Dr Singh Talks on her CFS XMRV study and the WPI's Response

[Jim]

Coffin Theory & Prostate XMRV

if coffin is right that xmrv was created in a lab in the 90's, and that the probability of it being created in the wild are near zero, how did it get into so many men with prostate cancer?

 

[joshualevy]

if coffin is right that xmrv was created in a lab in the 90's, and that the probability of it being created in the wild are near zero, how did it get into so many men with prostate cancer?

As a lab contaminant (not as a tissue/cell contaminant).
Remember, with XMRV the danger is that it contaminates the lab equipment, not that it contaminates the cells being tested. One theory is that XMRV was never in men with prostate cancer. Instead it was the lab that tested them. (Ditto with CFS.)

Joshua

 

[Jim]

As a lab contaminant (not as a tissue/cell contaminant).
Remember, with XMRV the danger is that it contaminates the lab equipment, not that it contaminates the cells being tested. One theory is that XMRV was never in men with prostate cancer. Instead it was the lab that tested them. (Ditto with CFS.)

Joshua

yes, i know that lab contamination is pointed out, but with singh's prostate and switzer's (?) the claim is no contamination. if there was no contamination in those cases. how does a lab virus get into the population so readily? i would not think vaccines, as men with prostate xmrv are probably not getting vaccines in the 90's.

 

[RedRuth]

Just as a matter of interest has this question

I do not know why Lo et al or Lombardi et al used a process prone to contamination like the nested PCR, and then did not use the dUTP-UNG system (you'll have to ask them). But I could not risk contaminating my lab with PCR amplicons - then every subsequent test we did would be suspect.

been answered? Also, are the WPI comments about using the VP62 clone about the ELISA or the western blotting, or both?

 

[eric_s]

I don't know. But in the next one or two months results of phase III of the XMRV Blood Working Group should be available and they might answer the question if XMRV is really there or not. And even if they used a process more at risk for contamination that could still not explain the difference between cases and controls and the antibody results, i think.

 

[RedRuth]

It can explain the antibody results. If they have cells contaminated with MLVs or with the VP62 plasmid then they could find viral proteins, RNA and even EM of budding virus.

I think it's pretty clear now that the Lomabardi et al PCR results are contamination.

 

[eric_s]

And how would they be more present in the samples of ME/CFS cases? I think the testing in Lombardi et al. was blinded.

And what about the other groups that have found XMRV or related viruses? Did they all have contamination?

 

[RedRuth]

You mean why were more ME + samples contaminated? Does it matter if it's contamination? The PCR data was never the most convincing data anyway, especially the way they did it. Everyone knows how easy it is to contaminate PCR. The data that got the Lombardi paper published is the antibody and FACS results. As for other labs, yes they could easily have contamination. As I said on the other thread PCR reagents have been contaminated with Mouse DNA, cell lines have been contaminated with MLVs and some of the labs will have used the VP62 plasmid, all sources of contamination.

 

[eric_s]

No, i woudn't call them contaminated. What we know is that more ME/CFS samples came back positive and the numbers are so that chance is more or less ruled out. If the experiment was blinded that makes contamination higly unlikely, unless the controls were collected, stored, etc. differently before the blinding and the contamination occurred then. As far as the other labs go, i find it hard to believe some of the people involved there would not find out they are looking at conatmination for years. Frank Ruscetti, for example, has now worked with XMRV for probably 3 years or more (i'm guessing). He has applied a number of different methods and looked at different types of samples in different illnesses. I think contamination with mouse DNA is not likely, since they have very sensitive assays to test for that and also they have sequenced what they've found.

Even if it was contamination, what i don't believe, i think it would matter why ME/CFS samples would be contaminated more often. Because if the testing was blided, this should not happen. They should find out what happened.

In the lab or institution where you work, did they ever study XMRV or related viruses in humans?

 

[currer]

I think Frank Ruscetti can get his tests right.

 

[eric_s]

Just yesterday or so i saw Senator Reid on TV, because of the debt ceiling problem. That made me think about the Whittemores and the WPI. Of course you can't answer a scientific question this way, but i thought could it be possible that the WPI has got it all wrong? Would people like the Whittemores let Judy Mikovits and her team either do bad work for 4 years (studying a contaminant and not realizing it) or partner in a fraud with them? And these are the only two explanations i could see if XMRV was not really there. I just find it hard to believe this. Their reputation would suffer a lot, i guess, and they would have burnt a lot of money for nothing. Would they just let this happen and not stop it for 3 or 4 years? They could only lose, if the WPI is wrong about XMRV.

 

[markmc20001]

I'm with You Eric. Not to mention the studies from the FDA that back up HGRV findings.

Nobody would go thru such a morass without being damn sure they are right.

If I weren't more familiar with M.E. history, Burzynski, Lyme folks, or Dr Andrew Wakefield and autism history. I would think it all is some kind of bad dream or mistake.

However, if there are millions of people thinking something is wrong, there is definitely something wrong.

 

[RedRuth]

It depends were they got contaminated though given the sequences the WPI have submitted look very much like VP62 it could be in their lab, especially as they have used the VP62 plasmid. Though as Dr. Singh points out in the paper

Control populations were often small, with as few as 43 in one study (25), and patient and control samples were often collected at different times, sometimes several years apart (11), leaving open the possibility that patient samples might have been handled more, and thus possibly contaminated more easily, than control samples. Additionally, in all except a subset of samples from one study (12), the identity of the samples was not hidden from the investigators.

Inadequate blinding and different sample conditions for the two groups. What do you think is wong with Dr. Singh's methodology? She's been incredibly thorough as far as I can see.

 

[RedRuth]

I think Frank Ruscetti can get his tests right.

What about Dr. Singh?

 

[Jemal]

What about Dr. Singh?

Dr. Singh still believes in her XMRV and cancer research and stands by her earlier results (she detected XMRV in people with prostate cancer). At least she said so right after the XMRV and ME/CFS study she did. She's in a weird position...

 

[Deatheye]

Dr. Singh still believes in her XMRV and cancer research and stands by her earlier results (she detected XMRV in people with prostate cancer). At least she said so right after the XMRV and ME/CFS study she did. She's in a weird position...

Doesn't this kinda fit the ape studies? Not detectable in blood but in organs?

 

[Jemal]

Doesn't this kinda fit the ape studies? Not detectable in blood but in organs?

Yeah, she was looking for the virus in tissue in her cancer research, while looking for the virus in the blood of ME/CFS patients (if I remember correctly).
The blood doesn't look like the most reliable or easy place to find this virus.

 

[eric_s]

It depends were they got contaminated though given the sequences the WPI have submitted look very much like VP62 it could be in their lab, especially as they have used the VP62 plasmid. Though as Dr. Singh points out in the paper

Control populations were often small, with as few as 43 in one study (25), and patient and control samples were often collected at different times, sometimes several years apart (11), leaving open the possibility that patient samples might have been handled more, and thus possibly contaminated more easily, than control samples. Additionally, in all except a subset of samples from one study (12), the identity of the samples was not hidden from the investigators.

Inadequate blinding and different sample conditions for the two groups. What do you think is wong with Dr. Singh's methodology? She's been incredibly thorough as far as I can see.

If contamination happened at the WPI then i think it's difficult to explain the difference between cases and controls. The quote refers to different studies, so i think it's not really objective to make it look as if all of this applies to one study. I'm not qualified to judge Dr. Singh's methodology, but as far as being thorough, she admittedly had contamination during this study. But she found out about it. Interestingly, the contamination affected cases and controls at the same rate. For me, that the possibility that ME/CFS samples were handled more often than control samples is left open is not enough to prove that there actually was contamination. By far not enough, it's no proof at all. Also i don't see why the older control samples should have been handled less often than the fresher ME/CFS samples. That doesn't really make sense to me. Contamination is a possibility, but i still find it more likely that many groups have just not yet been able to find the virus. It has also been reported that some of the groups that found XMRV at first didn't find it and only after consulting with the WPI were ableo to find it.
I think Maurren Hanson's study that was not yet published was blinded too, but i'm not sure about that. And hopefully there will be more blinded studies.

 

[Mark]

You mean why were more ME + samples contaminated? Does it matter if it's contamination?

What an extraordinary question Redruth! Where is your scientific curiosity?! Surely it's obvious why an answer to that question would be so crucial to the debate, and such a valuable piece of knowledge in itself?

Did you read Prof Robin Weiss' paper reviewing historical contamination incidents? It's a very readable overview, albeit a very carefully-timed political paper from a pillar of the establishment, of course. The highlight for me was learning that, in most of the incidents he highlighted as previous contamination, there had actually never been any proper proof that they really were contamination, and no satisfactory explanation of how the contamination had occurred: it had just been accepted, eventually, that they probably must have been contamination, and everyone had moved on. Most particularly, he admitted that there was no satisfactory explanation of why the contamination had sometimes affected patient samples at much higher rates than controls, and the only real hypothesis was that maybe the patient samples had been handled more often (and there wasn't even any evidence that they had been handled more often). The remarkable thing to me was: such "contamination" incidents have (allegedly) been confusing research, creating controversy, and diverting research funds inappropriately for decades...and yet there appears to be no desire on the part of those claiming this is the case to actually get to the bottom of the matter, figure out how this mysterious contamination keeps happening, and thus find out how it can be prevented in the future. That lack of curiousity seem curious to me...

Yes, it matters to know precisely how the alleged contamination occurred, and an explanation is required for how it could be that the patient samples get contaminated at higher rates than the controls, and how it was that the controls all got contaminated at roughly the same rate in multiple positive studies (I'm including the positive prostate cancer studies there, because everything that wasn't 0/0 has found roughly the same background rate of XMRV in controls; in a contamination scenario the statistical likelihood of that is infinitesimally small and that requires an explanation too).

It would matter how such contamination keeps affecting patient samples so disproportionately even if it had been proved that it is contamination: one would surely want to improve experimental design to avoid this happening again, no? But it is not at all proved that it's contamination, and (here's the crux of the matter, for me) the contamination theory should be subjected to the same kind of rigorous scepticism that has been applied to the positive studies. Posing this question of how it can be that the patient samples get contaminated at such high levels compared to controls is a reasonable question: it's something that the contamination theorists ought to be required to explain, and they should also explain where the contamination came from and how it took place. But where is the rigorous so-called "scepticism" now? Where are the self-styled 'sceptics' when you really need them, eh? They're certainly not busy poring over White and Wessely's garbage and asking searching questions about that, more's the pity - they appear to prefer softer, less well-defended targets, for some reason...

I really do find this whole reaction of "oh, nobody else can reproduce it, it must have just been contamination, let's move on" quite incredible. I realise that there are budgets to juggle with, and masses of other priorities to consider. But the lack of curiosity here, the lack of desire for a full and proper explanation of observations, just astounds me. When you consider what's at stake, to just let the matter drop without ever getting to the bottom of it would be the height of irresponsibility, and the willingness - nay, the enthusiasm - of the establishment to close down questions like this is just one more reason why so many people (myself included) are losing faith in the integrity of the modern scientific process.

But I suspect I can guess your answer to the above: Contamination in labs is very, very common, actually; despite our best efforts, there's rogue DNA all over our labs and the products we use, and when it happens in experiments we just shrug it off - even if it's contamination with a novel human retrovirus that was created in the lab and has spread unintentionally through an unknown process. That sort of thing is par for the course, and when it happens we just move on because we haven't got time to study every little thing. Somehow, I still don't find that revelation very reassuring though. Speaking as somebody with "bizarre" and "impossible" symptoms of permanent immune damage (lasting more than 16 years now) that are completely unknown symptoms to medical science (yet familiar to many members of this forum) and which nobody in the medical world seems to have the slightest interest in investigating or even acknowledging in any way...small wonder, really, that when I see a scientific blind spot like this one, in an area of science that would offer a perfect explanation of what has happened to me, that I don't want to see the scientific investigation finished without a proper explanation before it's even begun.

So: I am going to continue to demand a proper investigation and explanation of this science, and I'm going to continue to apply my scepticism not to those who are trying to help, but to those authorities who have so completely and systematically failed the millions who have suffered with ME/CFS/FM/MCS/GWI/WTF/etc for so many decades.

 

[asleep]

What an extraordinary question Redruth! Where is your scientific curiosity?! Surely it's obvious why an answer to that question would be so crucial to the debate, and such a valuable piece of knowledge in itself?

Did you read Prof Robin Weiss' paper reviewing historical contamination incidents? It's a very readable overview, albeit a very carefully-timed political paper from a pillar of the establishment, of course. The highlight for me was learning that, in most of the incidents he highlighted as previous contamination, there had actually never been any proper proof that they really were contamination, and no satisfactory explanation of how the contamination had occurred: it had just been accepted, eventually, that they probably must have been contamination, and everyone had moved on. Most particularly, he admitted that there was no satisfactory explanation of why the contamination had sometimes affected patient samples at much higher rates than controls, and the only real hypothesis was that maybe the patient samples had been handled more often (and there wasn't even any evidence that they had been handled more often). The remarkable thing to me was: such "contamination" incidents have (allegedly) been confusing research, creating controversy, and diverting research funds inappropriately for decades...and yet there appears to be no desire on the part of those claiming this is the case to actually get to the bottom of the matter, figure out how this mysterious contamination keeps happening, and thus find out how it can be prevented in the future. That lack of curiousity seem curious to me...

Yes, it matters to know precisely how the alleged contamination occurred, and an explanation is required for how it could be that the patient samples get contaminated at higher rates than the controls, and how it was that the controls all got contaminated at roughly the same rate in multiple positive studies (I'm including the positive prostate cancer studies there, because everything that wasn't 0/0 has found roughly the same background rate of XMRV in controls; in a contamination scenario the statistical likelihood of that is infinitesimally small and that requires an explanation too).

It would matter how such contamination keeps affecting patient samples so disproportionately even if it had been proved that it is contamination: one would surely want to improve experimental design to avoid this happening again, no? But it is not at all proved that it's contamination, and (here's the crux of the matter, for me) the contamination theory should be subjected to the same kind of rigorous scepticism that has been applied to the positive studies. Posing this question of how it can be that the patient samples get contaminated at such high levels compared to controls is a reasonable question: it's something that the contamination theorists ought to be required to explain, and they should also explain where the contamination came from and how it took place. But where is the rigorous so-called "scepticism" now? Where are the self-styled 'sceptics' when you really need them, eh? They're certainly not busy poring over White and Wessely's garbage and asking searching questions about that, more's the pity - they appear to prefer softer, less well-defended targets, for some reason...

I really do find this whole reaction of "oh, nobody else can reproduce it, it must have just been contamination, let's move on" quite incredible. I realise that there are budgets to juggle with, and masses of other priorities to consider. But the lack of curiosity here, the lack of desire for a full and proper explanation of observations, just astounds me. When you consider what's at stake, to just let the matter drop without ever getting to the bottom of it would be the height of irresponsibility, and the willingness - nay, the enthusiasm - of the establishment to close down questions like this is just one more reason why so many people (myself included) are losing faith in the integrity of the modern scientific process.

But I suspect I can guess your answer to the above: Contamination in labs is very, very common, actually; despite our best efforts, there's rogue DNA all over our labs and the products we use, and when it happens in experiments we just shrug it off - even if it's contamination with a novel human retrovirus that was created in the lab and has spread unintentionally through an unknown process. That sort of thing is par for the course, and when it happens we just move on because we haven't got time to study every little thing. Somehow, I still don't find that revelation very reassuring though. Speaking as somebody with "bizarre" and "impossible" symptoms of permanent immune damage (lasting more than 16 years now) that are completely unknown symptoms to medical science (yet familiar to many members of this forum) and which nobody in the medical world seems to have the slightest interest in investigating or even acknowledging in any way...small wonder, really, that when I see a scientific blind spot like this one, in an area of science that would offer a perfect explanation of what has happened to me, that I don't want to see the scientific investigation finished without a proper explanation before it's even begun.

So: I am going to continue to demand a proper investigation and explanation of this science, and I'm going to continue to apply my scepticism not to those who are trying to help, but to those authorities who have so completely and systematically failed the millions who have suffered with ME/CFS/FM/MCS/GWI/WTF/etc for so many decades.

Hear, hear Mark! Fantastic post!