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Addenda to the Science paper

Discussion in 'XMRV Research and Replication Studies' started by V99, Jun 4, 2010.

  1. V99

    V99 *****

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    Don't think this has been posted?

    http://www.landesbioscience.com/journals/40/article/12486/

     
  2. Megan

    Megan Senior Member

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  3. dannybex

    dannybex Senior Member

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    I posted this on the other thread...but am puzzled:

    How did the 67% reported in the original paper turn into 75% in this addendum?

    I don't get it...but my brain isn't working and am certainly no scientist.

    ???

    "In that study, we used a combination of biological amplification and molecular enhancement techniques to detect XMRV in more than 75% of 101 patients with chronic fatigue syndrome (CFS)."
     
  4. V99

    V99 *****

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    They say they used a combination of
    and that

     
  5. V99

    V99 *****

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    This is from the science paper:
     
  6. ixchelkali

    ixchelkali Senior Member

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    NCI used CDC's Assay!

    So maybe that's why Bill Switzer is giving the presentation on developing XMRV assays at the XMRV conference in September.


     
  7. SOC

    SOC Senior Member

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    And yet Switzer didn't find XMRV in any samples in the latest Retrovirology paper? Not even a background amount in the control group? Was the sample size too small to find 2-4% infection in the general population?

    NCI? This is Ruscetti we're talking about -- who used Switzer's assay?
     
  8. usedtobeperkytina

    usedtobeperkytina Senior Member

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    See Susan Vernon's response.

    Tina
     
  9. firefly

    firefly

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    Anyone a Harry Potter fan? It's starting to look like the loyalties, alliances, institutional maneuverings, CYA countermeasures ecc. are all going to turn out to be far more complex than a linear CDC versus NCI/FDA/WPI confrontation. Perhaps Switzer=Snape. That could be kind of fun.
     
  10. cfssufferer

    cfssufferer

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    I may have overlooked something but I think they only used Switzer's assay to rule out contamination. All of the cell lines and 101 patient materials tested negative for mouse contamination.
     
  11. SOC

    SOC Senior Member

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    Ah, thank you. That probably explains it. :)
     
  12. George

    George waitin' fer rabbits

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    (big grins) yeah Snape turned out to be a major player and more or less a good guy. But man I love to hate him!

    I noticed this statement. Does anybody see anything or know of anything about "Highly Viremic" aspect of this?

    also
    But not released for pre publish till July 4th and not e-published till July 29th and it looks like this is for the Sept/October print edition. Man, I hope PNAS doesn't do this with the Alter Paper.
     
  13. ixchelkali

    ixchelkali Senior Member

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    That's right. And somehow I don't find that reassuring. Um, "We know we didn't have contamination, because we checked for it using an assay from the guys who can't find XMRV even when it's there." What's wrong with this picture?

    I'm sure the science gurus would reassure us that it's much more complex than that and we shouldn't worry our pretty little heads.
     
  14. Megan

    Megan Senior Member

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    Tina, what response?
     
  15. Megan

    Megan Senior Member

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    Judy talked about using this assay in her webinar in January, so that was a long time ago, and this paper has obviously been written a while back, so both would have happenned well before the release of the CDC results.
     
  16. George

    George waitin' fer rabbits

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    A nice Summary of the problems from the other papers

    This paper was written in Feb of 10 and revised for publishing in May. When was the CDC paper written does someone have the date handy?
     
  17. Hope123

    Hope123 Senior Member

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    Tina is correct. I have somewhere in my notes that Dr. Mikovits mentioned that "Bill Switzer" helped eliminate the idea of contamination in their studies. If I understand right, it's not just about finding XMRV but finding subtypes of MLVs commonly known to be contaminants in labs.
     
  18. George

    George waitin' fer rabbits

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    Exactly! So this quote

    Means that Switzer et al turned around and stabbed everybody in the back when they published the CDC study. It was not only Dr. Alter and Dr. Lo who were "surprised" by both the results of the paper as well as the "lie to your face" factor here. WTF mates????
     
  19. acer2000

    acer2000 Senior Member

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    I read through the PDF posted earlier in the thread and came away with both more knowledge about how they did the experiments in the Oct 2009 Science study and also with more questions.

    1) It was nice that they listed all 101 patients in a table along with the testing methodologies they used and the results. But why didn't they test all of the samples using all of the methodologies? That doesn't make any sense to me. Maybe they tested them in a stepwise fashion, using the least sensitive/easiest assays first, and only moving on to the more sensitive ones if the samples were negative from the first tests. Is this the case?

    2) Also, is there a similar table for the controls? Did they test all of the controls using all of the methods? Did they test them in a stepwise fashion, using the least sensitive methods first, and then only proceeding to the others if the samples were negative? ie. did they just do PCR on the controls, or did they do cultures and "stimulate" the cells before PCR as they did with the non-controls? I am assuming they did, since to be a real "controlled" study you have to use the same methodology on both the cases and controls. Anyone know more details?

    3) Finally, although they tested the prostate cancer cell lines for evidence of mouse cell contamination:

    Did they assay the LNCaP cell lines for MLV or XMRV contamination (not just mouse cells) before they used them in experiments? Is it even possible that MLV could be growing in a cell line independent of mouse tissue? Is it possible that those lines were not contaminated with mouse cells or MLV, but may have had human XMRV already growing in them "from the factory"? (They are *prostate cancer* lines - a cell type supposedly associated with XMRV). It seems that every culture would be positive in that case, even in the controls, but since we don't know what tests they did on the controls, its hard to say. And there was a single sample in that table that was cDNA nested PCR positive but not positive by culture. Which would re-affirm that the cell line didn't already have XMRV in it before the experiment. But then you'd think if the blood was positive via PCR, for sure it would culture positive? Kind of confusing.

    [EDIT: Maybe line 7 in Table 2 shows the LNCaP cell line testing negative via PCR, indicating that the LNCaP line itself was free of human XMRV before it was used in culture experiments? Is that what this means?]

    Perhaps some others can take a look at this addendum and let me know if they addressed this stuff. Its entirely possible that I am just misreading it. But those were the questions I came up with.


    Thoughts?
     
  20. V99

    V99 *****

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    I believe they said they could not do every test because of time constraints and money.
     

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