaves rather little to talk on and eventually you feel pretty violated from having been forced to make something up or be fake positive.

So yes I think that there are many who also just think it is an attitude issue of making a big thing about something that is less debilitating and could do more on etc. too. Delude themselves with these wordings they slowly the first time gently and cagily say out loud and then it expands from there. And underlying that therefore is the 'mind' thing.

That's why the nonsense fops of 'had a virus but' or 'not all psych' really dog whistles that lot. Funnily enough it is those who in their mind are obsessed with not letting others be lazy because they will pick it up, and it comes from people who I might have worked with at various points and can say for fact they weren't the workhorses as I was, so it isn't even a self-preservation issue that it started from. When I think back I might have had a few years when I was maximum 12-13yrs old when I thought like that para above of the 'maybe if they just see if they could do more' but was able to mature out of it. So imagine how shocked I was to realise I'd been listening to thsoe red flags from people with respectable jobs and just assuming it wasn't what it was until they expanded it further and slowly like a boiling frog to the point it was undeniable and unjustiable and unaccpetable bigotry.

And then I look back and realise what on earth was I doing or how coerced was I that I was listening to these escalating things for about 5yrs and having incredibly mean things done to me (as things escalated beyond the 'could do a bit more' in the context of 'another friend who has the same') because, for what I guess was actually no good evidence in them at all other than me 'looking for the best' in their statements, I assumed it must have been a bad day or they mustn't mean it because they apparently were good people as I'd known them for a decade. But no I'd just been closing my eyes to it now I've not just seen them but had them bang me over the head with such grim vitriol so they made sure I knew what they thought that it isn't just without doubt but eventually became them being frustrated that I wouldn't see what they thought and were actually saying and thought they had cultural permission to say.
 
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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?
Just a guess, but I think the UK BioBank data might not be open access like 1000 Genomes is. Maybe worth checking though.
 
Hi Woolie, great to see you again - though I may have missed you previously.

That's true - here's one at the top of the tree on Google

At the same time, research studies are always strongly skewed to higher SES, amongst many things. Yet for 15 years, GWAS have been finding biological differences linked to disease that either explain symptoms or chime with existing known mechanisms. The question is, are the differences that could be attributed to ME/CFS strong enough to explain anything like 8 loci and p< 5 x 10^-8?

I don't know if the team looked at things like SES - but it should be easy to do. I don't know if anyone here can look at e.g. known SES loci/genes vs ME/CFS?

(There seems to be no limit to what some people here can do, it is so impressive. I can't help wondering if any other part of the ME/CFS research community is making as much use of the data, though Chris did say in the webinar that there have been 42 downloads of the summary stats.)


DecodeME restricted the initial analysis to those with European ancestry, and within that spent a lot of effort controlling population ancestry, which can create such effects (immune ones are the strongest, esp on HLA genes, as particular common variants have proved protective or risky for historical pandemics). It helps that UK Biobanks is so big, making it much easier to find controls well matched by ancestry. So such an effect is unlikely. I think @ME/CFS Science Blog also posted a graph showing minimal such effects on more common variants, though higher for less common ones, though they said the more common ones were more prominent in the findings.
Thanks for the reply, @Simon M!

I do see that the proof of the pudding will be in the eating, as it were. As an exercise that can generate new research questions, this study is amazing!

I also get your point that we could identify SNPs that could be linked to certain possible confounding variables, and look at those. Nice idea.

I just think we should take care when making the "biological proof" argument based just on these data, because its a bit fragile.
 
It's hard to know how widely held the belief is but my idea of getting some big medical guns to make a statement is primarily to convince people in the medical profession, since they're the ones likely to read it and the ones who don't listen to anyone else.
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 the findings of DecodeME is a positive and persuasive way of doing it. If these prominent people are involved in doing so that is the message itself. That is the path for others to follow.

A campaign based around how people have been persuaded, a letter saying ‘I was wrong and now I’ve seen the light’ ‘it’s not all in the mind’ to me may feel nice but isn’t the most effective way of actually persuading or educating the people who we need to and can be. People really don’t like to admit they’re wrong, so let’s not force them to, let’s just show them the evidence and let them think they’ve worked something out or found something new for themselves.

It is tragic that we have been ignored. But that is I think the real problem here. And it is possibly unsurprising that most people subjected to different forms of bullying or abuse have to put up with it for so long at least partially through being ignored rather than the perpetrators having widespread support.
 
Just a guess, but I think the UK BioBank data might not be open access like 1000 Genomes is. Maybe worth checking though.
Yes looks that’s probably the case. The eligibility criteria seem to make that clear and I can see them being able to use the data in a publicly accessible tool like FUMA but not being able to share it. A shame as it limits our ability to remove variables that may be causing differences in results.
 
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 the findings of DecodeME is a positive and persuasive way of doing it. If these prominent people are involved in doing so that is the message itself. That is the path for others to follow.

A campaign based around how people have been persuaded, a letter saying ‘I was wrong and now I’ve seen the light’ ‘it’s not all in the mind’ to me may feel nice but isn’t the most effective way of actually persuading or educating the people who we need to and can be. People really don’t like to admit they’re wrong, so let’s not force them to, let’s just show them the evidence and let them think they’ve worked something out or found something new for themselves.

It is tragic that we have been ignored. But that is I think the real problem here. And it is possibly unsurprising that most people subjected to different forms of bullying or abuse have to put up with it for so long at least partially through being ignored rather than the perpetrators having widespread support.
Sadly with the degree of cognitive dissonance and sunk cost this will take time , which to be honest noone has- it's already been too long to get to this point.
It needs persuasion and an " off ramp" .
What would an " off ramp" look like to work?
 
What would an " off ramp" look like to work?
I think the off ramp is as described, a path of least resistance for people based upon new evidence and solid science. Public displays of damascene conversions are unlikely and probably not helpful.

Having prominent and respected people involved is part of the answer to me. As it looks as if is happening with SequenceME

Chris said about Ewan Birney
" t"he's] a co-principal investigator on this who has been a long-term advisor for Oxford Nanopore Technologies and is a very eminent member of the genomics, genetics, and biological communities in Europe.
Birney is Executive Director of the European Molecular Biology Lab (EMBL), and non-executive director of Genomics England, among many things
 
I hope you are right .
This is a paradigm shift and there's bound to be a lot of noise from some until the science is bottomed out.

That noise , whilst hopefully becoming increasingly irrelevant, can still cause significant harm.
 
Some more thoughts on the local MAGMA results above. The difference in the gene based analysis is worth looking at too. It would be useful to understand why (discussing with @forestglip we wondered if it was the difference in SNP conversion methods and assemblies used, or perhaps the reference panels, but we don’t really know) and if this tells us anything.

The following were in the official DecodeME results but not the local MAGMA results
  • DNAH10OS (couldn’t find anywhere in my results, maybe lost in translation?)
  • HIST1H4H (p-value of 2.2675e-06 or higher in my results so fell outside threshold)

And these were in the local MAGMA results (in groups mentioned) but not the official DecodeME ones (apart from in table S3 where mentioned)
  • ATG12 (gwas1_male only)
  • CACNA1E (both gwas1 and gwas1_female) (also in table S3)
  • DCC (gwas1_female only) (also in table S3)
  • H4C8 (gwas1, gwas1_female and gwas1_infectious onset)
  • PLCL1 (gwas_1 and gwas_2) (also in table S3)
  • ZPBP (gwas1_female only)

While these were in both

Do the similarities mean we can be more certain of those results? Should we discount the differences in the local MAGMA analysis (that half were also in supplemental table S3 from the paper is perhaps reassuring). Or are both results telling us something? What do the subgroup findings tell us?

I’d like to better understand if/what is wrong in my method and accounting for differences seems a good place to start. It may be we can recreate things with FUMA and get the full output to compare results more closely (maybe differences are subtle with some things falling just in or outside the p-value thresholds). If anyone who knows these tools has any thoughts please do chip in. Now it’s all setup it should at least be trivial to change variables and rerun.
 
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