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

Dolphin said:
I see Chris Ponting shared this on Twitter last month:

Oxford Nanopore announces landmark UK Government partnership to advance genomics-driven healthcare innovation in the UK
https://nanoporetech.com/news/oxfor...nomics-driven-healthcare-innovation-in-the-uk
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Also: "Oxford Nanopore’s breakthrough genetic sequencing tech to analyse 50,000 samples from UK Biobank, to create a world-first ‘epigenetic map’." https://www.gov.uk/government/news/...ership-to-probe-causes-of-cancer-and-dementia
 
This looks really interesting. So good to see Chris, Sonya and others working together on the next steps after DecodeME. I’m sure the trials and application processes have taken a lot of time and effort.

And thanks to @Chris Ponting for the links to the paper and info on other uses of the technology.

I’d be interested to know who the project is hoping to get funding from. Hopefully we’ll find out in time and the application is a success.
DecodeME was I think largely this £3.2 million Medical Research Council and National Institute for Health Research grant. So SequenceME is twice that, but if they’re able to prove the worth with and build upon DecodeME…
 
Kitty said:
It sounds like a really exciting project. Let's hope they can raise the funding!
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given it’s Xmas and new year coming up it seems a good time to have a positive thing to disseminate

I don’t know whether there is any done thing like birthdays where someone can say instead of a card or present please donate to - but it might feel a bit late to ask people to do that as they might already be sent
 
bobbler said:
given it’s Xmas and new year coming up it seems a good time to have a positive thing to disseminate

I don’t know whether there is any done thing like birthdays where someone can say instead of a card or present please donate to - but it might feel a bit late to ask people to do that as they might already be sent
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This is going a bit off-topic as you can’t fundraise for this project yet but I do that with two friends with ME for our birthdays and Christmas where we donate in lieu of presents to an ME charity. One of them is bedbound and she suggested it, possibly after being not so happy with the presents I had gotten her! (It can be hard to get something for someone bedbound with severe ME if they have their basic needs met by family carers). Birthday fundraisers for charity are big on Facebook.
 
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Nightsong said:
Subject to funding, SequenceME would be the largest global single-disease ‘long read’ genetics study, which gives richer, clearer data, as well as the first in ME to use Oxford Nanopore’s new generation of nanopore-based technology.

The collaboration is supported by Edinburgh Innovations, the University of Edinburgh’s commercialisation service.
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I wonder if it would be possible to offer a commercial service that could subsidise the project analyses? I mean, it sounds as though Oxford Nanopore is a private company, and Edinburgh Innovations exists to commercialise UofE innovations. So, could a whole genome genetic reporting and analysis service be offered to people around the world who have ME/CFS?

I ask because I'm currently on the look out for a quality whole genome sequencing service for a person (diagnosed) with very severe ME/CFS. Some people like that might be willing to donate multiples of the actual cost in order to get their own sequence data, while also supporting this study. Later, maybe a company might offer a service to analyse individuals' data, in the light of any findings from the study.
 
Chris Ponting said:
Also: "Oxford Nanopore’s breakthrough genetic sequencing tech to analyse 50,000 samples from UK Biobank, to create a world-first ‘epigenetic map’." https://www.gov.uk/government/news/...ership-to-probe-causes-of-cancer-and-dementia
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That study, also by Oxford Nanopore, is looking at epigenetics. A large-scale epigenetic analysis would be another very useful ME/CFS study.

What I like about the latest ME/CFS study announcement, aside from the rather important possibility of it telling us something useful about the disease, is that it's sort of like insurance, a Plan B. I've been thinking that if DecodeME doesn't find anything very remarkable, doesn't produce leads, then there will be a lot of shattered people in the ME/CFS community. And that's an enormous burden for the people undertaking the DecodeME study to bear.

But, here we have the next thing. So, it's less important that DecodeME gives us the breakthrough because we know that an even more detailed genetic investigation can and will follow. And, after that, the epigenetics... There must be answers in all of that somewhere. We will eventually get some answers. We just need to get the next project funded.
 
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Hutan said:
I wonder if it would be possible to offer a commercial service that could subsidise the project analyses?
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The ethics of that might be...complicated?

The data wouldn't be any use until something is found, and even if something were found, it still might not help an individual get care, treatment, or even a diagnosis.

Struggling for clarity today, but I think the notion of payment for a service is really difficult. Some research teams can't even ask for freely given donations.
 
Hutan said:
I ask because I'm currently on the look out for a quality whole genome sequencing service for a person (diagnosed) with very severe ME/CFS. Some people like that might be willing to donate multiples of the actual cost in order to get their own sequence data, while also supporting this study. Later, maybe a company might offer a service to analyse individuals' data, in the light of any findings from the study.
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This is a good shout. I was looking for a possible genetic analysis service myself in the past but they nearly all have either
(1) Major privacy flaws (ie. they sell your data)
(2) Don’t have my trust because they offer “personality”, “skincare”, “exercise” and “diet” recommendations based on your genetics which strikes me as quackery.
 
Chris Ponting said:
Right on cue, a preprint came out today that spells out the benefits of applying both GWAS and Whole Genome Sequencing: https://www.biorxiv.org/content/10.1101/2024.12.12.628073v1.full.pdf
“GWAS and LoF burden [whole genome sequencing] tests reveal distinct but complementary aspects of trait biology, with important implications for interpreting and using association studies.”
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This article is beyond me at the moment. Can anyone explain in relatively simple terms how GWAS + WGS could tell us more than WGS alone? I wasn’t aware that GWAS could tell us anything that WGS cannot.
 
I remember a team in INIM in NSU (Florida, where Nancy Klimas is based) tried to collect data from people with ME/CFS who had bought commercial DNA tests. They got hundreds of submissions. I think others said there were lots of flaws with the data. There may be a thread on it here.

ETA: The pool for that was much larger as lots of people buy cheap tests for family history reasons.
 
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Robert 1973 said:
This article is beyond me at the moment. Can anyone explain in relatively simple terms how GWAS + WGS could tell us more than WGS alone? I wasn’t aware that GWAS could tell us anything that WGS cannot.
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The way I understand GWAS (30,000 data points) does a sort of birds eye view check of the genome and highlights common variants and associations.

While Whole Genome Sequencing (3 billion data points) tests the entire genome. So a lot of stuff could be missed by a GWAS that WGS might pick up. It could help identify specific rare mutations and stuff like that.

Even if GWAS picks something interesting up, we would get a sort of blurry signal, but with WGS we can zoom into that signal and see exactly what it’s saying.

The problem with WGS alone might be that it picks up so much random noise that useful analysis is basically impossible. So complemeting areas of interest highlighted by a GWAS by using WGS might offer the best of both worlds.

[I never finished a biology class so take this with many grains of salt]
 
For those who might be considering, or might consider, a donation to AfME in support of this project, I saw on one of their social media they give this reply to another member of the community,
"It is possible to restrict your donation to support our research work, including the setup of the work packages and fundraising for studies. This can be done by letting us know, when making a donation, that it is for research.”

Link to the donation page on their website
 
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