Discussion in 'XMRV Research and Replication Studies' started by omerbasket, Sep 25, 2011.
I wasn't aware of that either Sam... Have you got a link for any info on that please?
I don't understand much of it at the moment Daffodil.
But they are specifically saying that the VP62 strain of XMRV is a result of contamination, not the other XMRV/PMRV/HGRV sequences.
The reason VP62 got into the samples is because they were using it as a positive control.
And a coupla teasers -- look for, respectively, "unwilling to provide their data for examination" and "highly viremic":
Here's a quote for other people:
Sam, how do you think the "highly viremic" paragraph applies to the partial retraction, if you don't mind sharing your thoughts?
The argument I want to advance, Bob, is really a probabilistic one [ETA this is my pompous way of saying "this looks kinda likely to me" ]:
-- in the 2010 paper Judy says that the samples she sent to Silverman for confirmation came from patients with "persistent viremia" and that it was possible to detect XMRV in them using only single round PCR without culturing ie. as far as she was concerned these were bona-fide, barn-door-obvious positives
-- Silverman took extraordinary steps to avoid contamination [see the partial retraction] and treated all samples identically but (eventually) found VP62 plasmid contamination and, amazingly, it was only in the patient samples, not the controls!
So what is more likely, that Silveman managed to selectively and exclusively contaminate patient samples or that the samples were contaminated on arrival (remember: persistent viremia == lots of testing, retesting, sample handling) ?
If you listen to the last TWiV you'll hear Racaniello and guests discussing this and it's pretty clear where they think the problem is.
I see your point Sam.
So do we know if the WPI had the VP62 clone in their lab?
I think so, Bob.
False Positive Jon Cohen and Martin Enserink:
She soon enlisted Ruscetti, who had worked in Gallo?s lab when it
discovered HTLV-I, to screen blood samples from Peterson?s patients
for viruses. Intrigued by the RNase L link to XMRV, Mikovits and
Lombardi -- who by then had joined WPI as well -- met Silverman in
October 2007 at a prostate cancer conference in Lake Tahoe, where
they discussed the possible role of XMRV in CFS. Silverman was
happy to collaborate and sent WPI a clone of the virus, known as VP62.
The institute could use it as a reference to start hunting for the virus in
CFS patient blood samples that Peterson had stored.
From page 8 of the supporting online materials for Lombardi 2009:
Lysates were prepared from XMRV-VP62-infected Raji (lane 1), LNCaP (lane 2) or Sup-T1 (lane 3).
That looks like a definite 'yes' then, doesn't it!
Just to add to Sam's comments. Jon Cohen has been bugged by those claiming WPI never had VP62 in their lab. In the comments beneath his last article here:
You will see that he repeats the claim, and then engages further more recently:
'We're going around in circles here. We never stated that VP62 contaminated samples at WPI. Whether WPI had VP62 is a separate question, and, as I have detailed, both Mikovits and Silverman say the institute had it. I'm uncertain why you continue to insist otherwise, and this is my last reply on this question.'
He also points to the retraction paper and how in the supporting online material:
'it states in reference to Silverman's group at Cleveland Clinic: "In particular, neither plasmid XMRV VP62/pcDNA3.1(-) nor XMRV PCR products were ever taken into the clean room."'
He further adds:
'I also refer you to figure 3 in the original supplementary material for Lombardi et al., which adds more details about the use of VP62 for serology tests.'
So with the Cleveland Clinic saying that the contamination came from outside their lab, and WPI seemingly using VP62 or at least having it (contrary to some peoples claims), as well as the lengths that Silverman went to in order that his 'clean room' was kept isolated and well 'clean' for any samples stored there... one can perhaps see how claims are now being made that the samples sent from WPI were contaminated.
Whether or not any such claims are 'true' I don't really know.
Jon Cohen seems like a decent guy, or at least, he's dealing in a respectful way with some frustrating comments. It looks like he's willing to do some work and research to respond to them properly. He also passed out his e-mail address on twitter so that a patient could talk things through in more detail - I think that sort of willingness to engage in a real discussion is something to be respected.
It seemed like he was only interested in the XMRV stuff at the CFS conference though, rather than having any interest in CFS generally, and the problems that surround it, which is a bit of a disappointment.
The WPI has already sent their samples to an independent laboratory and has them checked out. No sign of contamination from VP62.
So they are ahead of the gossip and innuendo here.
I think we're just discussing the possibilities here ukxmrv.
One of the articles says that the WPI wouldn't hand over their data, whereas Silverman was totally transparent.
I wish the WPI would be a bit more transparent, but I understand that there might be many reasons why they aren't.
Even if the WPI's lab was contaminated with VP62, it wouldn't explain them finding other HGRV sequences (e.g. PMRV), so it doesn't really answer any questions for us anyway.
Yes sorry. Have been logged in here and wasn't actually sat at the computer.
I did read that Bob. Hang on will try to find it...
That was quick!
'Bradford, Sciences executive editor, tells Retraction Watch that two of those authors, Robert Silverman and Jaydip Das Gupta of the Cleveland Clinic:
determined that the experimental results contributed by them to the Lombardi, et al. paper were the result of contamination, and they requested that we retract those parts of the paper. While we were aware that other co-authors had tested samples and claimed to not find evidence of plasmid contamination, those co-authors were unwilling to provide their data for examination so we were unable to comment on the validity of the other experiments. Since all of the other co-authors agreed with Silvermans conclusion that his samples were contaminated, we felt it was in the best interest of our readers and the CFS community to publish this information and to label the notice to make it clear that part of the original paper was not valid.'
I think that's what you mean Bob. Though I guess one could argue it doesn't refer to the Independent Laboratory.
Silverman's claim he had a clean room is no more guarantee than WPI saying they had a clean room. If you doubt WPI claims, you must also doubt Silverman's claims. Since Silverman had much more contact with VP62, I know where I would be putting my money.
Am trying to catch-up on all the reading as well Bob. This might be of interest. Haven't read it myself yet but extracts have been posted elsewhere:
Supporting Online Material for Partial Retraction to Detection of an Infectious Retrovirus, XMRV, in Blood Cells of Patients with Chronic Fatigue Syndrome
Vincent C. Lombardi, Francis W. Ruscetti, Jaydip Das Gupta, Max A. Pfost, Kathryn S. Hagen, Daniel L. Peterson, Sandra K. Ruscetti, Rachel K. Bagni, Cari Petrow-Sadowski, Bert Gold, Michael Dean, Robert H. Silverman,* Judy A. Mikovits
View attachment science.1213841.full.pdf
Yes, that's what I was refering to.
Yes, that explains Silverman's work.
Good luck to anyone reading it! Expect a headache for 24 hours afterwards!
ah thank you!
so that's what folk reffered to
I only read what I can read. It does show the lengths Silverman went to in order to preserve the samples sent to him by WPI for the Lombardi paper. But where and how those samples came to be contaminated remains the question doesn't it? (Well one of many I suppose).
I do wish the WPI were more 'open'. I mean if an independent lab had screened those samples why not release the data? It also seems strange that Science never asked for that information at the time (or later).
I've just read through the BWG published paper. (I've only read it once, so I can't remember it all, and I haven't got to grips with all of it yet.)
And I have to say that this is the first time that I've thought that XMRV research looks like it's not going anywhere.
Of course the results are not absolutely conclusive, but there are striking multiple reasons why this research shows XMRV testing to be weak.
Many of the arguments that I have previously used to say that the study could be ignored, do not stand up after reading the paper.
The only argument that I can see really remains is that the collection and preparation of the samples were done in such as way as to not preserve the viruses (i don't recall seeing any info in the paper with regards to that part of the methodology.), but even this looks like a weak argument when some of the other aspects of the study are taken into account.
After reading it, I'm not surprised that the VIPdx have withdrawn their testing, based on the following conclusion in the paper:
"Based on these findings, we conclude that currently
available XMRV/P-MLV assays, including the assays
employed by the three participating laboratories that
previously reported positive results on samples from CFS
patients and controls (2, 4), cannot reproducibly detect direct
virus markers (RNA, DNA, or culture) or specific antibodies
in blood samples from subjects previously characterized as
XMRV/P-MLV positive (all but one with a diagnosis of CFS)
or healthy blood donors."
However, the conclusion of the paper was slightly more nuanced than I had been led to believe:
"However, we cannot definitively
exclude the possibility that the levels of XMRV/P-MLV
markers in blood may be at or below the limit of detection of
all assays and/or fluctuate over time as recently described in
experimentally infected macaque studies (22)."
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