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

[Yann04]

Perhaps the sequencing of the post-covid ME/CFS samples coule be funded by the Schmidt Initiative for Long COVID (a billionaire ex-Google CEO’s intiative that claims to have a global focus)

 

[Braganca]

Or by Vinod Khosla.. ask him on Twitter. He’s replied to me once before but is only online periodically.

@Chris Ponting Maybe you could connect with him via his Khosla Ventures website if the team is soliciting funding. Or Ron Davis could connect you.

 

[RedFox]

This is a great idea. if I were an ME charity, I would be digging though my couch cushions to fund this, because I expect it to teach us things that are well worth 7 million quid.

 

[hotblack]

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.

This isn’t something I’m an expert on, but with a £7 million cost I expect the target will be institutional/government funding. And while there may be a mix of funding sources, anything attempting to combine those with commercial services would I agree get very difficult in terms of ethical and wider approval. I just do not see this happening.

@Andy mentioning charitable donations is interesting as they obviously fund things directly but I also wonder if he work for the funding applications themselves have been funded by donations to charities (in this case AfME) or out of goodwill.

 

[Andy]

@Andy mentioning charitable donations is interesting as they obviously fund things directly but I also wonder if he work for the funding applications themselves have been funded by donations to charities (in this case AfME) or out of goodwill.

I've not been involved in SequenceME but I do know that AfME have put a lot of work into getting things to this stage. As you say this project is likely to need institutional/government funding but without the work of AfME, who like all charities rely on donations to fund their work, it is unlikely that this project would exist to need such funding.

 

[EndME]

To me this seems like a project very much worth the effort. If there are people that would like to contribute, similar to how @Andy and @Simon M contributed heaps to DecodeME, is there anybody they can reach out to @Chris Ponting?

 

[Chris Ponting]

To me this seems like a project very much worth the effort. If there are people that would like to contribute, similar to how @Andy and @Simon M contributed heaps to DecodeME, is there anybody they can reach out to @Chris Ponting?

Yes - please email me if/when funding is announced for SequenceME.

 

[hotblack]

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’m only recently teaching myself this stuff, biology also wasn’t my thing educationally so I may not be right but…

This paper is I think more looking at two different analysis techniques (GWAS and rare variant/loss of function burden tests) than partial or full genome sequencing. You can do GWAS with either just partial which just looks at areas of common variation or with the whole genome where you get everything. While the rare variant/LoF tests cannot be done with just looking at the areas of common variation.

So having the whole genome is always ‘better’ (but more costly). But what the paper says is using two different analysis techniques allows understanding of different information within the large amount of data you end up with.

Does that help? Please anyone jump in if I’m talking nonsense!

 

[tuha]

If I understand correctly the saliva samples donated to DecodeME will be used for SequenceME study.
How much time does it take sequencing of 10,000 participants and then to analyze the data?

 

[Andy]

If I understand correctly the saliva samples donated to DecodeME will be used for SequenceME study.

With each individual DecodeME sample, half was used for DecodeME and half was saved for exactly this kind of opportunity, so it is that remaining half that will potentially be used here.

How much time does it take sequencing of 10,000 participants and then to analyze the data?

Someone far more knowledgeable than me is needed to answer this but the commonly quoted time for sequencing the whole genome of one sample is about 24 hours. I don't know how many samples Nanopore can sequence at once, and whether their technology is any faster than existing methods, so it is a bit difficult to guess how long they might take to process 10,000, or the planned 17,000 - analysis of all that data, and it is a lot, will also take a significant amount of time.

So ultimately until I know any better I will be setting my expectations as it all taking at least 18 months from once it is funded.

 

[josepdelafuente]

Thanks Andy!

Regarding funding - I have nothing specific at all in mind - but is this the kind of project that would be able to receive funding from individual members of the public (as I believe the OMF do - I get emails from them),

or is it just a case of waiting for institutional / government funding?

(This question is addressed to anyone who would like to answer, not specifically to Andy)

 

[butter.]

Yes - please email me if/when funding is announced for SequenceME.

So, funding is secured? Thank you!

 

[Sasha]

So, funding is secured? Thank you!

I read that as saying that funding is not secured! I think that Chris is saying that if funding is secured, that is the time for anyone to come forward who wants to help.

 

[hotblack]

or is it just a case of waiting for institutional / government funding?

(This question is addressed to anyone who would like to answer, not specifically to Andy)

I have zero information on this but I would be 99% sure it’s government/institutional. Most UK research linked to universities is I think government, national academies/institutes, european commission, etc. There’s sometimes charities involved too but individual donations seems much more a US thing.

edit: oh, apart from industry funded, but yeah, that doesn’t seem applicable here

 

[Dolphin]

From what I can see, the amount charities and similar give to medical research in the UK overall is similar if not a bit more than government sources like the MRC, NIHR, etc.

The problem here is the size of the funding being sought (£7 million) is not the sort of money UK ME/CFS charities are raising or likely to raise any time soon (Peter White says Parkinson’s Disease and Multiple Sclerosis charities raise twenty times the amount that UK ME/CFS charities raise (per patient?) so for another condition it might be feasible).

 

[Yann04]

Isn’t the MEA sitting on a couple unused millions. I mean it’s kind of like going “all in” but could be a good use IMO.

 

[Kitty]

Isn’t the MEA sitting on a couple unused millions. I mean it’s kind of like going “all in” but could be a good use IMO.

Yes, and even half of it would help.

But I think this should be one for government funding. They haven't put much into ME/CFS so far, and as it's likely to have relevance well beyond the initial questions, it's a good investment. If it produces answers that could lead to effective treatments, the economic payoff is potentially huge.

 

[Yann04]

But I think this should be one for government funding

I doubt anyone here disagrees with that. But the speculation is how it might be funded if only partial funding or even an outright rejection is recieved from the gov.

 

[bobbler]

I have zero information on this but I would be 99% sure it’s government/institutional. Most UK research linked to universities is I think government, national academies/institutes, european commission, etc. There’s sometimes charities involved too but individual donations seems much more a US thing.

edit: oh, apart from industry funded, but yeah, that doesn’t seem applicable here

I think universities in the U.K. have departments that are set up to support research that link in with eg major gifts (another dept - and they might be looking to find matches between projects that mightnt only be research but eg scholarships or music or whatnot ) and whatever dept they might call business development which includes anything from spin-offs of patents into a business to teaming up with industry or indeed funding of projects (but that will vary in how much and which depts/the infrastructure) so its there in the U.K. but perhaps less obvious.

And maybe there is less of a culture of the philanthropic things you see certainly on tv programmes from the US , maybe it just seems less obvious. Lots of buildings might have names of benefactors for example (although some might be people honoured fir different reasons)

I do remember over the years things like protests when some unis or depts took money from players in the tobacco industry for example. Reading has a centre within psychology dept for mental health that trains for ISPT )hence me looking at it) and is very CBT focused that was set up and funded a lot by a charity in the name of a family who lost their son

I don’t know how it works when a project is designed independently and then funded re:the conflicts of interest declaration and if that affects usage depending on who it is and I don’t know about whether the bigger chunks are often broken up into smaller chunks to make it more likely to get x donations of a smaller size vs one big one. Or whether (id probably have to think on it) it can just be a fund/campaign open to all donations (we assume it has to go through a charity and I guess these normally would link up with those if doing it that way) ?

 

[bobbler]

From what I can see, the amount charities and similar give to medical research in the UK overall is similar if not a bit more than government sources like the MRC, NIHR, etc.

The problem here is the size of the funding being sought (£7 million) is not the sort of money UK ME/CFS charities are raising or likely to raise any time soon (Peter White says Parkinson’s Disease and Multiple Sclerosis charities raise twenty times the amount that UK ME/CFS charities raise (per patient?) so for another condition it might be feasible).

I think there is chicken and egg we haven’t tested regarding ME research and we can’t assume. Ie the project does have to be a slam dunk that it would help and the good thing with this sort of thing is it’s helping to narrow down where to look (vs might be a theory that comes up empty)

mot would need to be very carefully thought about how to market it (DecodeME did well on being future - focused , people like missions that can ‘cure cancer by 20xx’ or ‘reduce poverty’) and do a good job of describing the condition (why is it needed) without saying too much it gets bogged down.