Lapp Reports XMRV is Found in CFS Using Genome Detection Technology/Ampligen News

[insearchof]

DanUSAAS

I agree with what you wrote, and this was my understanding also. But why hasn't there been more talk about this and more discussion in the forum and elsewhere? Has it got lost in the hype about Apligen? is it simply because it is a technology announcement unsupported by published scientific data in support of it's claims? Even I'd the later, shouldn't this be presented to the FDA/BWG for them to consider/look at? Does the WPI, NCI, Cleevland Clinic know about this?

 

[toddm1960]

Or did this find catch everyone off gaurd and they have no response yet? I thought the same thing when this came out, we'd see WPI, NIH and the Cleveland Clinic jumping in backing up the great news backing up their research.

Add me to the list................no lunulas, only small ones on my thumbs

 

[Esther12]

We have had a few rumours like this before.. some of them ending up in published papers, some didn't. That's limiting the seriousness with which I'm treating it. The fact the company mentioned seems serious, and genuinely involved in some cutting edge stuff is a big boost for me though. I had pretty much given up on XMRV, but it would only take one strong positive paper to really turn things arround.

 

[garcia]

We have had a few rumours like this before.. some of them ending up in published papers, some didn't. That's limiting the seriousness with which I'm treating it. The fact the company mentioned seems serious, and genuinely involved in some cutting edge stuff is a big boost for me though. I had pretty much given up on XMRV, but it would only take one strong positive paper to really turn things arround.

I agree with Esther. I think we should wait until seeing something published first.

 

[insearchof]

Does anyone know If WPI are aware of this new cell free DNA chrimea tech ?

For the Luna poll: None at all. ...and no finger prints!

 

[August59]

This sentence in the letter struck me as something that may now be pursued:

"Because AMP-511 is a treatment protocol and not a drug study, insurance may cover some or all of the expenses involved."

 

[SOC]

Does anyone know If WPI are aware of this new cell free DNA chrimea tech ?

For the Luna poll: None at all. ...and no finger prints!

Mini-poll at our house: 2 PWCs with lunulas only on thumbs, 1 non-PWC with lunulas on all fingernails.

 

[August59]

Just to make sure I'm on track here. The "lunulas" are the lighter colored area that kind of arcs across the bed of the fingernail?

 

[WillowJ]

This sentence in the letter struck me as something that may now be pursued:

"Because AMP-511 is a treatment protocol and not a drug study, insurance may cover some or all of the expenses involved."

I thought insurances always excluded experimental (esp. non-FDA-approved) treatments?

 

[Bob]

Just to make sure I'm on track here. The "lunulas" are the lighter colored area that kind of arcs across the bed of the fingernail?

Yes that's right August... the half moon at the base of your nails.

Maybe we could set up a lunula forum survey?!
It could be a bit of fun, and an interesting (sort of scientific) survey, at the same time.

 

[kurt]

Before getting excited about this, not only does it need to get published, but this needs to be validated by other labs. How many labs now have thought they found XMRV only to discover contamination? At least three or maybe four by now. Some questions I would ask, how have they ruled out contaminants? Have they run ALL the tests that are now indicated to rule out contamination? (more than just testing for mouse mitochondria DNA). I believe finding fragments of a virus is one sign of a contaminant. Yes, this was found in human DNA sequencing, but that is also a new technology, is that a proven test? There are about 10 companies now saying they will have very inexpensive full genome sequencing soon, so there is a big race, I think we need to give this some time, see how this plays out.

Also, that improvement on Ampligen, sounds similar to the rate of improvement from other treatments for CFS. Such as B12 therapy, and there was a gut dysbiosis treatment study a few years back that had fairly high rates of improvement.

Speaking of nails, I read somewhere online that pink nails indicate B vitamin deficiency. Given the B12 problems with CFS I wonder if other people also have pinkish color to the nails? I have that, as well as the missing lunulas on my fingers (thumbs still have them) which I believe can be caused by chronic stress.

 

[Sing]

This thread reminds me of the "Follow the money!" suggestion. Presumably big insurers, including the government, are interested in minimizing their services and payouts to chronically ill people. But presumably also, big pharmaceutical companies sniff around looking for opportunities for profitable drugs, and labs look to develop new tests which large numbers will need. As patients, we are looking for accurate diagnosis and treatment, but we also benefit from watching and influencing what happens on a basis of "Follow the money!"

 

[SOC]

This thread reminds me of the "Follow the money!" suggestion. Presumably big insurers, including the government, are interested in minimizing their services and payouts to chronically ill people. But presumably also, big pharmaceutical companies sniff around looking for opportunities for profitable drugs, and labs look to develop new tests which large numbers will need. As patients, we are looking for accurate diagnosis and treatment, but we also benefit from watching and influencing what happens on a basis of "Follow the money!"

So true, Sing. Big pharma may ultimately be our "friend" as they will earn much more money treating us with expensive drugs than they will if we continue to go untreated.

 

[insearchof]

Thank you Kurt......but before you go killing peoples enthusiasm completely, please understand that the ppl on this thread are not new to science 101 or the possible ''issues'' pertaining generally to the matter of the discovery of XMRV and the chrimera found here.

We are celebrating a new possibility, that may further the science in this area and science generally as well as, ''following'' a possible new money trail, as Sing said.

As for a lack of luna's caused by chronic stress, was that a study undertaken by Wesley et la by any chance?

 

[kurt]

Thank you Kurt......but before you go killing peoples enthusiasm completely, please understand that the ppl on this thread are not new to science 101 or the possible ''issues'' pertaining generally to the matter of the discovery of XMRV and the chrimera found here.

We are celebrating a new possibility, that may further the science in this area and science generally as well as, ''following'' a possible new money trail, as Sing said.

This is a strange 'possibility' and that is all I am trying to say. Full genomic sequencing is a lower sensitivity test than PCR, so this report just does not make sense to me. If XMRV fragments can be found in plasma by a low-sensitivity test, then all these highly sensitive PCR tests should have had no problem at all finding XMRV. And at least one of the 0/0 studies did include whole blood testing, so they searched the plasma, and using many times more sensitive test than a full genome sequence.

Also, how did they determine that fragments found floating in plasma were integrated ('chimera')? Just because they were in the plasma, they deduced that these must be from integrated strands in destroyed cells? How did they know these fragments were XMRV? I wonder whose PCR test they used to validate that, and whether they calibrated that to VP62 as WPI and all the others did?

To make this more clear, the sensitivity of the most recent CDC/Cooperative PCR test run for XMRV was about 1,000 times more powerful than full genomic sequencing. In other words, to detect XMRV with a full genomic sequence, the plasma would have to be literally flooded with XMRV fragments. If that were the case, nobody would be having trouble finding XMRV in blood samples of infected patients.

Also, not having LTR sequences, that is strange, how can that be a chimera? From wikipedia:

Long terminal repeats (LTRs) are sequences of DNA that repeat hundreds or thousands of times. They are found in retroviral DNA and in retrotransposons, flanking functional genes. They are used by viruses to insert their genetic sequences into the host genomes.

So if these fragments have no LTR sequences, how were they inserted to form the chimera?

 

[ixchelkali]

...to detect XMRV with a full genomic sequence, the plasma would have to be literally flooded with XMRV fragments.

Why?

(adding misc letters here because the forum doesn't allow one word posts)

 

[lansbergen]

To make this more clear, the sensitivity of the most recent CDC/Cooperative PCR test run for XMRV was about 1,000 times more powerful than full genomic sequencing. In other words, to detect XMRV with a full genomic sequence, the plasma would have to be literally flooded with XMRV fragments. If that were the case, nobody would be having trouble finding XMRV in blood samples of infected patients.

They have a method called next-generation sequencing.

I can not find what exactly they did in the ampligen trial, have to wait till they make it public.

They have a paper published called: Disease-specific motifs can be identified in circulating nucleic acids from live elk and cattle infected with transmissible spongiform encephalopathies

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632913/?tool=pubmed

 

[free at last]

POSTED BY kURT

If XMRV fragments can be found in plasma by a low-sensitivity test, then all these highly sensitive PCR tests should have had no problem at all finding XMRV. And at least one of the 0/0 studies did include whole blood testing, so they searched the plasma, and using many times more sensitive test than a full genome sequence. End

Really Kurt, then we will have to assume that Dr Alters comments recently, mean that Alter is indeed contaminating hes own samples. Not to be correlating with the CDCs testing. Because if we find out at some point Alter is not contaminating hes own samples ( to explain the negative positive discrepncies of the NIH CDC ) then those comments Will really be in trouble. Once one trusted groups Testing is shown to have problems ( CDC Alter NIH ) then likely possibly others do too. Its not clear whats going on yet is it. but either Alter is indeed contaminating hes samples ( but apparently they are testing negative to that ??? )
Or the CDCs testing ( and by virtue maybe others too ) really is in trouble. The discrepencies reported by Alter recently should have alarm bells ringing loud and clear. Really those that belive testing is fail proof. probably are hoping Alter is contaminating hes samples because if hes not. There goes your 100% fail proof belief on all or most of the 0/0 studys. Maybe Alter is contaminating hes samples. But i guess the guy isnt a idiot. and is testing for all possibillities ? whats the truth. At the moment we dont know. But Alters recent comments are alarming to say the least. If people are convinced as you are Kurt. that the testing is fail proof. Untill we know more. theres indications that it is just not so. But i agree. maybe we will find Alter has contaminated hes samples. But is that likely if the testing is showing otherwise ?

 

[omerbasket]

He reports that the MLV's Lo found are similar enough to the XMRV the WPI found to warrant their being included in the same group - that is definitely a matter of contention.

I don't think that it is a matter of contention. If you'd use the "BLAST" tool in the NCBI website, you'd find out that the similarity between XMRV (for example, the very much known VP62) and the PMRV sequences found in the Lo/Alter study have at least the percentage of similarity that different isolations of HIV-1 or HCV (Hepatitis C Virus) have between them - and still, for some reason, sequences that shares 79% of similarity are still being called - for both of the sequnces - "HCV", while sequences that share more similarity (and perhaps, much more), are being treated by persons such as Myra McClure as "different viruses". McClure deals with HIV-1. I wonder if she calls the sequences of HIV-1 that are only 85% identical to one another by different names (one is HIV-1 and the other, I don't know, HIV-III? I've never heared of it, but I have found HIV-1 sequences that are only 85% identical to other HIV-1 sequences - and I'm talking about full genomes. From the sequences that we currently have regarding PMRVs, they are as least as identical as those HIV-1 sequences, and possibly more identical, perhaps much more).

 

[Bob]

This is a strange 'possibility' and that is all I am trying to say. Full genomic sequencing is a lower sensitivity test than PCR, so this report just does not make sense to me. If XMRV fragments can be found in plasma by a low-sensitivity test, then all these highly sensitive PCR tests should have had no problem at all finding XMRV. And at least one of the 0/0 studies did include whole blood testing, so they searched the plasma, and using many times more sensitive test than a full genome sequence.

Also, how did they determine that fragments found floating in plasma were integrated ('chimera')? Just because they were in the plasma, they deduced that these must be from integrated strands in destroyed cells? How did they know these fragments were XMRV? I wonder whose PCR test they used to validate that, and whether they calibrated that to VP62 as WPI and all the others did?

To make this more clear, the sensitivity of the most recent CDC/Cooperative PCR test run for XMRV was about 1,000 times more powerful than full genomic sequencing. In other words, to detect XMRV with a full genomic sequence, the plasma would have to be literally flooded with XMRV fragments. If that were the case, nobody would be having trouble finding XMRV in blood samples of infected patients.

I'm sceptical about these reports as well, and sceptical about when we are likely to see any benefit from the supposed findings. I'm sceptical partly because of the lack of information, and also because of the way the information has been presented... It's all just speculation at this stage.
I'm hopeful about finding XMRV being integrated into the human chromosome, but I don't think these reports tell us what we need to know.
And as there's absolutely no solid information about it at all yet, I guess we just have to wait and see exactly what there is to be excited about here.

Also, not having LTR sequences, that is strange, how can that be a chimera? From wikipedia:

Long terminal repeats (LTRs) are sequences of DNA that repeat hundreds or thousands of times. They are found in retroviral DNA and in retrotransposons, flanking functional genes. They are used by viruses to insert their genetic sequences into the host genomes.

So if these fragments have no LTR sequences, how were they inserted to form the chimera?

It has been suggested, I think by Gerwyn, that the bit about the missing LTR's was misinformation.
But I don't know what either Gerwyn or Lapp are basing their information on, and whether Gerwyn has actual knowledge about this or is just being hopeful.
So it's all just speculation at this stage.