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Researchers propose deep trawl of DNA to help uncover the causes of ME/CFS (Simon McG blog)

Discussion in 'BioMedical ME/CFS News' started by Simon M, Jun 26, 2019.

  1. Simon M

    Simon M Senior Member (Voting Rights)

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    Researchers propose deep trawl of DNA to help uncover the causes of ME/CFS

    Analysing the DNA of thousands of patients can help to uncover the genetic roots of diseases and shed light on the underlying biological mechanisms. This can reveal targets for drug development.

    A new and very different type of genetic research has emerged this millennium – the genome-wide association study (GWAS, pronounced “gee-was”). By probing small genetic differences between people, such studies can help to uncover the biological roots of disease and have already helped to guide drug development. Researchers including Professor Chris Ponting, an expert in biomedical genomics, are asking the main UK research funders to finance a large GWAS for ME/CFS.

    The genome is our complete set of genetic information – all our DNA – and is made up of more than three billion DNA nucleotide base pairs. These nucleotides, usually referred to by their initial letters of A, T, G and C, spell out our genetic content. That includes all our genes, which are the bits of our genome that tell the body how to make all its proteins.

    There are roughly ten million places along the human genome where these individual letters can vary from person to person. For example, one person might have a G while another has an A. Each site where the letters vary is called a single nucleotide polymorphism, or SNP (pronounced “snip”) and a GWAS reads out around a million of these SNPs.

    SNP-close-up.jpg
    ...
    Researchers look for when a particular SNP version is strongly associated with a disease or a characteristic such as intelligence. For example, the “G” version of a particular SNP might be more common in people with ME/CFS than in healthy controls. This demonstrates a genetic influence on the risk of disease or on the characteristic – and what genes are involved, and what those genes do can reveal a great deal about the underlying biology.
    read the blog

    ...
    As a result of GWAS (confusingly, the same acronym is usually used for both the singular and the plural), we now know that hundreds of genes affect height, but each gene typically increases or decreases height by around 1 mm. (Environmental factors such as childhood nutrition affect height too.) Ponting told me in an email conversation:

    “SNPs are like small pieces of paper that – placed under the legs of a pool table – tip the balance of the table so that a ball rolls in one direction more than another.”
    ...
    With ME/CFS, scientists have pursued many different hypotheses about its cause over the years but have yet to make a breakthrough. University College London’s emeritus Professor Jonathan Edwards @Jonathan Edwards argues that it is time for broad approaches like GWAS with the potential to generate new avenues to explore. He told me in a recent email,

    “The success of research into causes of disease hinges on someone suddenly having a brilliant idea… yet for ME/CFS nobody has a strong enough lead to show everyone the way forward. So it makes sense to set up a comprehensive fishing trip to see if we can trawl up some clues. Genetic screening [a GWAS] is probably the best bet for finding such clues.”
    ...
    GWAS successes
    Despite these limitations, GWAS studies and follow-up work have already thrown light on the mechanisms of several diseases and have helped to identify new or promising drug therapies.
    ...

    Other autoimmune disease

    Analysing DNA from one patient reveals little, but combining data from thousands of people in a GWAS can reveaal much more.
    Researchers have compared GWAS results from different illnesses to see if they have something in common – and autoimmune diseases often do. Findings from these studies have led to the identification of a common pathway for several diseases, one that includes an immune-regulating molecule called IL-23. As a result of this insight, existing drugs that are used to inhibit the IL-23 pathway in other diseases have become a mainstay treatment for several autoimmune conditions, including psoriasis and ankylosing spondylitis.

    ...
    GWAS can sweep across the whole of human biology looking for potential mechanisms that might cause ME/CFS, even unsuspected mechanisms. It’s a remarkable technique and this is the ideal time for an ME/CFS study.

    UK researchers, including Chris Ponting, colleagues from the CMRC and the CureME team are aiming to put a proposal in for a large GWAS later this year. The study might need as many as 20,000 patients.


    But recruiting so many ME/CFS patients would pose an unprecedented challenge for the researchers. The study would be the largest ever conducted in ME/CFS.

    DNA-people.jpg

    However, recent years have seen rapid growth of an action orientated patient community around the world. MillionsMissing events, for example, have shown what patients can come together to achieve. Chris Ponting says,

    “we can get this done, and done fast – but it will be people with ME who make it happen.”
     
    Last edited: Jun 26, 2019
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  2. arewenearlythereyet

    arewenearlythereyet Senior Member (Voting Rights)

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    I think this is very exciting if we get the funding. I’m already thinking of ideas on how to drive recruitment. 20,000 is a big number.

    @Simon M would this be a simple case of signing up and being sent a spit tube/cheek swab that can be sent and returned in the post?
     
  3. Andy

    Andy Committee Member & Outreach

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    An interesting question, to my mind at least, is will all those 20k patients need to be assessed to confirm their diagnosis, or will it be OK if the participants self-report a CFS/ME diagnosis? I'm assuming that the larger the sample size, theoretically the less of an issue that it becomes?
     
  4. wigglethemouse

    wigglethemouse Senior Member (Voting Rights)

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    Thank you @Simon M !!! Some questions if you are able to pass them on.

    1. Would the study need controls or could it leverage and use labs/sequencing chips from previous GWAS studies to keep costs down.

    2. Would patients submit a survey to try and better group data being that we are a likely hetergenous group. I'm thinking this is also a good chance to leverage some of the ME Biobank data surveys that they do. And also best results are obtained with a well defined case and control group - which is likely hard with 20,000 patients. Needs some good GWAS experience to well define the study I imagine.

    3. Would it be a mail in saliva sample or lab blood sample?

    4. Would it be UK only or wider? I assume the population stratification of control group needs to match that of patient group so ties into (1) above.

    5. Approximate cost per sample? I have no idea how much a GWAS study would cost.

    6. What are @Chris Ponting thoughts on the value of GWAS as described vs WGS of families with multiple people effected to find the significant genes. I'd like to understand the pros and cons. Probably both have a place......
     
  5. Medfeb

    Medfeb Senior Member (Voting Rights)

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    Thank you, @Simon M!! Interesting.

    My question is similar to @Andy's. How will they confirm that the 20,000 people all have ME?

    In the US, CDC has piloted a survey, called the "Behavioral Risk Factor Surveillance System that used a patient report of a diagnosis of CFS by the doctor. The pilot reported a lifetime prevalence of 1.6% and a current prevalence of 1.2%. That's significantly higher than Jason's prevalence estimate of .42% and if I remember correctly, Nacul's prevalence estimate of .19% for Fukuda and .11% for CCC.

    The CDC survey was self-report of a diagnosis by a doctor which is better than just self-report. But IMO, even that is not enough as a CFS diagnosis at least in the US has been based on Fukuda, is often inaccurate, and is too often used as a wastebin diagnosis for unexplained fatigue. Two studies from the UK also reported diagnostic inaccuracy with something like 50% of the patients referred to a CFS clinic being diagnosed incorrectly. So I expect its likely that the CDC survey captured people who had all been given a CFS label by their doctors but some significant percentage actually had something else.

    For the 20,000 person "CFS" GWAS study, I appreciate the power of these technologies. But I also question how much power the technologies have if faced with a cohort that is poorly defined and wildly heterogeneous to the extent of including significant numbers of people with other conditions. My assumption, which could be wrong, is that this problem does not go away just because you have a huge cohort.

    Will Oxford CFS patients be included? NICE criteria? What other criteria will be used and just as importantly, how will they be operationalized to ensure consistency in application across the centers doing the study? Will there be a clinical confirmation of the diagnosis?

    If the plan is to cast a wide net, is there precedent for applying these technologies and this approach in such an ill-defined space? If so, could you share so I can better understand how they deal with such a situation?
    Thanks
     
  6. Lisa108

    Lisa108 Senior Member (Voting Rights)

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    Could pwME share their already existing WGS-data?
     
  7. Trish

    Trish Moderator Staff Member

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    I note the article says the CureME/UK ME biobank team will be involved. So I'm sure they will want to make sure there is a proper diagnostic process. But for 20,000 participants, they won't be able to do the personalised approach they do now, presumably. I hope they will make it an international study with data collected in other countries too.
     
  8. Simon M

    Simon M Senior Member (Voting Rights)

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    Thanks for the excellent questions and I am delighted that so much interest in this. I will answer as much of this as I can myself as I don't know if Chris Ponting is available at the moment.
    Yes, it is an enormous number! I am not sure if that many patients have ever come together for a single project. It is simply a spit and post in terms of sample collection.

    This is the key question. Not all the details have been finalised yet. Certainly it will include self-report of a ME/CFS diagnosis (I'm not sure this will be bright simply a doctor or by a consultant). There will also be some questionnaire screening (note that the UK ME/CFS biobank is involved).


    There's also the possibility of a validation step: taking a subsample of those people who pass the questionnaire screen and giving them a thorough medical assessment/diagnosis.


    Yes, with larger sample sizes you have more leeway (because non--cases should be easier to identify in a cluster) but I think it's important there is some quality control of who exactly is passing the standard screen.

    1. The controls would be from existing very large samples using the same lab/sequencing chips.

    2. Note that the project does involve the ME/CFS biobank and will involve those with good GWAS experience (and will tap into yet more experience).

    4. I think to get numbers it will have to recruit beyond the UK, that might be limited to only a few countries for logistical and ethical (approval) reasons.

    5. I am not sure, I think it's a better hundred pounds per sample, maybe less as costs fall generally and because of scale.

    6. Hopefully Chris Ponting will apply here but I know from discussions I have had with him that he believes that both GWAS and WGS (whole Gene sequencing) are important.

    No I don't think the CDC-type survey with weak patient selection is what we are discussing here, see above.

    There will be a detailed screening question that will aim to find ME/CFS, not some broad definition of CFS such as Oxford, AFAIK.


    Not sure, but I suspect that the numbers will be tiny.
     
    Last edited: Jun 27, 2019
  9. Amw66

    Amw66 Senior Member (Voting Rights)

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    How many other bio banks/ DNA sampling data is there worldwide?

    A coordinated, standardised format may be able to glean existing data .

    Both omf and klimas have requested and received genetic data. Could some who have forwarded this previously be interviewed ( Skype?) / complete a diagnostic questionnaire to push this on.

    To me epigenetics would seem to play a key role: it's the interaction of multiple gene's that may give some of the heterogeneity.

    There is an end state, but many paths in - that's both the fascinating and frustrating aspect .
     
  10. Michiel Tack

    Michiel Tack Senior Member (Voting Rights)

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    I like the idea of a GWAS, as it could further the field with some reliable clues into ME/CFS. But I'm skeptical that a study with 20.000 ME/CFS patients is feasible. If a study uses more than 100 ME/CFS patients that's already considered a big deal. And using questionnaire screens to diagnose ME/CFS and bypass the time-intensive clinical examination is constantly being tried by researchers like Jason and Baraniuk, but I'm not aware of much progress in this area except perhaps for the DePaul Symptom Questionnaire.

    I don't know if there is a study that tested the reliability of a self-reported diagnosis of ME or CFS. But the reported prevalence of self-reported ME/CFS is often higher than 1% which seems implausible. The epidemiologic studies point to a figure of 0,2%-0,4% with the majority of patients being undiagnosed. This suggests that self-reported diagnosis of ME/CFS is very unreliable (one caveat: This could partially be a result of severity requirement in case definitions. Patients might have received a diagnosis of ME/CFS and gotten a little better. So they might no longer fit case definitions but consider themselves to still have ME/CFS, and perhaps rightly so).

    In the epidemiological studies, they started with questionnaires to identify patients with a CFS-like illness. This meant that patients confirmed to the Fukuda-definition requirements but without having a clinical examination by an expert to check whether those requirements were really met. In the Chicago study, 166 persons with such a CFS-like illness were examined by an expert and afterward only 32 (19%) of them were diagnosed with CFS (42 had idiopathic chronic fatigue, 89 had a medical explanation for their fatigue). Results were similar in the Wichita, Kansas study. 299 patients with a CFS-like illness were examined by a clinician and only 43 (14%) were found to have CFS afterward.
    upload_2019-6-27_0-15-0.png

    So if a study were to use questionnaires to look for patients satisfying the Fukuda CFS-criteria, approximately 80% of the patients selected would not currently have a diagnosis of CFS, if they were examined clinically by experts. Perhaps there are better questionnaires to screen for ME/CFS patients but I doubt that this figure of 80% would drop anywhere near to acceptable levels. Sorry to dwell on this issue, but I suspect this will be the major hurdle for this project: whether it is realistic to go for a sample of 20.000 ME/CFS patients.
     
  11. Simone

    Simone Senior Member (Voting Rights)

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    I hope whoever runs this project (presumably Chris Ponting?) learns the lessons from the MEGA project: don’t let psychosocial researchers anywhere near it because, even if you have the best project design in the world (not that MEGA was), the patient community won’t trust you if you include anyone with a whiff of the psychosocial school. Have a Patient Advisory Group, and actually collaborate with them. If they’re just a token, it won’t work.

    With needing 10,000+ samples, whoever runs this project needs to listen to and engage with the community. Not MEGA-style PR and spin, but genuine engagement. For a project like this to succeed, they will need the community to be behind it.
     
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  12. Cinders66

    Cinders66 Senior Member (Voting Rights)

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    After several years keeping us as a community baited with this as the big “project in the pipeline”, if they do eventually get this off the ground , I’m guessing it won’t be funded until mid next year potentially, started at the end of 2020 to finish 23-25?
    Since this was THE research project we were, from the little information given at CMRC conference and minutes, all waiting on, I would have liked much more transparency from the start. I don’t know how content, since 2016, the community would have been to just wait on this and nothing else, if they’d known it would take until end 2019 to even put in applications for funding. When MERUK recently gave that suggestion m that time had actually just been spent securing support for an application, I couldn’t get this really clarified by the charities when asked. There’s not been much communication with the community but clearly certain groups have been busy.

    I’m not qualified to say if this is worth the wait and the resources. I’m guessing as a big project it will amount to the totality of uk effort and funding if the likes of K Morten are getting turned down. I personally think by 2023 25 other groups will have found some of direct significance findings, possibly translated in treatment. Simon has listed where it’s helped with other illness , so well and good if it eventually helps us too, if we are stil around waiting; A Severe disappears every few months. I personally don’t agree with how this has been almost sole focus of CMRC and the potential only MRC funds on table.
     
    Last edited: Jun 26, 2019
  13. Simon M

    Simon M Senior Member (Voting Rights)

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    I am not aware of any biobanks with significant amounts of relevant DNA data. There is Klimas but I don't know if it's feasible to incorporate that data.

    Epigenetics is a different approach. Critically, epigenetics reflect gene activity, which can be an effect of other things upstream, which may not be specific to the illness. Whereas GWAS gives causal data. See this from the blog:

    Thanks for those points and the incisive analysis. The Chicago and Wichita studies are very relevant. A couple of things: they only used a Fukuda questionnaire, which does not require PEM, even though most researchers consider that the cardinal symptom of the illness. And critically they did not also require a (Self reported) medical diagnosis ( I think that most cases were undiagnosed ). And there are much better questionnaires around, including the DePaul one.

    Also, do you know what's thresholds they used for fatigue and function? My dim recall is that a lot of the non-CFS cases were simply not severe enough.

    So using better questionnaires, requiring diagnosis (perhaps by a consultant which means that at least some level of medical examination, nb most cases in the study were undiagnosed) and some sensible thresholds for fatigue and function will probably produce much more accurate diagnosis.
    This is key. That is why I think it's important there is a validation step in the GWAS, with proper medical assessment of a subset as a quality control.

    It hasn't been finalised who will be running the GWAS but it will be run by biomedical researchers and there will be a patient advisory group who will have meaningful involvement. Certainly, Chris Ponting is very keen on a patient advisory group taking a key role. Not least because, as you say, this project will only succeed with the community behind it.

    I certainly agree it is disappointing that CMRC activity hasn't translated into biomedical research projects yet. I don't know what the timescale is to get final results but it's certainly going to be a number of years. It is possible that ME/CFS would have been solved by them: I would be extremely surprised and delighted if that is the case.
     
    Last edited: Jun 28, 2019
  14. arewenearlythereyet

    arewenearlythereyet Senior Member (Voting Rights)

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    I presume the 20,000 number accounts for misdiagnosis and will be able to still generate enough power to give some meaningful findings that will generate enough leads to do more in depth studies?. It may also help (in conjunction with screening questions) to identify the rate at which misdiagnosis occurs?

    I think in order for recruitment to work to get the 20,000, we will need a full social media campaign to drive recruitment off of multiple platforms with all charities supporting it and encouraging their members to participate. I’m not sure how many members the mEA or other charities have?

    We could also have posters for GP surgeries if this is ethical/allowed? I hope the charities would spend some money sending out mailers to its members as well as ambient posting on their websites.

    Getting 20,000 might not be as difficult as it sounds. I think from memory the MEA petition to stop GET was over 15,000 signatures in quite a short space of time

    I think signing a petition is one thing (some of which will be friends and family without ME), but providing DNA material may be viewed with suspicion or reluctance so convincing the community as to the anonymity of how it will be used and stored will be key during recruitment. Also how much effort is required may need to be explained (e.g. return address envelope, sample collection). I would also advise that the questionnaire needs to be short and take no longer than 10 min to complete and be available to fill online as an alternative to a paper version.

    Recruitment copy will need to demonstrate the value of the project in a clear way to show relevance and context. We need to be really clear on this.

    We should also allow enough time for recruitment so leaving this open as long as possible seems sensible.

    Targets and feedback back to the community will also help motivate and keep the campaign running during recruitment.

    I hope they consider allocating some marketing funds for recruitment in the proposal, and don’t just rely on the rather amateurish, passive and lacklustre activity we have seen from some charities of late.
     
  15. Sly Saint

    Sly Saint Senior Member (Voting Rights)

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    I would worry that they ended up recruiting from fatigue clinics.
    Personally, I would prefer research to concentrate on some kind of fairly reliable biomarker first to ensure participants in this kind of genetics study were patients with ME.

    Could they not just do the analysis on the all the existing Biobank samples for pwME and see what it reveals first? (or have they already done this?)
    (is this or similar genetic analysis not done as a matter of course when new samples are received?).
     
  16. strategist

    strategist Senior Member (Voting Rights)

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    That was unlikely to be 15000 patients but included friends and family members. It's also much easier to sign a petition than to give a saliva or blood sample.
     
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  17. It's M.E. Linda

    It's M.E. Linda Senior Member (Voting Rights)

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    Certainly, as a starter @Simon M , I would think all current participants with the U.K. ME/CFS Biobank would be keen and willing to provide samples.

    A spit and post trial could be done very easily within this group - the Biobank has already completed screening, confirmation of diagnosis and every participant is satisfied that their data is properly anonymised. Just some spit in a pot is quick and easy to do at home in comparison to the usual collection procedure for the current research.

    As a participant, I think any sort of fundraiser the Biobank created specifically for this project (if they were able to take the lead on the screening of volunteers) would also be supported by many of those signatories from the ME Association petition.
     
  18. arewenearlythereyet

    arewenearlythereyet Senior Member (Voting Rights)

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    Yes I agree, which is why I mentioned it in my post.

    I think anyone who is resistant to participating will need convincing ...so a passive campaign like the one for the stop get signatures will be inadequate imo. The charities will need to significantly up their game if they are going to drive recruitment on this. Particularly MEA and AFME. They will need to allocate in the region of £5-10,000 (at least) to directly market it to their members. I hope within the proposal some funds can be made available to do this, but I confess I do not know whether this is a “normal” thing to do? I hope the charity membership databases are fully compliant with GDPR.

    A normal uptake for any marketing campaign would be anywhere between 2-25% of the target group. So if we have say 250,000 people in the uk and we want 20,000 this does fit in the range. How well this goes depends a lot on the communication plan and the incentive to participate.
     
  19. Simon M

    Simon M Senior Member (Voting Rights)

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    Thanks for all the suggestions. This is a huge target but I think of the whole community gets behind its we could do this and establish the world's largest ME/CFS study. From the blog:

    But recruiting so many ME/CFS patients would pose an unprecedented challenge for the researchers. The study would be the largest ever conducted in ME/CFS.

    However, recent years have seen rapid growth of an action orientated patient community around the world. MillionsMissing events, for example, have shown what patients can come together to achieve. Chris Ponting says,

    “we can get this done, and done fast – but it will be people with ME who make it happen.”

    It’s rare that any patient can take part in research about their illness, but this study gives us all this chance. It would be an incredible project, the world’s biggest ME/CFS study, that could help uncover the biological roots to our disease.​

    So the 20,000 does assume that diagnosis won't be perfect. Nobody knows what is the "right" number (and the final figure might be less than 20,000 to this study). Until you've done a GWAS, there's no actual way of knowing how big a sample you need. But 10,000+ is a reasonable guess.

    And yes, identifying the rate of likely misdiagnosis is important, I believe.

    GWAS have used questionnaires and spit and post before, so there is a proven methodology for this. Though I am sure there will be extensive piloting of the specific questionnaire for this: on the one hand it needs to be short to get high completion rates, on the other hand getting an accurate diagnosis means collecting a lot of data.

    I agree with all the things you've said and this is going to require an enormous effort with the community. Personally, I think that could be incredibly exciting.

    Unfortunately, people have spent the last 30 years trying to find a reliable biomarker, without success yet. And biomarker screening would be expensive. The key thing is to get of reliable diagnosis and if a questionnaire approach (as outlined above, with Screening) can do it, that's probably more cost-effective.

    The biobank has a couple of hundred ME/CFS samples and that's way too small to get any usable GWAS data, unfortunately. It's very much a big data approach, because it is looking for small effects.

    Yup, and that's a couple of hundred for starters.

    Stuggling to keep up! hope I haven't missed anything.[/QUOTE]
     
    Last edited: Jun 27, 2019
  20. Amw66

    Amw66 Senior Member (Voting Rights)

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    Thanks for the clarification @Simon M . I have a feeling in our case that epigenetic expression helped create the conditions for a trigger to tip things over. I could be very wrong. So not causal but a facilitator.

    This seems a study that needs to be done. The difficulty, given history, may be targeting the patient group without alienating ( or being seen to denigrate) those who don't meet strict selective criteria.

    We are divided enough amongst ourselves as it is.

    This would require significant and ongoing diplomatic efforts and coordination across charities and advocacy groups to garner the amount of samples required even without any spanners being thrown in from outside.

    Could this be the project to drive wholesale cooperation?
     

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