1. Patients launch $1.27 million crowdfunding campaign for ME/CFS gut microbiome study.
    Check out the website, Facebook and Twitter. Join in donate and spread the word!
Ergonomics and ME/CFS: Have You Hurt Yourself Without Knowing It?
Having a chronic illness like ME/CFS can make it hard to avoid problems that come from bad ergonomics. Jody Smith has learned some lessons the hard way ...
Discuss the article on the Forums.

XMRV and Culturing, HERV's and more

Discussion in 'XMRV Research and Replication Studies' started by kurt, Mar 23, 2010.

  1. ukxmrv

    ukxmrv Senior Member

    Messages:
    3,442
    Likes:
    1,940
    London

    I am glad that you brought up the scandelous waste of money by the teams using their own methods for finding XMRV. If there had been one step missed out by WIP and if the WPI had not been willing to share information, then you would have been right.

    However, the facts do not support this argument.

    The wastage of respources is important to every patient. The money needs to be in the right hands and not in the hands of teams who designed studies that were not even attempts to replicate the WPI finding from the very start.

    The labs who attempted to find XMRV did not follow the protocol in even the most basic way. They did not use a similar cohort, they did not use the same methods as per the Science paper and they included researchers who may have a vested interest in a negative coutcome.

    They wasted precious funding in a series of repeat errors.

    Is it a conspiracy or just plain incompetence. I don't know.

    We are sick not stupid.
  2. Gerwyn

    Gerwyn Guest

    I dont know who told you that the importance of amplification varies with the sensitivity of the test "proper" extraction of DNA whatever on earth that means is irrelevant .Amplification is paramount


    You would have to extract the RNA from the pMBCs and make copy DNA.Once again you cant detect a latent virus using PCR no matter how sensitive--I know facts can spoil an argument
    FOR PCR TO WORK YOU NEED REPLICATING VIRUS.If you look for a non replicating virus in blood you will never find it with PCR

    Nothing to do with Herv read study

    You need replicating virus for PCR no matter how sensitive the test lok in the blood for as long as you like It is time wasted


    No one but a complete idiot would try to figure out if a test worked.A scientist would calibrate the test first against a known positive. It has nothing to do with tinking it is effective enough not for a scientist anyway
    It is nothing to do with mathematics basic or otherwise oh and by the way they got the sample volume wrong anyway good maths eh!

    Amplifying positive laced controls is childs play It does not mean the test worked

    Why do they want more information when they could not be bothered to use the information in the study read said study

    If they did not want to waste money they should have followed the instructions Simple really is it not
  3. Cort

    Cort Phoenix Rising Founder

    Messages:
    7,025
    Likes:
    439
    Raleigh, NC
    This still seems innocuous to me. Are you saying that XMRV can only be picked up when its replicating? Aren't lymphoid cells in the blood? IF they didn't concentrate the lymphoid cells and then look for XMRV couldn't they make up for this by using a more sensitive technique?

    Sure the review went fast and that looks suspicious but that doesn't mean the paper itself is bad - the fast review doesn't necessarily mean anything about the study - it simply suggests something about the Journal. The paper stands on its own. Sure in a quick review they could have missed something..the question is did they?

    I don't get your conclusion that the patients had no symptoms like the WPI cohort or even the lab tests. Most of the abnormalities reported by WPI (RNase L, cytokine upregulation....) are not necessarily signs of a specific illness - they are simply abnormalities. Saying that any abnormal lab test will get you disqualified from a study is going way, way too far in my view. They would have to disqualify everyone who has low cortisol, for instance, and they've done study after study on low cortisol patients. That group found evidence of cytokine activation in one of their studies. Does that mean they can never test those patients again? That interpretation is far too reaching for me.

    Again, my question which no one has answered or rather you have not answered :) - is there any evidence in the Science paper that WPI researchers activated cells prior to testing them for PCR. I don't see any?
  4. dannybex

    dannybex Senior Member

    Messages:
    2,176
    Likes:
    518
    Seattle
    I'm not certain of course, but I think this may be part of what Kurt's referring to -- from the Prohealth webinar/interview with Dr. Mikovits:

    "Question: Im confused about something. You say you cant find it very easily by PCR, so you are culturing it. Then how did you find it for the Science paper?

    Judy: Well, because I found it in 67%, by PCR, of the patients, but I looked several times, at any given time. I just said it's like an EEG. So I got lucky and found it when the patient was high. Theyll come to the doctor when theyre sick which might mean theyre replicating more WBCs and theres more virus in their WBCs.

    Question: So you checked these patients multiple times over time?

    Judy: No, I did them all at the same time because they were in the repository. So we collected those samples multiple times over time.

    Question: So you took like 10 samples from one patient?

    Judy: No, usually it was four. A Poisson distribution, the copy number could be as low as 5 or 10 copies per mil of blood, so theres a statistic called Poisson distribution, you might find it one out of three times so we went more than one and in most people we found it.

    Question: So the UK paper had studied patients. If they would have looked at 4 or 5 per patient, do you think they might have found it?

    Judy: They might have certainly found more, yeah."


    Correct me if I'm wrong, but it's my foggy-brained recollection that the need to collect or test at least four samples in order to come up with a positive, was not reported in the Science study.

    Is that a critical piece of information that wasn't in the original study?

    ???
  5. Cort

    Cort Phoenix Rising Founder

    Messages:
    7,025
    Likes:
    439
    Raleigh, NC
    That was not in the original study. If they did need to activate/culture cells in order to find the virus and didn't mention it that would be a spectacular 'boner' and I just can't imagine that that would happen. I assume that every author of the paper - looked at it closely - and as we know these were no lightweights - some of them had long resumes - I can't imagine they would have missed that. The best explanation for me is that they didn't do it.
  6. Esther12

    Esther12 Senior Member

    Messages:
    5,259
    Likes:
    5,436
    re studying multiple samples: Could this have just been left unclear if the Science paper talked about 'patient samples' (plural) but made no specific mention of taking multiple samples from the same patient?

    I remember at the time hearing that Science were apparently uninterested in publishing lots of additional details with this paper. I can't remember where I read that though, and it sounds a bit strange now I repeat it.
  7. julius

    julius Watchoo lookin' at?

    Messages:
    785
    Likes:
    5
    Canada
    Does anyone remember, and I think it was in the same interview, when Dr M said that there were many more details they wanted to give, but science edited them down? And I'm not talking about wanting them to not mention CFS, I mean technical details.
  8. kurt

    kurt Senior Member

    Messages:
    1,132
    Likes:
    176
    USA.Earth
    Correct, the sequencing would distinguish the type of antigen very well. However, the lab where the sequencing study was probably sent (Silverman's) had previously conducted extensive studies on that exact same XMRV antigen. So if there was a false result, contamination is one possible explanation for the sequencing study.

    Each test in the Science article has to be evaluated separately, if the study failed there would have to be an explanation for every part. But there could be multiple problems involved. MuLV cross-reaction for antibody, culture and antigen studies, contamination perhaps for sequencing study. I don't know of an alternate explanation for the PCR, but false positives can have many different explanations.

    The purpose of external validation studies is to sort through all this, and verify that WPI found what they said they found, using alternate test designs where possible (which strengthens the case). So far all we have seen is a few PCR tests that could not find XMRV, and one antibody test that appeared to find something else in controls. So jury is still out.
  9. Gerwyn

    Gerwyn Guest

  10. kurt

    kurt Senior Member

    Messages:
    1,132
    Likes:
    176
    USA.Earth
    A technical note for Gerwyn and others. For the record, to include a quote in your post, you must have both the quote start at the beginning (that is the word 'Quote' in brackets [] which may include the person's name you are quoting but that is optional) and quote end statements (that is the word '/Quote' also in brackets []) at the end of the quote. That can be just written in the regular message text.

    This would be helpful because otherwise it is hard to know where the quote ends and your comments start.
  11. Gerwyn

    Gerwyn Guest

    origially posted by Kurt

    when are alternate test designs possible? How does using an unproven assay method strenghen any case?
    if you want to validate a test you cant use a different test
    Everyone in the field of retrovirology including Groom and McClure accepts that the WPI isolated XMRV---Are you really suggesting otherwise .Are you putting your lay opinion ahead of theirs?

  12. julius

    julius Watchoo lookin' at?

    Messages:
    785
    Likes:
    5
    Canada
    The XMRV that WPI was looking at is said to be different from the prostate one Lombardi was studying. Could someone here have a look at the two complete genomes (if Lombardi did one?) and see if they are the same or different?
  13. natasa778

    natasa778 Senior Member

    Messages:
    1,409
    Likes:
    1,208
    London UK
    Re the need to collect multiple samples (at different times) in order to 'hit' on the active period of the virus... that was exactly what was suggested should be done/considered in Q&A session following abbots diagnostics guy CROIT presentation - they were puzzled as they were getting so few positives through antibody tests (just developed xmrv-specific antibodies). Although they were looking at healthy blood donors they only got about 4-5 clear positives if I remember correctly out of hundreds of samples (was it 800 or something like that?).

    Then someone suggested it would be interesting to retest the same cohort at different times to check if this could be down to viral activity phases....
  14. Knackered

    Knackered Guest

    Post deleted by moderator - insulting to another forum member.
  15. julius

    julius Watchoo lookin' at?

    Messages:
    785
    Likes:
    5
    Canada
    And it's always great to read your insightful, intelligent posts as well knackered.
  16. Knackered

    Knackered Guest

    It's just a bit of fun.
  17. Jody

    Jody Senior Member

    Messages:
    4,048
    Likes:
    534
    Canada
    No Knackered, it's not fun and it's not going to be tolerated.

    No more of these types of posts please.
  18. Gerwyn

    Gerwyn Guest

    98.6% similarity
  19. Knackered

    Knackered Guest

    It's not a barrel of laughs having this illness either Jody as you know. Being berated by seemingly vitriolic posts about the only valid cause about my illness I've ever heard isn't much fun either.

    I appologise, but it's just a joke, no harm intended.
  20. julius

    julius Watchoo lookin' at?

    Messages:
    785
    Likes:
    5
    Canada
    Yeah, so if one of you sciency guys could take a look at the complete sequence the WPI did, and compare it with a complete sequence by Lombardi (if he did one), we could see whether it is a contamination issue.

    And before anybody jumps on me, I know that there wasn't contamination in the WPI lab, but there is the possibility of it in Lombardi's.

See more popular forum discussions.

Share This Page