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Due to the following fact - is contamination even possible?

Discussion in 'XMRV Research and Replication Studies' started by omerbasket, Mar 26, 2011.

  1. Bob

    Bob

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    England, UK
    Thanks omerbasket.

    I assume that the WPI also test their cell lines for contamination from XMRV, before they expose it to XMRV+ patient samples.

    What I don't quite understand is how anyone can test XMRV positive samples for mouse contamination if XMRV is made up from a combination of endogenous mouse viruses. Surely contamination tests would always test positive if XMRV was present, due to the composition of the XMRV DNA/RNA?

    Do you know if 'one other method' includes the sequencing of the PCR product?
  2. omerbasket

    omerbasket Senior Member

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    I know, Bob, and it does not include the sequencing of the PCR product. One other method would probably be antibodies, western blot or other things, probably pretty similar things.

    Regarding the WPI testing their cell lines for XMRV - I think that Dr. Mikovits said so in the last "state of knowledge" conference, and anyway it's almost certain that they do it because it's basic.

    Regarding the test for mouse contamination - what you've said is not correct. The test for mouse contamination looks for MOUSE DNA, as opposed to the retrovirus DNA. If a mouse contaminated a laboratory and therefore caused that laboatory to find a virus (which came from the mouse), it is almost certain that the mouse also left some other stuff there - his DNA. the virus is not the mouse DNA, or at least not his entire DNA. In order to find a contamination by a mouse you seek for something that exist in many many copies in a mouse, but does not exist in things that are not mice. This way, you make almost certain (you can never make such things absolutely certain, but you make it somethings like 99.9% certain, I think) that if there is a mouse contamination there, you would detect it, but also that you wouldn't detect something that exist in things that are not mouse (for example, polytropic MLVs) and mistakely think that it is a proof for mouse contamination. The test the WPI used, and the test that the FDA used (although there are differences between those two tests) relied on mouse mitochondrial DNA, which exists in many many, many many, many many copies in a mouse, so if the mouse left a virus in the lab, he almost certainly also left some copies of his mitochondrial DNA. Coffin used another thing, called intracisternal A-particle, or IAP, which also exists in many many many many copies in a mouse - but Dr. Lo, who used this assay exactly as Coffin asked him to do (and actually used two of these assay - the regular one and the improved one) did not find any evidence for mouse contamination via this assay or via his mtDNA assay - and he also showed that his mtDNA assay is more sensitive and so should find contamination, if it's there, better than Coffin's assay (but that doesn't really matter - because he used his mtDNA assay as well of the two assays "prescribed" by Coffin, and found no evidence of contamination. He also did some other very important things that made the argument that there is no contamination there even stronger).

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