XMRV Buzz - Take a Deep Breath/the Big XMRV Meeting, Singh On XMRV, Sample prep?

[Otis]

I would have had to stifle the urge for a flying tackle (which would have put me in the hopsital) and I didn't mean to imply you messed up, just that a direct answer to those questions would have been very telling.

 

[Cort]

I would have had to stifle the urge for a flying tackle (which would have put me in the hopsital) and I didn't mean to imply you messed up, just that a direct answer to those questions would have been very telling.

I agree! Honestly I just do not understand why I didn't (or anybody else) directly ask that question. Part of it may have been that before his presentation we weren't really thinking about the big C. I did ask Houghton and he did agree that the antibody findings, etc. were pretty compelling and not easy to explain away. This was from somebody who had just given his warning on XMRV. (By the way, because I'm afraid people are going to assume the worst of him - he is very interested in EBV's connection to CFS and is going to push for a trial - he seems very sincere and troubled about the lack of assistance for people with CFS.)

I meant that the onus is being put on the WPI - not that it should be on them; before the emphasis was on the poor nature of the first studies...now there is a bit of a change. I should say that we are really relying on only a few people for our understanding of what the emphasis is right now; Dr. McClure, Dr. Weiss and Dr. LeGrice....They may be representative of the field as a whole or they may not be - they just happen to be the ones that have been public lately.

On the other hand there is Dr. Ruscetti, Dr. Singh, Dr. Alter and Dr. Lipkin. I would point out that the NIH and the NIAID are very cognizant of the arguments pro and con XMRV (the NIH has several representatives in the blood working group) and yet they chose to go forward, at this late date, with a quite expensive study featuring a top pathogen hunter. (I've never seen a $1,000,000 plus one year study for CFS) That doesn't sound like the actions of a group that believes the case on XMRV is closed or nearly closed - that sounds like the actions of a group that believes that all options are open. Lipkin is a major scientist and he does believe pathogens play a role in CFS (and other mysterious disorders).

I don't think you hire a guy like that to prove a negative - you hire somebody like that to genuinely explore what's going on and to make sure you get it right. They could have hired some junior scientist somewhere but instead they hired a major figure. That suggests that the push it under the rug scenario does not apply here.

 

[MarxyGrouch]

Reposting from another thread:

Not only are MuLVs NOT benign, they also tend to cause a disease prgression that is eerily similar to CCC ME/CFS. Too much so to be mere coincidence. Too bad people spouting lazy and unsupported theories of contamination and opportunistic infection are too lazy to actually look at the huge body of research on CCC ME/CFS and the real deficiencies and abnormalities that have been found, and then compare to MuLV research.

Calling all scientists that are not lazy and corrupt please!

 

[alex3619]

Hi, I have another reason why there might be attempts to slow down XMRV research. It is similar to George's cure suggestion. They need a feasible, commercially available, high throughput blood test for XMRV that can detect it reliably in blood. Until they have that, "they" want everything to be doubted (and pick your own "they"). This is because if the finding is "controversial" and "not proven" then they can say that they could not be held responsible for not testing the blood supply, and therefore are not responsible for anybody being infected from tainted blood. Legally, just not having a valid commercially available test may be an insufficient defense, because there are tests and the argument can be made that it was required of every blood bank, hospital and doctor to run those tests - everyone involved could be sued. It could be simple fear of litigation that is the driving force.

Bye
Alex

 

[Cort]

Regarding the blood test issue in general, I agree with the point you're making here Cort, it does make sense to try to detect XMRV in blood given that's what the WPI claimed. And it also makes sense to pursue blood tests because they're cheaper and easier; that's not an irrelevant argument. It's just that the point about tissue reservoirs is valid as well and researchers should rather explore those possibilities than just dismiss the whole thing.

Finally, since we are discussing "contamination" yet again (yawn), it seems relevant to mention that the WPI fully sequenced 2.5 of the XMRV samples they isolated. These sequences were not mouse DNA, nor human DNA, and since they were sequenced I don't really see how there can be much dispute about that: whatever it was that WPI detected in the Lombardi/Science study, it was not mouse DNA contamination. It was XMRV: they sequenced it.

So (along the lines of some posts above in this thread) if there were a contamination issue, it really has to be contamination by XMRV itself, surely? In which case, if this XMRV contamination is so widespread, one has to wonder whether the contamination-theorists think this XMRV that's floating around in labs and/or reagents has the potential to infect humans? I can't really understand how one can accept XMRV is an infectious retrovirus that can infect human cells in vitro and establishes an efficient spreading infection in monkeys, say that XMRV is a widespread contaminant in laboratories, and then dismiss the idea that XMRV is present in CFS patients on the basis of negative studies that can't find any XMRV anywhere.

Yes, good point - it has to be XMRV itself also because they sequenced it and were able to grow it. So we're not talking about a bit of mouse DNA floating through the air here but the intact virus itself which would I think make the contamination arguments much more difficult. I imagine it could be a mouse cell full of viruses - which is why I guess they wanted to see XMRV embedded in the genome in the Alter/Lo paper. Retroviruses do not, I don't think, generally survive well outside of the body - so I guess it would have to be an intact cell from somewhere that had viruses in it.

Which brings to mind Alter/Lo's work at a) sequencing the 'pMLV's' they found and b) isolating the virus. Dr. LeGrice said the first was 'easy' to do; he didn't say how time consuming it was. Hopefully they will report on those two facets soon.

By the way, the Lipkin meeting did take place and mum's apparently the word. I think the fact that the meeting took place means the BWG has finished their assessment of blood storage and contamination (?). THe NHLBI rep at the CFSAC meeting said the news would be released quickly - but nothing yet; the participants were apparently sworn to silence which means ???? God knows.

 

[Cort]

Here's the latest from the Buzz page by the way

The ‘Big’ (Little?) Lipkin Meeting - did occur. It does appear to have been focused on Dr. Lipkin’s study. Why federal, research and advocacy representatives or invited to it is a question whose answer we will presumably get at some point. Since the Lipkin study is using the Blood Working Groups findings we have to assume that they have come to some conclusion about storage/sample preparation/contamination, etc. yet for some reason we’ve heard nothing as the contents of the meeting have apparently been embargoed...which means what? Big news? A really secretive researcher? Is the BWG waiting for the right time (whatever that could be?) Who Knows? The ME/CFS community was promised, however, a quick release to the BWG's findings - and that has not occurred.

Three compelling fundraising video’s from the Whittemore Peterson Institute. Stating “As far as I’m concerned the WPI brought us out off the darkness into the light” Dr. Jamie Deckoff-Jones at times emotionally relates the difference the WPI has made in her and her daughter’s life using treatments based on the WPI’s XMRV findings. Another video features parents of children with a different neurological disease. The last was the most compelling for me; it features a father who used the WPI’s technology to find three viruses in his daughter - who almost overnight was able to speak coherently for the first time using antiviral therapy and goes on talk about the importance of private funding.

Never Easy - The Singh’ Study Proceeds - The Singh/Bateman study appears to have wrapped up but like just about everything else in XMRV the data does not appear to have come easily. Patients were first told to expect results in July/Aug (remember Dr. Bateman’s webinar in which she hoped to be able to present some results?) now it’s November and they’re still waiting.

I really liked that last video from the WPI; it related for me, how effective the WPI can be even without XMRV. They have those great pathogen panels and they apparently used them to great effect to find viruses - the treatment for which apparently turned a young autistic girl's life around. Amazing...

The Singh study apparently has had a hiccup or two along the way - perhaps not surprising with this new pathogen and all the testing Dr. Singh is doing. This is such an exciting study in so many ways...she is replicating part ofthe WPI study, using immunohistochemistry, a PCR technique she says is essentially impervious to contamination, a highly selective batch of patients from Dr. Bateman, some patients who tested positive for XMRV from the WPI, all the blood is treated the same and the patients are from the same area. They'll be able to quickly determine if functionality/severity or onset (I would guess) or several other factors correlates with XMRV positive rate. Exciting stuff.

 

[Cort]

Hi, I have another reason why there might be attempts to slow down XMRV research. It is similar to George's cure suggestion. They need a feasible, commercially available, high throughput blood test for XMRV that can detect it reliably in blood. Until they have that, "they" want everything to be doubted (and pick your own "they").
Alex

I hope this is wrong! because as I remember it takes much longer to produce a viable, effective high throughput test than to produce a clinical test for your doctors office. You could also argue that if they knew it was there and didn't say so publically that could put people at risk from catching xMRV who might not otherwise - if they had known to stay away from infectious people with ME/CFS. There would be legal implications to that as well.

 

[Sean]

I don't think you hire a guy like [Lipkin] to prove a negative - you hire somebody like that to genuinely explore what's going on and to make sure you get it right. They could have hired some junior scientist somewhere but instead they hired a major figure. That suggests that the push it under the rug scenario does not apply here.

Agree with that.

 

[Esther12]

Badly want to know more about the Singh study and what was said at the BWG meeting. This is internet age - info's meant to travel instantly! I'm not used to waiting.

 

[Otis]

The Singh study apparently has had a hiccup or two along the way - perhaps not surprising with this new pathogen and all the testing Dr. Singh is doing. This is such an exciting study in so many ways...she is replicating part of the WPI study, using immunohistochemistry, a PCR technique she says is essentially impervious to contamination, a highly selective batch of patients from Dr. Bateman, some patients who tested positive for XMRV from the WPI, all the blood is treated the same and the patients are from the same area. They'll be able to quickly determine if functionality/severity or onset (I would guess) or several other factors correlates with XMRV positive rate. Exciting stuff.

It would be nice if they have all that data (are they looking at onset type?) but mostly I hope for a rock-solid confirmatory study.

I think it's likely that the review process for a complex study like this is a larger component of the schedule delay. I imagine that even without the specter of Rumor Contamination this would have been tough to get through peer review after what transpired with the Lo/Alter paper.

 

[urbantravels]

I gotta figure that everyone being "sworn to secrecy" means Something Big's Going Down. I.e., I don't think the announcement is going to be "It was all contamination, nothing to see here, move along..."

 

[Cort]

It would be nice if they have all that data (are they looking at onset type?) but mostly I hope for a rock-solid confirmatory study.

I think it's likely that the review process for a complex study like this is a larger component of the schedule delay. I imagine that even without the specter of Rumor Contamination this would have been tough to get through peer review after what transpired with the Lo/Alter paper.

That's exactly what she said. NOW every journal is being very, very careful; multiple reviews, looking under every stone....I'll bet its harder to publish a positive paper now; she said it was harder to publish period because its a controversial subject - I imagine its even harder to publish a positive paper. However, she is a respected researcher - she's got a great study design, her paper very well could illuminate something very important about the disparities in the results - in short, it could be a significant paper - which journals also really want to publish.

 

[Cort]

I gotta figure that everyone being "sworn to secrecy" means Something Big's Going Down. I.e., I don't think the announcement is going to be "It was all contamination, nothing to see here, move along..."

I just don't know. I emailed Holmberg and the other co-chair of the study - and said, you know, you promised us the results-----where are they? We'll see if they answer.

It could be that they are still at sea - they haven't uncovered any sample problems or any contamination or anything - that is a possibility. Wouldn't that be something? Then they would move onto the next phase.

 

[Mark]

I'm finding it pretty hard to think of a reason why the BWG would swear everyone to secrecy and fail to release their findings despite promising to do so as soon as possible...other than the obvious explanation that what they've found out is the hugely significant explanation we're all hoping for (and which most of us, I guess, are expecting).

If their results were inconclusive so far then I can't see any reason why that would require secrecy, nor the calling of a big meeting like this. So you have to figure they have found something out. I guess if they want to wait until they're 100% confirmed before going public, or if they're about to publish something, that would make sense.

If their findings were negative - i.e. identifying a source of contamination - then I suppose they might want to demonstrate or prove that before going public with the explanation, especially if the WPI were contesting the point.

But if their findings were positive - i.e. they figured out why the negative studies were failing - then we would be back on, with an infectious retrovirus that has gone unchecked for more than 25 years while the evidence of patients' experience was dismissed by the responsible bodies, and now about 5% of the population is infected...yes one can very easily see why that scenario might call for some secrecy and some control over how the information was managed...

Since they clearly have something very significant that they don't want to tell us yet, it sounds like the next move is going to be decisive. To say that I'm on the edge of my seat now, is an understatement!

And surely, they can't hold onto this information for very long. Given that they know that we know that they know something...how long can they resist the clamour for the rest of us to know what that something is?

ETA: The more I think about it, the more I think it has to mean they have an announcement or publication imminent that they don't want to pre-empt. Which could mean just about anything, I guess...

 

[Mark]

Yes, good point - it has to be XMRV itself also because they sequenced it and were able to grow it. So we're not talking about a bit of mouse DNA floating through the air here but the intact virus itself which would I think make the contamination arguments much more difficult. I imagine it could be a mouse cell full of viruses - which is why I guess they wanted to see XMRV embedded in the genome in the Alter/Lo paper. Retroviruses do not, I don't think, generally survive well outside of the body - so I guess it would have to be an intact cell from somewhere that had viruses in it.

Indeed: so for starters we are talking about contamination with XMRV itself, if we must talk about contamination at all. Not contamination with mouse DNA - although some people have talked about just that.

Next, we have the evidence that the Swedish group detected XMRV in 2/3 +ve samples from the WPI. That has to mean that any contamination by XMRV was in the blood itself when the WPI supplied it to the Swedes (rather than in their detection equipment). It also has to mean that there's nothing much wrong with the Swedish group's ability to detect XMRV - so therefore if it's not contamination then the XMRV must have got lost or corrupted by the way the Swedes (and others) collected and stored the blood - or, there are geographical factors at play.

Then we have the point that lots of different groups have found XMRV in prostate cancer studies, including in healthy controls. So the contamination theory now has to state that all those different labs were contaminated with XMRV, and therefore XMRV contamination is fairly widespread, in the US, Japan, and Germany at least, and is somehow getting into blood samples.

SO: the contamination theory requires widespread XMRV contamination that is getting into blood samples.

And the non-contamination theory requires that XMRV gets lost if the blood isn't collected or stored in the right way - OR geographical variation in XMRV sequences.

By the way, Gerwyn made a strong point a while back about what would have happened if Alter/Lo had done the gold standard test and shown XMRV embedded in the genome: the naysayers would then have argued that they were detecting a human ERV sequence. With some people, you just can't win...

 

[Sean]

With some people, you just can't win...

True. Some will never concede they are wrong, they will just get pushed aside, and will go to their graves denying the truth.

But we don't have to win everybody over, just enough of those in the right places.

 

[biophile]

Is it possible that the BWG Phase II results will be delayed or censored because they will cause major embarrassment for one of its members eg the CDC?

As for Coffin not taking the lead as expected, well, I imagine he is being extra careful because he does not want to risk his reputation? Betting on the wrong horse in controversial science can ruin your career, and when all this retrovirus controversy is resolved, some people's names are going to be stained.

 

[Megan]

The Big (Little?) Lipkin Meeting - did occur. It does appear to have been focused on Dr. Lipkins study. Why federal, research and advocacy representatives or invited to it is a question whose answer we will presumably get at some point.

I just read Lipkins paper. It's clear why he's invited everyone when you look at that. Here's a critical quote:

Many scientists fail in impact because they consider only themselves and their peers in the study design. Over the course of many validation/invalidation projects, we have developed the following guidelines for study design.

1. At the outset, engage other scientists, including those responsible for the original findings, as well as representatives of professional, funding, and advocacy organizations. Ensure that key partners agree on study design as well as plans for monitoring of progress, release of results, and conflict resolution.

2. Collect samples (under code at a location not affiliated with the laboratory sites) from subjects who meet strict case definitions accepted by key partners. When appropriate to obviate the risk of geographic or temporal bias, use samples collected from different regions and in different seasons and different populations.

3. Establish concordance across laboratories for sensitivity and specificity using positive and negative controls. For PCR assays, we insert non-wild-type sequences into positive-control template constructs to differentiate bona fide
versus control products.

4. Prepare several aliquots for each sample using a minimum of two codes. This enables blinded duplicate assays and facilitates blinded reassessments in the event that results of assays are discordant within or between laboratories.

5. Distribute duplicate, differently coded aliquots of positive and negative controls and samples. To facilitate interlaboratory comparisons, we typically send replicates of multiwell plates wherein each control or sample is placed into two nonadjacent wells.

6. Report results to a central biostatistics core for an assessment of intra-and interlaboratory consistency. As needed to achieve intralaboratory consistency, assays should be done with coded specimens.

7. Release results simultaneously to key partners.

 

[Cort]

So the contamination theory now has to state that all those different labs were contaminated with XMRV, and therefore XMRV contamination is fairly widespread, in the US, Japan, and Germany at least, and is somehow getting into blood samples.

SO: the contamination theory requires widespread XMRV contamination that is getting into blood samples.

By the way, Gerwyn made a strong point a while back about what would have happened if Alter/Lo had done the gold standard test and shown XMRV embedded in the genome: the naysayers would then have argued that they were detecting a human ERV sequence. With some people, you just can't win...

Agreed - it has to be widespread.

Interesting idea from Gerwyn. I wish they'd had the chance to come up with that viewpoint - it sounds like somebody would have made that point. At some point the ideas on either side will get more and more tenuous. I remember DeFreitas came down to saying that you have to use this specific product instead of this comparable (and widely used) product at which point alot of people threw up and said that she was reaching and they started to stop listening to her. Ironically, her rgument would get listened to now - 20 years later. Technology is better and importantly, the WPI's initial paper was a lot more comprehensive than hers. Hers was easier to dismiss.

(In the end even she was unable to duplicate her findings and her retroviral findings in multiple sclerosis were also debunked - despite the fact that she was part of a very prestigious Institute working with a very prestigious researcher. Who knows? maybe if they revisited the issue things would be different. The WPI was unable to find any evidence of HTLV-like viruses in their big pathogen arrays though)

 

[Cort]

Is it possible that the BWG Phase II results will be delayed or censored because they will cause major embarrassment for one of its members eg the CDC?

As for Coffin not taking the lead as expected, well, I imagine he is being extra careful because he does not want to risk his reputation? Betting on the wrong horse in controversial science can ruin your career, and when all this retrovirus controversy is resolved, some people's names are going to be stained.

Agreed about Coffin - he's not willing to lead with his nose. He did lend his prestige, so to speak, in the beginning as he did allow himself to become associated with the paper publically. It does make sense, though, for one of the top retrovirologists in the world to address a hot new topic. He's being careful- which is probably one of the reasons (plus that huge brain) that he got to the position he has.

I was taught in graduate school that the biggest error one could make is overstating something. That is considered particularly bad science. Its far better in the research communities eyes to understate the significance of something than overstate it.