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The Fight is on...Imperial College XMRV Study

Messages
13,774
WPI official statement in up on their website

http://www.wpinstitute.org/news/docs/WPI_Erlwein_010610.pdf

Official Statement from the Whittemore Peterson Institute Regarding UK Study

The Whittemore Peterson Institute (WPI) has reviewed the paper entitled Failure to Detect the
Novel Retrovirus XMRV in Chronic Fatigue Syndrome. This study did not duplicate the
rigorous scientific techniques used by WPI, the National Cancer Institute and the Cleveland
Clinic, therefore it cannot be considered a replication study nor can the results claim to be
anything other than a failure not just to detect XMRV, but also a failure to suggest meaningful
results.

The scientific methods used by WPI are very exact and require specific techniques to ensure
accuracy. Differences in techniques employed by Erlwein et al. not only explain their failure to
replicate the WPI study, but also render the conclusions meaningless. These differences
include, but are not limited to the following:

1) blood sample volumes and processing;
2) patient criteria/population differences;
3) number and type of tests done to assure accurate results, including white blood cell
culture;
4) use of a molecular plasmid control in water versus a positive blood sample; and
5) different primer sequences and amplification protocol used to find the virus, which
were not validated by a clinical control.


The WPI study was published after six months of rigorous review and three independent lab
confirmations, proving that contamination had not taken place and that infectious XMRV was
present in 67 percent of CFS patients diagnosed according to the Canadian and Fukuda criteria.
In contrast, this latest study was published online after only three days of review. Significant
and critical questions remain as to the status of patient samples used in the UK study as those
samples may have been confused with fatigued psychiatric patients, since the UK has relegated
CFS patients to psychiatric care and not traditional medical practices.


Little is known about the prevalence of XMRV world-wide, much less the incidence of XMRV
in ME/CFS or prostate cancer emphasizes Dr. Judy Mikovits. WPI and its NCI collaborators
are actively engaged with international research teams to investigate these important questions.
WPI does not recommend the use of anti-retroviral drugs that have yet to be proven to be
effective in treating XMRV infection. However, several large pharmaceutical companies have
expressed interest in developing anti-retroviral and immune modulating drugs that will
effectively treat XMRV associated diseases.

WPI looks forward to the results of other scientific groups around the world, serious about
replicating its scientific results, by using the same techniques as WPI and its collaborators. The
fact that XMRV was detected in 67 percent of the CFS samples in the U.S. study determined a
significant association between XMRV and CFS, demanding a much more serious inquiry by
responsible health agencies around the world as to the cause of this debilitating disease.


Whittemore Peterson Institute
The Whittemore Peterson Institute for Neuro-Immune Disease exists to bring discovery, knowledge,
and effective treatments to patients with illnesses that are caused by acquired dysregulation of the
immune system and the nervous system, often results in lifelong disease and disability. The WPI is
the first institute in the world dedicated to X associated neuro-immune disease (XAND), and other X
associated diseases, integrating patient treatment, basic and clinical research and medical
education.

Sorry - pasting it lost all the formatting. Have put in some paragraph breaks now.

Quoted because no-one else has commented on this in twenty whole minutes - and I think it's the most interesting thing posted in this thread for some time. What a statement. I want more replication studies!! Surely the WPI wouldn't make a statement like this unless they were getting good news from the people they were working with? But it sounded like the Wessely lot had heard negative things from other replication studies? Maybe it's a bluff from the WPI to get a few more months of selling expensive tests before they take the money and run? This is exciting stuff.
 

spit

Senior Member
Messages
129
SPit, see also my prior message to you 20 min ago, a page back or so

Saw it, and am pondering a bit. IF they could get their concentrations of +plasmid to what would be expected in a positive sample relative to other DNA, I don't see a problem. Of course, that's a pretty unweildy IF, given that we have no idea what sorts of viral loads, and in what sorts of cells, we're talking about.

It looks to me like they did make sure they could amplify a single target at some point, but they're not specific on the concentrations used to get the bands we're seeing in their figures. And I'm not very satisfied with those bands. Those 2nd runs aren't great signals for the only known positive.
 
K

Katie

Guest
Just a few words as I'm helping my mum search for a new laptop (her's toasted itself quite literally, fitting due to the tea split into recently) but the WPI response is exactly what that contemptuous study required. As someone in the UK who feels at the bottom on the shoe of the psych-brigade I finally feel like someone is fighting not only for us, but for a fair shot at some decent science. Wessely has been on top of his totem unchallenged by big hitters for too long and the WPI just left him, McClure and their cronies with bloodied noses. If I get time tonight I'm gonna email the BBC with that, it's just bloomin' brilliant.


It's so lovely when someone in authority says what you're thinking. Oooh, the delightful little sideswipes dealt back after McClures clumbsy comments, just beautiful. I can't wait for a serious and legitimate study to come out next, hopefully in a few months when they've had a chance to do it properly. Happy, happy, joy, joy (showing exactly how old I am with that reference ;) )
 

rebecca1995

Apple, anyone?
Messages
380
Location
Northeastern US
It looks to me like they did make sure they could amplify a single target at some point, but they're not specific on the concentrations used to get the bands we're seeing in their figures. And I'm not very satisfied with those bands. Those 2nd runs aren't great signals for the only known positive.

Spit, this is interesting. Are you saying that the Wessely/McClure test seems to be not very sensitive?

We appreciate the input of you, Eric and others! :)
 

spit

Senior Member
Messages
129
Kurt -- I just disagree on several of these points.

I do expect labs to "do their own thing", to a degree. But using totally different tests can give totally different results, because the testing is still squishy. We've had long, long discussions on this forum about testing being squishy still. So it's not terribly helpful to try some new, potentially squishy test as "validation" of the other study, which had multiple kinds of testing to confirm results.

And they didn't just do one different thing, they did a bunch of different things at the same time, including with the cohort. Which means that it's nigh on impossible to say whether the results are different because they are different, or that they're different because of the several different methodological differences. Their results may be accurate, I don't know, and I'm not assuming that they aren't -- but I see quite a few reasons to wonder. To construct the study this way opens it up to that wondering.

Yes, we need other testing. But working out other testing is a different question than "is the original study replicable or not", and combining those is something that should be done very carefully.

It is not the case that getting a positive result on one single control validates an assay. Simply not true. It's a good sign, but it's not as end-of-debate as you're presenting it. Variance exists, and a sample of pure plasmid isn't necessarily going to act the same as a test sample with a bunch of other bits of genome.

Of course no healthy control is necessary if you get no positives. But if you don't know you're going to get no positives, you'd want to have a healthy control, because otherwise you can't do the statistical analysis of much of anything. Maybe they had a control waiting in the wings, who knows. But it's still an odd choice, that's all.
 

Eric Johnson from I&I

Senior Member
Messages
337
IF they could get their concentrations of +plasmid to what would be expected in a positive sample relative to other DNA, I don't see a problem.

Theres no way [ (XMRV copies) / (total amount of DNA ) ] can be the same for the plasmid as it is in the patient samples -- the plasmid is small and has XMRV in every copy. But extracting DNA from blood, I would imagine you would get less than one XMRV genome per human genome. And the human genome is of course extremely huge.

I looked up something on PCR inhibition by excess DNA:

Although it was originally reported that excess DNA does not affect PCR amplification reactions including real-time PCR (32), recent studies have shown that large amounts of double-stranded DNAs can completely suppress the PCR reaction (33, 34).

Found here: http://www.jbc.org/content/276/50/46946.full

It would probably not be the case that this phenomenon would stop an optimal PCR from working. But if a PCR were already non-optimal, perhaps this could push its sensitivity over the edge to where one gets false negs. Thus, I dont agree with Kurt that any + control is a fine + control.

They certainly succeeded in amplifying the beta-globin gene. But it is of course present at a rate of one per human genome. XMRV is probably much less abundant than that -- less than one XMRV genome per white blood cell on average.
 

spit

Senior Member
Messages
129
Spit, this is interesting. Are you saying that the Wessely/McClure test seems to be not very sensitive?

We appreciate the input of you, Eric and others! :)

Well, it depends. I don't know what initial concentration those bands represent. But it does make sensitivity more of a concern for me. I sure wouldn't feel confident in using a signal that weak as my -only- positive reference, but maybe they have reasons to feel more confident about it.

To be clear, I'm no PCR guru, by any stretch, or even really a gel electrophoresis guru.
 

fresh_eyes

happy to be here
Messages
900
Location
mountains of north carolina
Variance exists, and a sample of pure plasmid isn't necessarily going to act the same as a test sample with a bunch of other bits of genome.

In case anybody else - like me - is wondering what a plasmid is, this from ucbiotech.org:

Independent, free-floating circular piece of DNA in a bacterium, capable of making copies of itself in the host cell. Plasmids can be used in recombinant DNA experiments to clone genes from other organisms and make large quantities of their DNA.
 
G

George

Guest
If you haven't read the WPI's response Back up to Esther12 post (really Big Grins)

It's number #377
I have to say the response was impressive. Wessley/McClure took direct swipes at the WPI so I'm not surprised to see the WPI put them firmly in their place.

I think the response was appropriate, considering the snide "discussion" section of the Wessley/McClure paper I think the response was civil.

Significant
and critical questions remain as to the status of patient samples used in the UK study as those
samples may have been confused with fatigued psychiatric patients, since the UK has relegated
“CFS” patients to psychiatric care and not traditional medical practices.
I was a little surprised that they came right out and made the above statement. I mean these guys don't need to get involved in the politics of CFS/ME in another country. Eventually they'll be the winners anyway. But it was really nice to have them say it on behalf of all of the UK patients and well. . .patients everywhere who have been "redefined".
 

Kati

Patient in training
Messages
5,497
Sending a big cheer for WPI and CAA. Thank you both for prompt response. Time will tell.
 

spit

Senior Member
Messages
129
Theres no way [ (XMRV copies) / (total amount of DNA ) ] can be the same for the plasmid as it is in the patient samples -- the plasmid is small and has XMRV in every copy. But extracting DNA from blood, I would imagine you would get less than one XMRV genome per human genome. And the human genome is of course extremely huge.

You're right, of course, I shouldn't have said anything about relative to the total DNA. If [XMRV] itself is about the same regardless of the other constituents of the sample, the primers shouldn't really care about the other stuff much for sensitivity purposes -- that is, if you've got x copies of XMRV in each sample of given volume. It's sort of moot, since we don't even know what to mean by "the same".

Interesting about the inhibition, and yes, that's a place where it might make a difference that you're working with a 1:1 relationship of overall human genome to reference gene vs. a much different ratio of normal human genome to XMRV. I'm not really sure how that pans out in real life, but that theoretically could make sense to me.
 

Eric Johnson from I&I

Senior Member
Messages
337
Honestly, the gels seem ugly. Some of the worst looking data Ive seen. ROund 2 of nested PCR dimmer than round one? Not a lot of sense being made there. I wish I had more pertinent lab experience though. I am not too sure just how aberrant round 1 > round 2 is. So the caveat is that I'm not 100% confident in my assessment.

Also, I aggregated the prevalence data on healthy controls from the three prior studies including Mikovits. This calculation (chi squared, one-tailed fisher exact test) shows that odds are only 0.014 that a sample the size of Wessely's would find zero XMRV+s *even if he were studying healthy normals*. This is assuming, of course, that the virus has the same prevelence in normals in England, and so on.

Of course, it would probably be appropriate to throw out the Mikovits data from the calculation above. After all, thats the study whose veracity is (ultimately) what Wessely's study is about. WHen you do that, the odds go up to 0.127. Not implausible, but more unlikely than likely. Add this to the goofy appearance of the Wessely paper, and it basically amounts to that paper being not worth consideration. Indeed, I am much more disheartened by the rumors coming via McClure, as well as the now de-posted negative informal report fromt he big boys at Koch-Institut, than I am by today's paper in PLoS ONE.
 

Lily

*Believe*
Messages
677
It's number #377
I have to say the response was impressive. Wessley/McClure took direct swipes at the WPI so I'm not surprised to see the WPI put them firmly in their place.

I think the response was appropriate, considering the snide "discussion" section of the Wessley/McClure paper I think the response was civil.

I was a little surprised that they came right out and made the above statement. I mean these guys don't need to get involved in the politics of CFS/ME in another country. Eventually they'll be the winners anyway. But it was really nice to have them say it on behalf of all of the UK patients and well. . .patients everywhere who have been "redefined".

Ya - thanks for putting your 2 cents worth in, George! I had been wanting to repost that because so few people had commented on it, I figured they missed it or that it must be naptime. :victory::sofa::victory:
 

Cort

Phoenix Rising Founder
Feel to post the little Q and a with Dr. McClure. I am really out of depth here with what her answers mean. :)

It was nice to see the WRI state their findings had been replicated by three labs - I wondered if the NCI was in there, I guess it was.

Both groups, the Imperial College and the WPI, are getting a bit too aggressive in their comments for me. Of course there's alot at stake....
 

Holmsey

Senior Member
Messages
286
Location
Scotland, UK
It's number #377
I have to say the response was impressive. Wessley/McClure took direct swipes at the WPI so I'm not surprised to see the WPI put them firmly in their place.

I think the response was appropriate, considering the snide "discussion" section of the Wessley/McClure paper I think the response was civil.

I was a little surprised that they came right out and made the above statement. I mean these guys don't need to get involved in the politics of CFS/ME in another country. Eventually they'll be the winners anyway. But it was really nice to have them say it on behalf of all of the UK patients and well. . .patients everywhere who have been "redefined".

But we'd still need to see something, WPI found 3.75% in their control group, so we'd expect to see something even among fatigued psyc patients, so we're actually saying, the group was wrong and the science was inefective.

Any chance Spit and / or Eric from I & I can ask any of the researchers directly about their concerns, some I'm sure would be answered quite straight forwardly but if others were not we'd maybe get some clues as to whether there's parts of this that they're concerned about.
 

maryb

iherb code TAK122
Messages
3,602
Location
UK
Significantand critical questions remain as to the status of patient samples used in the UK study as those
samples may have been confused with fatigued psychiatric patients, since the UK has relegated
CFS patients to psychiatric care and not traditional medical practices.

I was so depressed this morming at the news of the IC research, I am now overjoyed with the response of WPI, I love it, thank you thank you
 

rebecca1995

Apple, anyone?
Messages
380
Location
Northeastern US
Also, I aggregated the prevalence data on healthy controls from the three prior studies including Mikovits. This calculation (chi squared, one-tailed fisher exact test) shows that odds are only 0.014 that a sample the size of Wessely's would find zero XMRV+s *even if he were studying healthy normals*. This is assuming, of course, that the virus has the same prevelence in normals in England, and so on.

Thanks for posting this, Eric! Those are pretty low odds. I don't have your science background, but my initial layman's response to the Wessely study was, "That's strange. Not even ONE positive? It must not be a very sensitive test!"

Of course, that's the way he wanted it.
 
G

George

Guest
Cort, ya little tired there dude (grins). I think it maybe nap time for all of us.

We had the highest number of people online today at around 1:48 Something like 290 visitors. We be important in this little game.