SequenceME genetic study - from Oxford Nanopore Technologies, the University of Edinburgh and Action for ME

SolveME sent a newsletter and has a page about providing funds for a couple projects, including SequenceME. I posted on the Solve thread.

This is from the email:
  • We're proud to announce Solve’s latest Catalyst Award-winning projects, which will expand whole-genome discovery and test a promising low-cost therapy targeting inflammation and energy dysfunction—key steps towardbiomarkers and clinical trials.
  • Dr. Jay H. Chung (National Institutes of Health) was awarded Catalyst funding for his study, “Mitochondrial stabilizer IVO-21 as therapy for ME/CFS," and will join Solve for a webinar on September 8. Register here.
  • The DecodeME Management Team was awarded Catalyst funding for their study, "Sequence ME & Long Covid," and will join Solve for a webinar on June 10. Register here.
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Is this new funding we hadn't known about yet?
 
forestglip said:
SolveME sent a newsletter and has a page about providing funds for a couple projects, including SequenceME. I posted on the Solve thread.

This is from the email:


Is this new funding we hadn't known about yet?
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This funding from Solve went towards phase one of SequenceME. I believe that we were unable to announce it at the time of the other funding as Solve wanted to announce it today, so it's technically not new funding but is the first time it has been made public.
 
Huge congratulations to all involved in achieving Sequence ME's success. This is mega news.

It does seem peculiar to fund the sequencing and not the analysis, but presumably getting funding for the analysis work will be much easier once there is a £4.75m dataset sitting there waiting to be investigated?

The NR comments validate the work by many to push him out of the MEA, but I find it a little sad that it has become a talking point today. Today I want to celebrate SequenceME's success.
Perhaps we can also celebrate that NR is no longer in a decision-making position at the MEA, or on how ME funds are spent.
 
Amazing news! Just what I needed haha. :)

A shame it's only partial funding but sequencing the ME/CFS samples does seem the most important thing to pursue right now. Would be hard to see the analysis not getting funded afterwards. That should already give us lots to work with.

Then maybe the Long Covid part will be able to attract LC specific funding.
 
Well done to everyone involved!

Andy said:
The definition is yet to be decided upon and forms part of the work already funded by previous supporters. I can't guarantee at this stage what the definition will be but we are well aware that it will need to be better than anything as vague as "3 months of any symptom at all after a Covid infection". Given that eventually we will be comparing them with DecodeME particpants I personally would like to see all LC participants evaluated with the DecodeME questionnaire for likely ME/CFS status.
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Yes, maybe it's even smart to have 2 sets of Long-Covid cohorts, one meeting the ME/CFS status per DecodeME questionnaire and one without PEM. You can then possibly get an understanding of whether or not PEM is driving the signal, which arguably you might not be able to get otherwise, but one may wonder how heterogeneous such a cohort would be in the first place and what they would consist of. If they aren't homogenous enough they might just as well look similar to healthy controls which in turn maybe wouldn't offer to much, but possibly there's a sufficiently large pain dominant or cognitive problem dominant LC cohort?
 
2 questions:

1) In the best case scenario, how long might it take for Squence ME and Long Covid to lead to development of effective treatments for ME/CFS that are available on the NHS? And what is a realistic range of timescales?

I know there is other research which could lead to treatments but for the purpose of this question, assume that Sequence is the only route.

2) I noticed that The Times article referred to SequenceME rather than Sequence ME and Long Covid. Was that a mistake or is phase II being referred to as SequenceME as it’s only looking as ME/CFS samples?
 
This is cool and I am hopeful that it shows us something. I think whole genome sequencing is better than looking at SNPs.

But I cannot suppress my contrarian streak: There is part of me that is skeptical of genetics being especially important in infectious-origin diseases.

It's a bit like trying to understand the plot of Midsomer Murders by looking at the blueprint of the Samsung TV.

The program is running on the system. And yes, okay, in one sense the architecture of the system decides what can and can't run, but a lot of different things can happen within the constraints of the system.

In the end I remain both hopeful and skeptical. Which I think is probably the right mental model for thinking about everything!
 
Robert 1973 said:
1) In the best case scenario, how long might it take for Squence ME and Long Covid to lead to development of effective treatments for ME/CFS that are available on the NHS? And what is a realistic range of timescales?
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Our official answer on the topic of treatments, "A core aim of Sequence ME & Long Covid is to identify genes and pathways that can potentially be targeted with drugs. Once biological drivers are understood, researchers can investigate whether existing medicines might be repurposed or whether new treatments can be developed and tested. This process can be long and iterative, but genetics tends to speed up this process and can give clear direction for targeted research."

The one thing I can tell you for certain is that phase 2, sequencing 6k ME/CFS samples, is funded and scheduled to take a year. Anything else would be mere guesswork which I do not feel qualified to do, particularly when we need to find the funding for the further stages, and especially on such an emotive subject. I'm sorry that I can't give what might be considered a more helpful answer.

Robert 1973 said:
2) I noticed that The Times article referred to SequenceME rather than Sequence ME and Long Covid. Was that a mistake or is phase II being referred to as SequenceME as it’s only looking as ME/CFS samples?
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The full project name is Sequence ME and Long Covid, we do not have different names for different phases. However, it can be easy for people, including me, to just refer to it as SequenceME and not pick up on our mistake in doing so, and this is what I think has happened here.
 
Murph said:
The program is running on the system. And yes, okay, in one sense the architecture of the system decides what can and can't run, but a lot of different things can happen within the constraints of the system.
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I think you are missing the point. With your analogy the question would be why on all TVs with system J4776 it turns out that Mrs Gubbins did the murder but for TVs that run on J4667 it was suicide after all. The great thing about genetics is that what you find is always causal because it is always antecedent as well as correlating with outcome. The causal matrix may be very complex and there are some fringe caveats but the fact that it always turns out to be suicide on a J4667 set must mean that the set system is part of the cause. And since the programmer knows exactly how he programmed J4667 and J4776 you have a way to work out why the outcome is different.
 
Murph said:
But I cannot suppress my contrarian streak: There is part of me that is skeptical of genetics being especially important in infectious-origin diseases.
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How confident we are that ME/CFS has a strictly infectious origin ? What about patients who have been exposed to organophosphates and got ME/CFS?

EUROMENE Report mentioning Organophosphates as a trigger :

https://pmc.ncbi.nlm.nih.gov/articles/PMC8073750/
 
Great news about the funding, thanks and well done everyone who helped get this over the line!

Not sure if it’s been asked yet:

Can meaningful analysis be done on 6,000 samples? If for some stupid reason we can’t get the additional 3,000 funded

How much would sequencing the extra 3,000 samples cost?

How much is the data analysis expected to cost, for 6,000 or 9,000 genomes?

Just trying to get a rough sense of what's still needed for the ME/CFS part of the study. I’m guessing LC would take up more than half of the total 20k budget since they have to start from scratch for that
 
Andy said:
For an organisation not involved with SequenceME and Long Covid, or responsible for securing the funding for it, the MEA sure seem determined to give the impression of the opposite, https://meassociation.org.uk/2026/0...ion-funding-for-sequence-me-research-project/
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I’m not up to date but the last I heard the MEA still had significant reserves in its bank account waiting to be spent on research.

Do you know if the MEA has been approached to ask if it would be willing to contribute to Sequence?
 
There is a short Reel [video] about Sequence on the Channel 4 Facebook page: https://www.facebook.com/share/r/1MtJRrzJWg/?mibextid=wwXIfr

The text says:

“The world's first genomic study into ME, or Myalgic Encephalomyelitis, has been announced.​

Researchers are hoping that by building a genetic map of the illness, it will help pave the way for a future diagnostic test and even treatments.​
​
But charities have warned that there is more to do and this must only be the start.”​

I guess this may mean that it will be on C4 News this evening.

Hopefully someone will have pointed out that it’s not first genomic ME/CFS study by then.
 
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I think it's worth making sure that people with ME/CFS understand how genetics could be important in a condition often triggered by an infection.

Here are some of the DecodeME FAQ that address this [underlining added] - might be useful for clarifying things on social media/Reddit/etc:
What do the genes found do?
We found that people with ME/CFS are more likely to carry certain DNA differences in eight regions of their genome, and these variants tell us about possible biological causes of ME/CFS. Most of these regions contain several genes. Our methods did not allow us to conclusively locate the ones most relevant to ME/CFS in each region, but public data allowed us to pick out the most likely ones. Three of the most likely genes produce proteins that respond to an infection. Another likely gene is related to chronic pain. Overall, our initial genetic results show that ME/CFS is partly caused by genes related to the immune and nervous systems.
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You mention a connection with infections at onset. Does this mean getting an infection causes ME/CFS?
Our results show that people with ME/CFS have subtle genetic differences in how their bodies detect and respond to infections. This doesn’t mean that infection itself causes ME/CFS, but it may mean the way their immune system reacts to the infection increases the risk of developing the condition. Further studies are needed to explore this potential link in more depth.
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Are people with ME/CFS born with these genetic differences?
Our genetic code is something we are born with, and it stays the same throughout the course of our lives. The differences we’ve found were present from birth in those who have them. However, this doesn’t mean someone was predestined to get ME/CFS, but it is a factor in whether or not the condition is later developed.
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What has DecodeME discovered about what triggers someone to develop ME/CFS?'
Our findings have pinpointed eight areas of the genome that are linked to ME/CFS. We don’t know exactly how these genetic differences interact with triggers, and further research is needed to understand this. However, our findings do support the idea that people with certain genes may be more susceptible to ME/CFS when exposed to a trigger such as an infection.
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