CAA - WPI only lab reporting false positive result. (Is this correct?)

[judderwocky]

Here it is for people.

Thanks for posting this V99. It is a bit worrying that the WPI got a false positive - but you're right that it seemed the FDA did too. Maybe this is why (some guy - forgotten his name) was talking about the possibility that identifying XMRV from patient samples is different to spiked samples? It would be extraordinary if they sent out a XMRV positive sample in a sample that was meant to be clean, but who knows at this point. If the FDA and WPI picked out the same sample, but that is what happened.

Were the FDA involved with the positive study we're waiting for? I'm getting my three letter acronyms mixed up - FDA, NIH, NCI...

If both positive studies were properly blinded, it would be strange that the contamination would be consistently more likely with the CFS samples.

ps: The CDC kicked arse at the spiked samples.

It sounds like to me that this is an artificially generated strain of XMRV, that was derived from prostate cancer cell lines.... the first test is for a single artificial spike of Xmrv

From what I have read and heard from Ruscetti, the envelope section mutates .... i doubt that an artificially created sample would contain the variations of the ENV section that seems to mutate and be present in humans... so this could actually explain why they (CDC) are thinking they were accurately testing for XMRV in general.... they have high sensitivity in all the calibrations showing that they are detecting it, but didn't have the same sensitivity in human tests because that section is mutating away from the strain they are testing for...

they are testing for a static copy of XMRV... and its fluctuating around in people that are infected... they can get the static version maybe, but not the one thats changing around...

does that make sense to anybody else... am i missing something?

i know ruscetti has said that most of the labs that had negative results were using the ENV section, but that it was the GAG that they were using...
so my guess is, since the ENV section mutates a lot in patients, and since its probably just a single strain in the spiked sample... they went into it probably thinking they had a really good test, and probably weren't aware they had missed those with mutated ENV sections... just an idea

i dont know how they are making these spiked samples.... if its all an identical virus though, its possible that the CDC is very good at detecting that single strain of XMRV... any containing that ENV sequence, but that it might mutate too much in people for them to have the same degree of sensitivity in blood...

also... the FDA study found more than just XMRV.. mlv's... so we know that there are different strains running around and we should suspect that there are some people that still haven't tested positive in any study and still are...

when the FDA study comes out, we might have to start referring to it as the "XMRV cluster of viruses" instead of just "XMRV"

 

[CBS]

Judderwocky,

That sounds a lot like what I took from the Ruscetti talk. I'd be interested in seeing the context of this slide (supposedly to be released 'soon'). If the samples are spiked and not "known" human positives then all bets are off as to the meaning of a so called 'false' negative.

 

[judderwocky]

Judderwocky,

That sounds a lot like what I took from the Ruscetti talk. I'd be interested in seeing the context of this slide (supposedly to be released 'soon'). If the samples are spiked and not "known" human positives then all bets are off as to the meaning of a so called 'false' negative.

Exactly.... also its very interesting if you look on the side of this graph... i can barely make it out... but it seems like it was run in batches... in other words... it looks like either 5 or 3 samples each at equal strength were used at increasing concentrations of the virus.... so it looks like the detection was only one out of five of those at the lowest concentration that they got the false positive on... and only on a single one out of the batch... i dont think its very startling at all frankly... a little background noise always spills in... the original science paper took multiple precautions to guard against that

 

[judderwocky]

Exactly.... also its very interesting if you look on the side of this graph... i can barely make it out... but it seems like it was run in batches... in other words... it looks like either 5 or 3 samples each at equal strength were used at increasing concentrations of the virus.... so it looks like the detection was only one out of five of those at the lowest concentration that they got the false positive on... and only on a single one out of the batch... i dont think its very startling at all frankly... a little background noise always spills in... the original science paper took multiple precautions to guard against that

i mean... really they've got to be scratching their heads about this one... because the CDC has better sensitivity, but the same false positive rate as the NCI, but the NCI is sitll finding it in patients when the CDC is not... that also seems weird....

 

[RustyJ]

From what I have read and heard from Ruscetti, the envelope section mutates .... i doubt that an artificially created sample would contain the variations of the ENV section that seems to mutate and be present in humans... so this could actually explain why they (CDC) are thinking they were accurately testing for XMRV in general.... they have high sensitivity in all the calibrations showing that they are detecting it, but didn't have the same sensitivity in human tests because that section is mutating away from the strain they are testing for...

they are testing for a static copy of XMRV... and its fluctuating around in people that are infected... they can get the static version maybe, but not the one thats changing around...

Good assessment. If I can understand this, and WPI and Ruscetti have reiterated it, and the Science paper explains it, then why hasn't the CDC tested it? It has to be deliberate on their part... to avoid CFS. It is not incompetence.

 

[Dr. Yes]

Hi judderwocky,

From what I have read and heard from Ruscetti, the envelope section mutates .... i doubt that an artificially created sample would contain the variations of the ENV section that seems to mutate and be present in humans... so this could actually explain why they (CDC) are thinking they were accurately testing for XMRV in general....

But the CDC did PCR testing for gag and pol sequences, not env.

 

[VillageLife]

I really hope they update there site soon.

 

[jspotila]

More details are coming

I'm told that a more detailed write up of the FDA meeting will be in this week's CFIDS Link. FDA is also supposed to provide the Powerpoint presentations from the meeting, and those will also be posted to the Association's website (as well as the FDA and CFSAC websites).

 

[George]

The way I understood it was that they took blood that was "known" to be negative, spiked with this "cloned copy" (so that everybody had the same chance of finding or not finding it) the spikes where different strengths to test "titer" type levels. They sent these kits to each lab and let each lab test their "serology" test on the kit samples.

This means that the kits were artificially made up. There was NO human XMRV involved at all in any way. And all the assays were tested on the cloned copy of XMRV. What does it mean? Well that all 6 labs more or less passed the first round of testing. Next up is to test the assays on human samples. These kits are being made up or will be made up by the WPI if I understand correctly, from "Known" human positives along with a set of negatives. Phase II has either happened or is happening as we speak and this is where I get confuzzed. . .

Why would Dr. Le Grice say that he had sent his assays out to labs overseas for manufacturing if we were only at phase two? You don't send your stuff off to 4 different manufacturing labs unless you are making up a BUNCH of kits to do a LOT of testing, right??? Wouldn't a lot of tests indicated that they are past phase II, that the above info is old, and that they are gearing up for phase IV which is the big 400 sample test????

I would think that if the DHHS wants to look good they would need to have the phase IV testing done before they unleash information regarding a new retrovirus to the public. Personally I think that folks worry more about looking right than doing right, but I really get the impression that the suffering we are doing now is due to "information control". We are going through a black out period while DHHS get's their ducks in row.

But it should be soon now, very soon.

 

[V99]

I think your right George, we must be at stage two by now, perhaps even further. Stage one though would not have a way of testing if the sample was negative, so how would they know? Therefore it could contain XMRV.

 

[George]

I think your right George, we must be at stage two by now, perhaps even further. Stage one though would not have a way of testing if the sample was negative, so how would they know? Therefore it could contain XMRV.

Sorry V I'm soooo not following that logic. Huh?

 

[V99]

It's not you, I'm not wording it well. If there is no test for XMRV, how can they know if the sample is negative.

 

[garcia]

It's not you, I'm not wording it well. If there is no test for XMRV, how can they know if the sample is negative.

I agree V99. No way of validating a negative sample at present. So if two labs got the same "false positive" you have to ask whether it was false in the first place.

 

[V99]

This reminds me of when I would ask my dad. "how do you spell..." He would tell me to look it up in a dictionary. My complaint was that I couldn't spell the word well enough to look it up in the dictionary.

 

[omerbasket]

Thanks for that Omerbasket. I didn't think the CAA were being as alarmist as Mikovits implied - the CAA didn't really do any interpretation for there to be a misinterpretation (other than not mentioning the apparent FDA positive). I understand it being a touchy issue though.

Still though - if it was a false positive, it does raise concerns about contamination while things are so uncertain.

You may not know it, but in Herbrew I usually don't make any spelling mistakes (by the way, I apologize for spelling mistakes in English, in this comment of mine as well as in others). I'm very good at spelling in Hebrew. But once at a time I do make an embarassing mistake. Let's say that I would write "he is fool of shit" instead of "full of...". I was typing fast and made a rare mistake.
But if a person that knows me and knows that I rarely makes spelling mistakes in Hebrew would take that mistake and show many people that don't know me my mistake, they would certainly think I am a fool, and would think that I don't know how to spell. That person would not mention that I'm very good in spelling and that it was a rare mistake by me.
Technically - he would'nt lie. I did make that mistake (in our little story...). BUT HE WOULD DEFINITLEY BE MISLEADING.

It's very clear now. The members of the panel were asked to test these artificial XMRV samples with qPCR. WPI did not use qPCR in any of their methods published on the "Science" paper. It's possible that their first qPCR teting were when they tested the samples of the blood panel. The WPI never claimed that they have a good qPCR test (although it does seem good, even if not 100% accurate). They do stand behind their tests that were published in the most prestigous scientific journal in the world after a long process of peer-review. They were never found to have even one false positives with these tests.

jspotila, you quoted a patient writing that Dr. Vernon is in that working group. So couldn't she provide the accurate and not-misleading picture?

Now, regarding that "contamination issue" which you mention: I'm sorry, but this is just nonsense, being made by people who either does not understand anything in science, or not to know the exact details of the WPI's tests, or have some interest by saying that (and that interest is not the public health). There are so many tests that were done to eliminate this opportunity. They even used a test develpoed by Mr. Switzer himself to make sure there are no mouse tissues in the patients samples as well as in the WPI's cell lines. They isolated the virus from every positive PCR they did (as Dr. Mikovits said, more than 600 positives by now). They showed genetic stuff that strongly suggests it cannot be a mouse contamination (as far as I understand it, the XMRV they found doesn't mach the genome of MLV's and even not the exact genome of XMRV from prosate cancer). They confirmed their findings by every method with a positive test by another method. They sequenced every PCR product. Their findings were rigorously review by the number one scientific journal in the world, "Science", for about 6 months. Dr. Alter, a very respected scientist, said about WPI's study:

Not only have they detected gag and envelope XMRV sequences, but they have infected prostate cell lines and recovered gamma retrovirus particles and have transmitted XMRV to rhesus macaques by the IV route and demonstrated infectivity.

The study was also confirmed by two major labs: the Cleveland Clinic and the NCI. Do you say they all contained contaminants?
Besides, neither the WPI nor the NCI labs have ever worked with mouse tissues!

And the best evidence for no infection whatsoever is, as I see it, the fact that they found antibodies to the virus. You can't find an antibody in a sample that it's XMRV was just the product of a lab contamination.

These are a lot of arguments, and I guess they aren't even all of the arguments. Therefore I say again: To say that the WPI's positives might have been a result of a contamination, you either have to understand nothing in science, or not to know the exact details of the WPI's tests, or to have a interest in make these allegations.

 

[George]

Got it! Think about it like this (If I over simplified, I'm sorry). . .

I'm a science teacher teaching my class to calibrate a weight scale, so they can tell me how many drops of water are in each of say 6 tubes.
I give each group of kids (NCI, CDC, WPI, FDA, NIH etc) in the class
1 empty tube
1 with 1 drop of water
1 with 2 drops
1 with 3 drops
1 with 4 drops
1 with 5 drops of water.
But the kids can's see into the tubes they are opaque and sealed. Everybody get the same sets. The group that get's each tubes water amount correct wins the big prize. An A. (grins)

Each kid has to figure out how to set the scale so that the empty tube is the base line (0 XMRV) and then be able to weigh each tube and say exactly how much water is in each tube. (1, 2, 3, 4, or 5 drops or in this case how many copies of XMRV)

All of the groups NCI, CDC, FDA, NIH got exactly the same tubes with the same amounts of XMRV in them. One had 0 ( I can't really make out the numbers but say for argument ) one had 20 copies of XMRV, one had 100 copies, 500, 1,000 and 5,000. Each team used the serology assay that they had come up with to see if they could determine how many copies where in each tube. They wrote down their answers and handed them in.
This chart is the result. If you got a red bar then you were dead on the money, if you got a yellow bar you were half right, (partial credit here) if you got a green bar you where wrong. Both the FDA and WPI got one wrong answer each.

What does that mean? Well, the WPI are still the smart kids in the class in that, even though their serology test wasn't perfect they are still the best at finding XMRV the old fashion way using the culture methods. They are still best at checking their work. Most likely the reason VIP hasn't put the serology test up yet is because the WPI had to fix the problem with their test. I have no doubt that they would not put out a faulty test. Once they figured out what the problem was they went back and fixed it. Which is why it's 6 weeks late from the original release date.

And so what, the CDC (the smarmy little kid in the back of the room, grins) got it right this time around. I don't think the CDC wants to be left out of XMRV research, too much money coming down that pike, they just don't want to find it in CFS. (grins) But I have to say thanks for whipping up an accurate serology test.

Not to worry because all of these groups will patent their revised tests and market them.

 

[V99]

I'm having trouble following the water story. ooops I think you said that the WPI and FDA (Lo) got the test wrong on that sample? but what if the sample was positive, and no one knew it was? Then WPI and FDA(Lo) were correct and everyone else was wrong.

 

[George]

It's impossible for the sample to be positive.

 

[V99]

I'm not sure it is. If they cannot test for real virus yet, how would they know?

 

[George]

I'm not sure it is. If they cannot test for real virus yet, how would they know?

ARRRRRGG, science.