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Negative study of CFSers cerebrospinal fluid for XMRV and other viruses

Discussion in 'XMRV Research and Replication Studies' started by Esther12, Feb 4, 2011.

  1. omerbasket

    omerbasket Senior Member

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    This does not look to me like a good study, Esther. They might have wanted to find the truth, but to me it seems slappy. For example, what is all that stuff with putting 20 samples together?

    Anyway, I ask a very important question: Is it reasonable that there was not even one of all of the viruses that they tested in the CSF? Is the percentage in the healthy population of that (these viruses in the CSF) is 0 or very very close to that? And what about the percentage in CFS patients?
    I think that that might be important not only for this study, but perhaps it can explain other negative studies as well. Is there something which they all do that kills the viruses while they don't know that?

    If someone knows whether it's reasonable that good tests (and I don't say that the tests used in this study were good or bad tests) would not find even one of those 43 patients to be positive to at least one of the viruses described in the study (such as EBV, CMV, HHV-1, HHV-2, HHV-3, Parvovirus B19 etc.), please comment about that.
    It just seems very odd to me that they did everything right and still found none of these viruses in those samples. I tend to think that somewhere in the process they did a crucial mistake.
  2. Esther12

    Esther12 Senior Member

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    I have to admit, I am still speaking from ignorance, and going off what others have said as I can't get the full paper (and would not have the knowledge to properly assess it anyway).

    If they'd not found any XMRV, maybe they thought combining samples for VIP would be a quick way of having VIP check a number of samples, before trying to narrow down what would cause the any difference. Maybe VIP weren't keen on checking 43 samples? (Which is a low number... I'm not normally so concerned by cohort issues on these studies, on the assumptio that most criteria will include some 'real' CFS patients. I thik this is probably still the case for XMRV, but with the other viruses there's more of a potential for subsets, and then 43 could be too small to give a meaningful negative).

    I googled one of the people doing this study, and it brought up news articles of him making breakthroughs in the ability to detect viruses in CSF, so I am willing to make the sort of excuses you see above for him unless there is a more compelling reason to think there's something actively bogus about the work.
  3. omerbasket

    omerbasket Senior Member

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    Actually, I'm more arfraid of those who found new ways to discover viruses... They tend to forget the old ways, which are better sometimes.
    Anyway, the fact that he found new ways of discovering viruses says nothing about this study, and the fact that you, Esther, sees nothing bogus about it is your right - but I still am wondering - how is it that they found no viruses whatsoever in there.
    You also have to remember that at least in the blood, the WPI - and VIP Dx works with WPI's best methods - found XMRV in 3.7% of the healthy population. So it's also wierd that they (was it VIP Dx or just their methods?) couldn't find XMRV in any of the people there. Also, I wonder why they didn't look for antibodies. Are there no antibodies in the CSF?

    With this grant, I think that could have, and should have, done a much better study before they publish negative results.
  4. acer2000

    acer2000 Senior Member

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    Not odd at all. Based on what is current knowledge, they shouldn't find any of those viruses in CSF of CFS patients (or controls). CSF is supposed to be sterile. The only thing I can recall is that HHV6 might have been found in the CSF of some small number of the incline patients.
  5. omerbasket

    omerbasket Senior Member

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    And what a surprise - they didn't check for that. Perhaps they thought this could cause them to lose some of their credibility?
  6. acer2000

    acer2000 Senior Member

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    I don't know. I think the issues with this study being accurate or not are mainly going lie with the methodology of the methods they used to find XMRV since that is the new thing.

    My main questions are - 1) does the VIPdx culture method that they ran on the CSF even work to find XMRV in CSF? (As far as has been documented in studies and being communicated commercially, its only been used on blood). 2) How were the samples collected/processed before they were tested and can that make a difference? 3) Does XMRV even exist in CSF - ie would it even be expected to be found there?

    I would have liked to see them compare blood XMRV results, CSF XMRV results to controls. That would have been pretty interesting.

    OTOH - I think one thing we might gather from this study is that contamination is even more an extremely unlikely issue with VIPdx and their process. If there was an issue with "passing through VIPdx lab space/method" that would cause contamination, well you'd think it would have shown up here - but all these samples were negative. We all kind of knew that accusation was bunk, but this, while indirect - is another nail in its coffin.
  7. omerbasket

    omerbasket Senior Member

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    I agree with you completely. The question about the other viruses is in order to see if we can find a very easy proof that we have a problem in the methodology.
    Anyway, even if these other viruses are not suposed to be found in anyone's CSF, we still very well might have problems with the methodology.

    I'll tell you guys what I think: I think that scientists here are forgetting why it is still important not to rush science. Yes, ofcourse, we would love to have a solution today or, you know what, yesterday. We would very much prefer that. But after the first negative study, the second negative study and the third negative study - scientists must understand: Rushing here is a fatal mistake.

    I said on the other forum that it won't harm to do the study using whatever methods, as long as you publish it only if it's positive and you take proper steps to avoid contamination - and if you don't, you state so. But I'm painfuly confident that publishing a negative study before doing everything, but really really everything (none of the negative studies until today got even close to doing everything - even though some scientists would consider them - "very well done". Perhaps they are forgetting that we're dealing with a new virus that might not act in the same way that we expect it would act), is disasterous and could keep people very ill, or even cause them to die younger than they would have if the negative studies are wrong.

    We just don't know, and can't know, what can go wrong with a study and cause it's results to be misleading. For example: One might say that his assays were good enough to find at least one or two positives, if the 67%-98% of positives reported by the positive studies are correct. Altough I think that this is a claim that he cannot prove, at least not at this point, let's assume for a second that he is right - that his assay would have detected at least one, or two, or three positives in a cohort of, let's say, 50 people. But who are these people? Are the people that Simon Wessely diagnoses as CFS sufferers have the same illness as those diagnosed as CFS sufferers by Dr. Peterson? They would say that at least 10 of them are probably are. Altough I'd argue with that also (It's possible, but it's also possible that it isn't - and the radical example of Wessely makes it understandable [altough sometimes it might be the truth and we would still not know that]: Wessely believes that physical symptoms are due to psychiatric problems, and it is very well possible that the vast majority of his "CFS" patinets - and all of those 50 selected for the study, wouldn't have been diagnosed by Dr. Peterson as CFS sufferers), let's go along with that example. Now, you have 10 CFS sufferers and 40 with CFS. Let's say you have 12 XMRV positives there - the 10 from CFS and 2 of 40 from the other sufferers (close to the percentage in healthy controls). Your test is good enough to at least find it in 4 people out of 50 that are all positive (or the vasy majority of them are positive). But who says that here, with the 12 positives, it would be able to find it even in one? Possible, but also possible that it won't be able.

    Let's go for another example: You cloned XMRV and put it, without any periphral blood, in a cell line that wasn't tried before. you test it after some time with a quantifying method and see that there is much more XMRV there now. You say to yourself: "That cell line is permissive for XMRV". So you take patients blood and put it in this kind of cell lines. What you don't know, and can't know, is that once peripheral blood comes in touch with this cell line, it creates a substance that kills XMRV. I mean, sometimes you need two to tango. The mitochondria, without oxygen and sugar/fats, wouldn't produce energy, but with them it keeps us alive. So it's possible that a reaction between two substances would cause something that you didn't think about and that would ruin your study.

    These are two examples. The thing is: There are thousands, and probably more, of such examples. Every little thing can matter. Therefore, and because we are dealing with people's health and life here, we must be extremely careful. The scientific world might move on and leave XMRV behind, because many studies didn't find XMRV - even if XMRV is very very real and does exist in the human population, and the studies didn't find it because they have done one thing, or more than that, wrong. For all we know, we should be very very gracious that a human being ever found a method that would find XMRV in real clinical samples.

    So you can do the CSF testing. And if you have a positive result, you can publish it. But if you have a negative result, don't publish it before you perform the things that leas scientists to finding XMRV in real clinical samples. So, the authors of the current study would say: "We did just that! We used VIP Dx's method!". Here is their mistake, and here is what I was refering to in all this long post of mine: No, you did not do what VIP Dx does. It's not just that you tested CSF and not blood. It's also that you might not have used the same test tubes, the same type of patients (patients who fulfill the Canadian Consensus Criteria), the same type of processing of the sample, the same type of storage (some scientists would say: "We tested fresh samples!". Well, it seems to me that the WPI, and probably also VIP Dx, only tested stored samples. Perhaps it caused the virus to be more easy to find? An example for how a thing that seems very much unlikely might very well be true is the results of the "Phase II" of the Blood Working Group - were they found that you can find the virus after 2 days and 4 days of storage, but not at the same day that it was taken. So, perhaps "We tested fresh samples!" is actually the reason for which you did not find the virus, even though the person might very well be positive for XMRV?) , the same assays, the same amount of blood, the same amount of tests in each assay etc. etc. etc. You just don't know what could have caused a problem here.

    Some would say that the XMRV thing is a result of lab contamination. I think that this is very unlikely, due to a number of reasons, but they are entitled to think so. They can think so, yes. But what they must not do is to speak about it as if it's a fact, or even to imply that it's a fact. It was not proven. Some people are probably pretty much sure about it, but some people are sure that it's a very real virus, and some are sure that antiretrovirals are good against that. The issue is to prove it. Perhaps proving that a virus is a result of laboratory contamination is not possible, I don't know (at the very least you'd need to think a lot in order to find out a way to prove it). But there is a simple way in order to make the claims very very strong: Replicate the positive studies, with the adjustments that the original authors of the studies would recommend due to the things that they have learned since that.
    But replicate it. Completely. Not just one assay, not just all the assays, not just the cohort, not just the collection, not just the storage, not just the processing. All of them.

    If you have a low budget or you are short in time - you can do a non-replicating study, with what you have. If you find a positive result, you should publish it, while taking serious steps to avoid laboratory contamination. But if you did a non-replicating study and came up with a negative result, do not publish it. If you'd have the possiblity, complete everything that needs to be completed in order for it to be a full replicating study, and then publish it with whatever results you have. If you can't do that, because of budget, time or other issues - don't publish it at all.

    If you can do science and reach absolute 100% proofs on a short period of time - that's better than to wait longer. But if there is any room for doubt, even 0.01% of doubt, you must complete the long process in order to find out the truth, this time with 100% certainty of all of the scientists.
  8. TerriK

    TerriK

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    A side note.. it would be nice to know if any of these CFS patients had oligoclonal banding. It seems to me it would be a significant finding in patients with no other dx; no infection or dx of MS etc. The bands have to come from somewhere, from a significant immune response within the body, one that effects the CNS. Even if a CNS microbe was unable to be identified if a significant number of CFS patients have oligoclonal banding that would be a major finding, would it not?
  9. WillowJ

    WillowJ Senior Member

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    I've seen this technique before in CSF studies (some of them with Natleson), when they found proteins that don't belong. Evidently (and this was explained in another paper) stuff is so diluted in CSF that you have a better chance of finding abnormalities like this, or so the theory goes.
  10. omerbasket

    omerbasket Senior Member

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    As you said, WillowJ, theory.
    I have another theory: perhaps those who really don't have XMRV in their CSF have some antibodies or other materials against it there, materials that would make all the XMRV from all of the patient's samples in the vial to die?

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