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Negative XMRV CFS study with Ila Singh's name on it (University of Utah)

Discussion in 'XMRV Research and Replication Studies' started by Jemal, May 4, 2011.

  1. eric_s

    eric_s Senior Member

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    Thanks CBS. I also think Switzer's study and the Macaque findings are interesting. Also what Vaughn (Miller's assistant) is about to publish. I don't know what the truth will be, but there are too many questions open and too many coincidences like that XMRV likes to go to the prostate in Macaques and has neurotoxic and immunotoxic properties to abandon it before all of this is answered, i think.
  2. Parismountain

    Parismountain Senior Member

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    Who's going to risk submitting a paper which is positive on XMRV now? A piece of lab equipment with the most minute particle could be a source of contamination? If you are in the middle of a study and you get the robot dna machine clue in from this just released paper, wouldn't you automatically discount all your findings and wonder might MIGHT that have happened to me too? I probably sneeze and mouse DNA flies out of my nostrils. Great just Great.

    Had a software engineer friend who use to have a poster of a rooster in his office with the caption - I'm so confused I don't know which way to point my pecker. That about sums it up.
  3. Mya Symons

    Mya Symons Mya Symons

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    Sorry if someone already mentioned this. I am too tired to read through all the posts.

    Have we heard anything more about the DNA evidence Dr. Mikovitz claimed to have? What happened to the $100.00 DNA mapping test that found Mouse DNA mixed in with the human DNA.

    What about HTLV 1 & 2? I posted a study that found that 38% of persons with HTLV 1 ended up with fibromyalgia. It was an old study from 6 years ago. I have access to some of the medical journals, and I could not find where anyone had attempted to do a follow up study. I know fibromyalgia isn't the same as ME, however, maybe this virus effects certain people much more negatively then others, depending on genetics? Would it have been possible for another retrovirus (not XMRV) to be causing ME symptoms?
  4. currer

    currer Senior Member

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  5. Parismountain

    Parismountain Senior Member

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    Yes it is scary and I don't want to go back to the times before WPI either. I agree it seems so simple if you took 500 people qualified by Bell or Peterson or Klimas or Chenney or Lapp and studied the heck out of those people you'd find it. I don't care anymore about criteria Faduko this and Canadian that. You could easily get patient sets to study from known points of light docs we've been flocking to.

    This whole saga fits well into the life isn't fair category. It's beyond crummy to be so ill but I don't think a Pulitzer prize winning author could write a concoction of a tale mirroring the way we've been treated and have that tale pass as believable. The ignorance of physicians, the psyche criminals and the lack of funding for research and the career ending knowledge researchers who get into this subject find, the CDC morons who headed CFS and directed the 10 cents in funds coming our ways to other illnesses, the tag-alongs who claim to have this disease because they're fatigued to, I could go on and on but what's the point.

    Discouragement bucket is full on me I'd say today.
  6. Cort

    Cort Phoenix Rising Founder

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    A True Replication Study

    After reading the study my conclusion was that this was a true replication study.

    PCR- On line 356 she says she used the PCR assay used in the first study to search for XMRV in the Utah patients. She repeated that statement at least twice more in the paper
    Antibodies - I don't believe she replicated this test.
    Culture - She worked with Dr. Ruscetti to used an improved culture test that lasted for 6 weeks. Later she noted the increased risk of contamination from using culture.

    She also used the Lo/Alter version of the test and except for some sequences later determined to be due to contamination, failed to find the MLV sequences they had.

    On line 421 she says "We also also analyzed the WPI samples using tests utilized in the two studies that found XMRV or XMRV-like viruses in CFS, a PCR assay for gag sequences both in single round (12) and nested formats and a test for viral growth in cultured cells (12)"

    On lines 436/438 she repeats those statements - stating we used the gag assays and culture tests used in the original study....

    #11 refers to the Lo/Alter study and #12 refers to the WPI study.

    This was a replication study...not only does she say she replicated the WPI's methods but she used her own methods - which should, given how much has been learned about XMRV since then, be more accurate.

    She really looked hard - she looked 9 different ways for XMRV in those 14 WPI positive patients; 4 qPCR tests developed by Dr. Singh, two antibody tests, a Ruscetti culture test, nested PCR (gag) (Lombardi) and nested PCR (Lo/Alter). That is alot of testing.
  7. Cort

    Cort Phoenix Rising Founder

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    THis is an interesting subject. Look at line 449 - it says "Our experience shows us that detection of XMRV in blood is fraught with difficulties". :This study was all about the blood - it had nothing to say about XMRV elsewhere.

    We know that she identified the source of her false positives in the blood - so you can throw those out. But there are still the immunohistochemistry resultsI thought would be part of this study but it weren't. Her IHC results have come under some fire lately with at least one study purportedly showing, I believe, where they felt she went wrong but they are yet to come. She still has the autopsy study to come as well.

    This was an intricate and detailed study... Dr. Racaniello called it the most comprehensive study yet and CBS pointed out how it took her a year to finish it up. We saw how she painstakinging tracked down the source of the positives (on both the healthy controls and CFS patients). The study then really supersedes any patent applications - which tend to be filed as quickly as possible.

    Even if the IHC results are outstanding the authors did state that they believe that XMRV is not associated iwth CFS - not just in Utah but anywhere - which would be an odd thing to say if they had IHC results which contradicted everything.
  8. kday

    kday Senior Member

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    By no means do I think it is a conspiracy. I think this is honest science.

    However, we must not forget history:

    http://en.wikipedia.org/wiki/And_the_Band_Played_On (From the book "And the Band Played On")
  9. alex3619

    alex3619 Senior Member

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    There are issues with contamination that are worth mentioning again in light of the Shin et. al. study.

    Contamination is only a big issue with two testing methods, both of which is based on polymerase chain reaction, PCR. PCR amplifies genetic material - so even a small amount is amplified and becomes detectable if it matches the starting primer. Nested PCR has the potential to further amplify the genetic material.

    Culturing relies on PCR testing to identify the virus, iirc. Chance mouse contamination will probably have a small risk (due to being able to test for mouse DNA), this is a major problem only if the contamination is a live virus that can replicate in culture. The problem with a culture is that it is at risk from the environment on more occasions. Otherwise the risk is mostly from the PCR testing itself, because trace amounts of DNA in the culture will be amplified.

    DNA and especially RNA are very vulnerable molecules. They are easily destroyed. So old sources of mouse contamination are not likely to be a problem, ongoing sources of mouse DNA is the issue, which means something is continually putting mouse DNA into the lab. Lab reagents are a possibility, but there are many other potential sources. To prove contamination, somebody has to definitively identify the source, lab by lab (because different labs might have different sources). I still think we should consider infected people as potential sources of MLV contamination, mice do not have to be a vector.

    Antibody based tests, including immunohistochemistry, have a different problem. They are subject to cross-reactivity. Antibodies typically react to epitopes, small amino acid sequences with a particular configuration. Because these sequences are so small, many different proteins may have the same sequence present. This is why we can get cross-reactivity. These proteins need to be isolated and sequenced in full in order to determine what they are.

    Isolation and sequencing of proteins is essential for immunological techniques to be robust. If something binds to your antibodies, it is always possible to use standard techniques to isolate the protein, after which it can be sequenced. If the sequence is a match for a known virus, or family of viruses, you have evidence for that virus, although there is always risk that another virus will have the same protein.

    So contamination claims could explain the XMRV findings, but this is much more likely to be contamination from real XMRV than from mouse DNA, if for no other reason than mouse contamination is routinely tested for. I find this extremely unlikely, as the claim is that different strains are being detected - and contamination would most likely be from one single strain in any particular lab. I wont bother discussing the control issue again, as it has already been discussed at length.

    Multiple contamination sources are the only way to explain this, although if the source is live, such as a person, they could easily carry multiple strains. Multiple sources will however make it easier to find the source, which makes me suspicious of this hypothesis.

    Cross-reactivity could be due to proteins with similar amino acid sequences. It is always possible to isolate these proteins, but I am not sufficienty up to date to discuss the quantities necessary for sequencing. We need sequencing to be sure of the identity of the protein, but there might be difficulty in obtaining enough of any one protein to be able to sequence it. Alternatively this could be a gap in study design due to lack of resources, which includes funding and lab time.

    These are all technical issues that can be resolved. It takes time, funding and will to do so. How many labs researching ME/CFS have adequate funding or other resources? I have a strong suspicion that the primary problem we are experiencing with the science is not the science, as this is a tough area of research, but the almost total lack of political will and funding. Its hard to do good science on a shoestring budget.

    Bye
    Alex

    PS Doh, I forgot to get to a major point of this post. Singh has mostly found XMRV in prostate and other cancers using immunohistological techniques. She is finding something, but it might not be from XMRV. Does anyone recall it has been published that these proteins have been definitively identified as XMRV proteins? If the technology is effective at isolating and sequencing XMRV proteins in prostate tissue, there is no technical reason, provided we pick the right tissues, that this can't be done in ME/CFS.
  10. eric_s

    eric_s Senior Member

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    Since post #103 people have started to sound a bit as if XMRV was dead. I don't think it's time to think that.

    Let's wait if Dr. Singh will really abandon her conclusion about XMRV in prostate cancer. The same for Switzer. And even in this case there would still be Silverman and Klein. Plus Alter/Lo and the WPI. This is not over.

    Once again, she did not find XMRV in 305 samples, 200 of them from healthy controls. In her prostate cancer work, she found it in 4% of healthy controls. Unless XMRV only exists regionally and she herself has said in her video that she does not think this is possible, either this one or the prostate cancer study must be wrong, unless i'm really missing something here.
    I'm certain she will want to be very sure it's really like that before she's going to say she was all wrong about her prostate cancer findings.
  11. liquid sky

    liquid sky Senior Member

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    I am waiting to hear from WPI and Lo/Alter as to whether they consider this to be a true replication study of their work. It will be very interesting to hear their take on the situation. They know exactly what techniques they used and whether this study followed them properly.

    Anyone read of a response from either of the 2 previous study participants?
  12. ixchelkali

    ixchelkali Senior Member

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    I went looking for the facts on this one, and found it in the response (by Judy Mikovits and Frank Ruscetti) to the comments on the original Science paper.
    http://www.sciencemag.org/content/328/5980/825.4.full

    So I don't know which studies they were referring to when they said "generally not blinded," but the original WPI/NCI study was blinded.
  13. Snow Leopard

    Snow Leopard Senior Member

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    A recent study by Schutzer et al. found it's not in spinal fluid either. And that study actually used VIPDx as a testing laboratory, so...
  14. Daffodil

    Daffodil Senior Member

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    snow.....i think schutzer only used 2 samples though...? and the virus is in brain tissue..not so much in spinal fluid, dr. mikovits said in the recent meeting.

    i emailed the alberta researcher, who said they are still "Trying" to find it. maybe they wont find it either.

    i DID put all my eggs into this basket..i have no time for another basket to come along!!!
  15. Snow Leopard

    Snow Leopard Senior Member

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    The Schutzer study clearly had a limited budget, hence the use of VIPDx in the first place. They pooled the fluid of 43 patients into two samples (which were tested by VIPDx - PCR and culture tests), they also tested 10 samples individually.
  16. ixchelkali

    ixchelkali Senior Member

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    It seems that Dr Singh found that not to be the case:
  17. August59

    August59 Daughters High School Graduation

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    Has Dr. Singh given any indication of her "autopsy" study that she worked on for most of last year. It was rumored to be complete back at the end of December and she was running into resistance getting it published. Just curious of that studies status?

    My opinion of things right now are "If it is not XMRV, then what is it?". Contamination cannot explain all of the "positive" findings and if some of the positives were cross reactivity with "like" viruses (or pathogens) then which ones?

    If you can't find a virus then would science please tell me what is causing my malfunctioning immune system? Endocrine system? Nervous system? Limbic system (I'm sure this is part of one of the others, but what the heck). I'm not pushing for a virus to be responsible for all and I honestly do not think a virus is the only culprit. I think what has hurt the research towards ME/CFS is that is has always been about finding a "single" cause for the illness. It's not going to happen!
  18. In Vitro Infidelium

    In Vitro Infidelium Guest

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    That is a very important observation and we need to understand that many of those who favoured the 'XMRV' hypothesis increasingly leaned toward a "XMRV = real M.E", and anyone not fitting that category was consigned to a "they have some other illness, not our problem" status. M.E/CFS is a labelling of 'illness of common symptoms' and the chances that it is not highly heterogenous in causation is vanishingly small.

    Most medical research ends in a dead end and it is a bad strategy to overly indentify the campaign for aetiology/treatment/cure of M.E/CFS with a single line of research because the probability is that, that particular research will lead no where useful; in consequence that 'failure' then attaches to the image of what we are campaigning for. It is important not to see those researchers who come up with answers that we do not like as 'the enemy' and those researchers who produce promising results as being on 'our side' - we have to plan for the long haul and there's every possiblity that the researcher who comes up with a negative today, will in the future be the one to discover a key piece of the puzzle, and it is just as likely that the researcher who appears to offer the 'grand solution' today, will prove to have only a handfull of miscalculated data tommorrow.

    Of course it's hard to be dispationate about hopes for research 'success', but treating every 'promising' result with religous fervour only makes us appear crazy. We have to be smart if we are going optimise research amd medical establishment interest in M.E/CFS and our collective expressed response to XMRV has been anything but smart. The question now for the future of M.E/CFS research may not be what the scientists choose, but what M.E/CFS affected people choose to learn from the XMRV experience. My hope is that those who have until now either been intimidated by the scientific language of the debate, or put off by the passion of 'the believers' will add their 'quiet' voices to the discourse.

    IVI
  19. Daffodil

    Daffodil Senior Member

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    whenever dr. mikovits is asked about the XMRV debate, she says that the politics will die down shortly, implying that there is a huge positive study about to be released....but where is it? i dont understand.
  20. heapsreal

    heapsreal iherb 10% discount code OPA989,

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    is it true that singh has been threatened to lose her funding for cancer research because of her cfs research????

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