Paolucci et al: 2 out of 12 CFS patients positive for MuLV

[RustyJ]

No. I was expressing an alternate opinion of what might explain your reference to 'negativity' and others reference to some sort of apologetic nature in the paper about which this thread is concerned. But, neither would it be the 'caution' employed by Dr Mikovits either if you wish to go down this route. Why not - seriously - contact the authors and ask? I have found in the past (with the exception of Ruscetti - though there were reasons for that I believe) that in general they are very receptive to polite enquiries. Give it a whirl, see what they say.

Ah, you're referring to science by consensus, because to say Mikovits was not cautious would be a naive oversimplification, especially since the very same researchers who had been dabbling in tissue steeped with contamination for decades, not knowing it was there, are the ones crowing about MRVs not being in humans. Notwithstanding that Mikovits took two years to come to her conclusions. Certainly she did not make any sweeping statements that she could not support with her data.

 

[natasa778]

Would this be the same caution exercised by those researchers who couldn't find MRVs, who promptly announced to the world that they aren't in humans, or perhaps those researchers who introduce their papers with the statement that "Xenotropic murine leukemia virus-related virus (XMRV) is a virus created through recombination of two murine leukemia proviruses under artificial conditions during the passage of human prostate cancer cells in athymic nude mice." http://www.sciencedirect.com/science/article/pii/S0006291X12013903

LOL spot on

 

[Tito]

Do we know why only 12 patients were tested and not 50 or 100?

 

[RustyJ]

Do we know why only 12 patients were tested and not 50 or 100?

Presumably to limit the number of positives, lol. Sorry, couldn't resist. It is a good question. I also would like to know the answer to this.

 

[Tito]

Lol
It is also what I thought but I did not want to publicly express my cynicism. Lol

 

[Firestormm]

Hmmm... you could always ask the study authors I suppose...

 

[JT1024]

As regards the statistics, there are various ways one could look at this, but one is to say that given that two positives are found out of 52 samples total, the chance that both of them are found in the 12 CFS patients is 12/52 * 12/52 = 5.3%.

However, to make sense of questions like this, and make use of the power of statistics, it would be necessary for all registered scientific experiments to publish their data openly, whether the experiments are successful or not. So, for example, if any studies have been done which found a couple of positives in controls but not in patients, and which decided not to publish the findings but instead ignore them or run some more tests to look for contamination, those initial results too should have been published with full data, and the same applies to any positive studies which are not deemed acceptable for publication in a major journal - they should all be published somewhere, with full data, so that the sum of the data can be objectively assessed.

That's partly why I support Open Access and Open Data, along with many other long-overdue reforms to scientific practice like open peer and public review and pre-registration of studies...

While I agree with "Open Access and Open Data", taking all registered experiments and counting that data would be not be appropriate use of statistics. Assay design matters... unless there is political or financial motivation as seems to be the case in much of scientific literature today.

In many cases, poor study design results in poor results. When negative controls are positive, something is wrong with your assay. That is why you utilize quality control. I work in a clinical laboratory and utilize this daily.

To throw the control values (0/40) in with the cohort being studied (2/12) is deceptive IMHO.

 

[Snow Leopard]

Do we know why only 12 patients were tested and not 50 or 100?

Because this was a pilot study with limited funding...

 

[Tito]

I understand but when a sample is so small, the whole study becomes irrelevant. And the money is completely wasted. Testing 48 patients instead of 12 does not cost 4 times the initial amount, because the setup of the protocol is the same, the statistical analysis of the results costs the same or almost the same, it is just the marginal cost of the "ingredients" and use of devices. So it might cost twice the cost of a 12-patient study but it would be much more relevant.

 

[Tito]

What puzzles me is that on one side we have 12 patients and on the other side 40 controls. Why not taking 26 patients and 26 controls? It would have cost exactly the same.

 

[natasa778]

O`Keefe on Paolucci paper;

http://okeefe-lab.blogspot.co.uk/2012/07/new-study-finds-low-levels-of-mlv-gag.html#comment-form


in the comments she discusses again the curious case of everyone finding gag sequences only...

... I mean that is certainly possible; most people are looking for sequences based on what we know of the XMRV VP62 sequence (yes, lab generated or not), or other MLV-type viruses. Is it possible that an MLV has recombined with something with a slightly different sequence that isn't picked up by these primer sequences - I think so -- is it probable? Other explanations may include more rapid degradation of the non-gag regions of MLV...is that more probable than the first suggestion? What I think is very interesting is that if every finding of MLVs in mouse negative human samples is due to undetectable contamination-- then why is the GAG region the only region consistently picked up?

 

[natasa778]

Very true RustyJ.

Now why would they entitle the paper in such a negative fashion?

Probably for the same reason that those with positive findings are not bothering or trying to publish at all, as mentioned by O´Keefe recently... Probably the same reasons that made them patent before attempting to publish, IF they do. The air is just too contaminated with reactionary noises at the moment.

 

[natasa778]

What puzzles me is that on one side we have 12 patients and on the other side 40 controls. Why not taking 26 patients and 26 controls? It would have cost exactly the same.

Yes would be good to know the reasoning, although it could be something as simple as them having quick access to that many stored samples in a fridge somewhere nearby... not having funds to collect fresh samples etc...

 

[asleep]

As regards the statistics, there are various ways one could look at this, but one is to say that given that two positives are found out of 52 samples total, the chance that both of them are found in the 12 CFS patients is 12/52 * 12/52 = 5.3%.

I believe the probability is actually 12/52 * 11/51 = 4.97%, which by convention is statistically significant (if only by half a nose hair). It would be nice, though, to see more detail about their methods.

As others have said, this result strikes me as about what one could expect from a positive study with a (possibly) less rigorous patient criteria, a (possibly) less sensitive test (considering known limitations of PCR esp. in the context of unknown sequence variation), and other issues such as transient blood viremia.

It is becoming comical what lengths researchers are having to go to in order to get past the publication censors with results that run counter to the ordained "consensus." Coffin's hypothetically assumed recombination must be referred to as an established "fact" if you want to be published. Any positive findings must be presented in the absolute most negative light, often involving logical and semantic contortion that would make the average Cirque du Soleil troupe blush.

 

[Mark]

I believe the probability is actually 12/52 * 11/51 = 4.97%, which by convention is statistically significant (if only by half a nose hair).

Ah yes, quite right, how foolish of me. Thanks for correcting that schoolboy error.

 

[Firestormm]

Anyone care to explain or help me understand/interpret the highlighted parts below from the full paper please?

'It is however intriguing that the only positive results were obtained in these patients. On the other hand, in both cases the positivity could not be confirmed by the amplification of a different virus gene. The proviral DNA amount was very low in our patients, which might explain the stochastic amplification of a single virus gene in each of the two positive patients. Another possibility is that only fragment of virus DNA might be present in biologic samples.

In conclusion, while it appears established that XMRV/MLV sequences are not detectable in a significant proportion of CFS patients, the frequency and the role of evolutionary relic retrovirus sequences potentially detectable in the human chromatin remain to be further elucidated.'

http://www.newmicrobiologica.org/PUB/allegati_pdf/2012/3/341.pdf

Thanks.

 

[Wally]

Finding any MLVs in humans is a serious matter if you take gene vector technology into consideration.

The "wild" MLV would not even need to cause disease. There would always be the theoretical possibility of recombination in humans of an introduced gene vector and a wild MLV.

If the retrovirology community is responsible, they have no choice but to get to the bottom of this.
So we ought to see much more research on MLVs and human infection, even if MLV s are benign and not causing disease.

This will be a good thing for us but the motive may be nothing to do with CFS/ME.

Maybe this is why there is so much willingness to believe Paprotka.
The viriologists can see their research funds and patented MRVs fading away.....

From information I have come across it seems that patented viruses are worth a vast deal of money
$$$$$$$ $$$$$$$

Currer,

I believe you are looking in the right direction. Sometimes when one issue hits a roadblock, it may have more to do with its impact on other issues. I think it is worthwhile to keep exploring these potential connections.

Wally

 

[alex3619]

Do we know why only 12 patients were tested and not 50 or 100?

My best guess is that given the controversy this number of patients was about all they could get funding for. Though I think the suggestion to ask the authors is a good one. I have done that in the past on papers, and found them very receptive. Bye, Alex

 

[natasa778]

Anyone care to explain or help me understand/interpret the highlighted parts below from the full paper please?

'It is however intriguing that the only positive results were obtained in these patients. On the other hand, in both cases the positivity could not be confirmed by the amplification of a different virus gene. The proviral DNA amount was very low in our patients, which might explain the stochastic amplification of a single virus gene in each of the two positive patients. Another possibility is that only fragment of virus DNA might be present in biologic samples.

In conclusion, while it appears established that XMRV/MLV sequences are not detectable in a significant proportion of CFS patients, the frequency and the role of evolutionary relic retrovirus sequences potentially detectable in the human chromatin remain to be further elucidated.'

http://www.newmicrobiologica.org/PUB/allegati_pdf/2012/3/341.pdf

Thanks.

see O´Keefe´s plus other comments on her blog

 

[Bob]

I've read it now, and the results don't seem very impressive.

Firstly, the fact that no controls contained any sequences, is the first indicator that control subject samples and patient samples could have been handled differently. I would expect that at least one of the control samples might show up as positive, if the positive results were not based on contamination. (But this would not necessarily be the case, considering the low numbers involved.)

Secondly, the sequences that they detected are not helpful, as per my current understanding. The first sequence, 'CFS Pavia-1', was similar to Lo's sequences, but not the same, but it was 100% identical to a polytropic mouse virus.
And the second sequence, 'CFS Pavia-2', was 100% the same as XMRV VP-62.

The fact that the sequences were 100% identical to XMRV VP-62 and an ERV is not helpful, with regards to proving it is a human virus. It suggests that it could be contamination.

That's my understanding so far, but I might have misunderstood something.