Any news on Lipkin study?

Bob

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If the 'Lipkin' research had been produced shortly after it had been commissioned (or even a year after) then I think it's impact would have been greater because by all accounts it will be a very thorough study. However, given the delay (for whatever reasons) they will hopefully have learned quite a lot from the studies that have been published since 2010 and their own research will be better for it. I expect this to be a more extensive and credible bit of work as a result.
Yes, that's what I'm hoping as well... That they've been able to build on all of the stuff that's gone on since Lombardi, until now, and use all their most up-to-date knowledge... So I hope they looked for p-varieties... And avoided contamination pit-falls... Used the best methodologies, that avoided both contamination and false negatives... etc. etc. etc. With Judy and Lipkin in the driving seat, I have the feeling that it will be a thorough study, with no messing about. I hope so anyway.
 

currer

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Patients taking Rituximab relapsed shortly after stopping treatment which had removed B cells from the body, suggesting that these cells are not the source of the disease.

This diagram (fig 1) reports on the rebuilding of B cell levels over time and would not correspond with a sharp return to disease status seen in several of the patients
http://bloodjournal.hematologylibrary.org/content/117/7/2275.full
This paper is interesting, Mula, because there is a group of ME patients who do not respond at all to rituximab and this paper suggests some reasons why ritux can have different effects where autoimmune disease takes a different pattern. Thanks for finding it.
 

Mula

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This paper is interesting, Mula, because there is a group of ME patients who do not respond at all to rituximab and this paper suggests some reasons why ritux can have different effects where autoimmune disease takes a different pattern. Thanks for finding it.
It may be applicable, but MECFS is unable to achieve a similar purity of cohort that can be studied in isolation when selecting people with chronic graft-versus-host disease (cGVHD).
 

Christopher

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Dr. Lipkin's Research Study



Okay, this was more difficult than I originally thought after further investigation. Because Montoya is involved in several research initiatives with Lipkin so it was difficult and confusing to determine which ones.

Here is the bottom line:

1)The NIH ME/CFS XMRV, MLV, HGRV, as well as other pathogens study involving a number of labs are conducting the research, he is providing oversight. Montoya is involved in this as well. Lipkin is just providing oversight over these labs.

2) a Stanford Chronic Fatigue Initiative - Detection of pathogens such as herpes viruses, the Lyme disease agent, xenotropic murine leukemia virus-related virus (XMRV), Toxoplasma gondii, or any unknown pathogen that may be a trigger for chronic diseases such as CFS, CLD or other diseases ("Stanford/Montoya Pathogen Study") study. Completed, Lipkin is NOT involved in this study and the research has been completed and the results will be published in the near future.

3) A privately funded research a Chronic Fatigue Initiative ("CFI") Pathogen Discovery and Pathogenesis study. I guess the confusion lies in similar names.
This does not involve Stanford or Montoya. The second effort is to pursue microbe and biomarker discovery in different samples. The NIH has no role in funding or approving that work.

Will any of these studies involve deep sequencing to find any and all pathogens in the blood, plasmid, serum of ME/CFS patients?
Lipkin: Yes.

4) There are a quite a few other Stanford research projects that cannot be disclosed at this time in which Dr. Montoya and Dr. Lipkin are corroborating together on . There will be no requests for patient recruitments. This is where, I believe all the confusion is within the patient community. So Montoya is working with Lipkin on #1, and #4.

#5) Dr. Montoya is not involved with Dr. Kogelnick's Rituxan pilot program

I really hope this clears up all the confusion!

As to the comment on 'we'. It was in Lipkin's original email stating 'we' meaning other researchers. I have no part or interest in any of these research projects nor am I involved with Dr. Lipkin's research. I have my own interest in another research project not listed here.

The good news is that there are several research initiative projects that Montoya and Lipkin are working on in behalf of the ME/CFS community that are not announced at this time. So there is a lot of research going on with finding a cause for ME/CFS.

I hope this answers everyone's concern on this topic. :D

Eco

PS: I wish to add that Dr. Lipkin is working 18 hours, 6 days a week to help the ME/CFS community. He receives each week, hundreds of emails from people asking him questions which takes away from his time on research and teaching. I would like to make a suggestion to the ME/CFS community not to write Dr. Lipkin with questions. This way, it would reduce the amount of emails he receives to lighten his load and stress level. Your thoughts on this?
Eco,

According to #1 here http://chronicfatigue.stanford.edu/about/projects.html

Lipkin is involved in the Stanford pathogen study. Is that out of date or what?
 

Bob

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Dr Lipkin is studying known pathogens for the CFI using deep sequencing, but he is not looking for retroviruses in that study.
That's what I thought as well. But listening to his TWIV interview, it seems that he is looking for known and unknown pathogens, and that would include retroviruses if they are there to be found. It seems that it is a really comprehensive study that he is doing.

The information that we are getting, about Lipkin's pathogen studies, is contradictory, so I'm a bit confused.
 

Mula

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Deep sequencing technology won't be applied to the retroviral sequences, unless, perhaps, he has changed his mind post the results detecting fragments and serology?

Some of the same sites participating in the NIH’s XMRV study will also help enroll patients in the Chronic Fatigue Initiative’s bio-bank and cohort recruitment project. Once samples start coming in to the bio-bank, Lipkin says they plan to do an initial search for 20-30 infectious agents implicated in the past to be connected to CFS, including the herpes and Epstein-Barr viruses.

XMRV won’t be one of them, Lipkin says. “This should not be taken as bias one way or another,” he adds. “Given we are already doing that in another context, it doesn’t make sense to invest twice.
http://blogs.wsj.com/health/2011/09/15/applying-venture-philanthropy-to-chronic-fatigue-syndrome/
 

Bob

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Deep sequencing technology won't be applied to the retroviral sequences, unless, perhaps, he has changed his mind post the results detecting fragments and serology?

Some of the same sites participating in the NIH’s XMRV study will also help enroll patients in the Chronic Fatigue Initiative’s bio-bank and cohort recruitment project. Once samples start coming in to the bio-bank, Lipkin says they plan to do an initial search for 20-30 infectious agents implicated in the past to be connected to CFS, including the herpes and Epstein-Barr viruses.

XMRV won’t be one of them, Lipkin says. “This should not be taken as bias one way or another,” he adds. “Given we are already doing that in another context, it doesn’t make sense to invest twice.
http://blogs.wsj.com/health/2011/09/15/applying-venture-philanthropy-to-chronic-fatigue-syndrome/
In his TWIV interview, he seemed to be suggesting that he will be implementing a number of methodologies which will result in a number of non-specific pathogen searches, looking for known and unknown pathogens. In other words, if I understood the limited information correctly, his methodology is such any pathogens present could potentially show up. So this would include potentially finding any retroviruses that are present. He has ruled out XMRV and pMLV being associated with ME, but that doesn't rule out other retroviruses. In any case, from the sound of what he's doing, if XMRV were to be present, it would show up. I can't remember if he specifically mentioned that retroviruses would be part of his pathogen search.

I can't remember the exact details of his TWIV interview, and there wasn't much detail, so I might have misinterpreted some of it, but I was very impressed with what I heard.

I think I'll listen to it again, or read a transcript.

Does anyone know if there is a good transcript of the TWIV interview?
 

Mula

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In his TWIV interview, he seemed to be suggesting that he will be implementing a number of methodologies which will result in a number of non-specific pathogen searches, looking for known and unknown pathogens. In other words, if I understood the limited information correctly, his methodology is such any pathogens present could potentially show up. So this would include potentially finding any retroviruses that are present. He has ruled out XMRV and pMLV being associated with ME, but that doesn't rule out other retroviruses. In any case, from the sound of what he's doing, if XMRV were to be present, it would show up. I can't remember if he specifically mentioned that retroviruses would be part of his pathogen search.

I can't remember the exact details of his TWIV interview, and there wasn't much detail, so I might have misinterpreted some of it, but I was very impressed with what I heard.

I think I'll listen to it again, or read a transcript.

Does anyone know if there is a good transcript of the TWIV interview?
He has said xmrv is not one of the pathogens, and he would know because to look for a sequence his primers would need to target the suspected infectant. It is confusing to say pMLVs as this is a form of mouse virus, so would be reasonable to say he could find xenotropic MLV-related viruses which are not xmrv? It is unclear what his intentions are, but other pathogens tend not to need the level of amplification supplied by deep sequencing.
 

Bob

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I've just been listening to the press conference and Lipkin says that the samples are now being used for deep-sequencing testing, and he says that if there are retroviruses that he missed, he would hope to catch them in deep-sequencing testing. He specifically refers to retroviruses.

It is confusing to say pMLVs as this is a form of mouse virus, so would be reasonable to say he could find xenotropic MLV-related viruses which are not xmrv?
I don't know which specific retroviral sequences they searched for because I haven't read the paper in detail.
I assume that Harvey Alter would have looked for the p-variety of MLV-related virus that he detected in his previous study, however they are labelled/categorised. I don't know which sequences Judy and Frank Ruscetti looked for.
 

Mula

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I've just been listening to the press conference and Lipkin says that the samples are now being used for deep-sequencing testing, and he says that if there are retroviruses that he missed, he would hope to catch them in deep-sequencing testing. He specifically refers to retroviruses.



I don't know which specific retroviral sequences they searched for because I haven't read the paper in detail.
I assume that Harvey Alter would have looked for the p-variety of MLV-related virus that he detected in his previous study, however they are labelled/categorised. I don't know which sequences Judy and Frank Ruscetti looked for.
It is not conducive to retroviral discovery if those patients were not the correct disease to begin with. Placing such a burden on a handful of people lowers the chances of discovery. Dr Alter and Dr Lo moved to another tests with pMLV primers, but it is not possible to know whether those tests could find those sequences previously identified. Dr Mikovits and Dr Ruscetti had primers as they used previously and found gag.
 

RustyJ

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It is not conducive to retroviral discovery if those patients were not the correct disease to begin with. Placing such a burden on a handful of people lowers the chances of discovery. Dr Alter and Dr Lo moved to another tests with pMLV primers, but it is not possible to know whether those tests could find those sequences previously identified. Dr Mikovits and Dr Ruscetti had primers as they used previously and found gag.
I agree. I was dismayed to see they are using the same samples. Lipkin and the CAA, it seems, are moving to make these samples 'gold standard', to ensure they will be used in future studies. This means that if a study chooses not to use these samples it may be viewed as irrelevant. If there is a problem with this cohort, it will corrupt and skew me/cfs findings for many years to come.

The CAA has never been behind retroviral findings, even before the negative studies came pouring in. The CAA has actively campaigned against HGRVs. It could be strongly argued that a retroviral discovery as the cause for me/cfs would make the CAA irrelevant.

http://www.occupycfs.com/2012/09/22/thos...n-samples/
 

jspotila

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I agree. I was dismayed to see they are using the same samples. Lipkin and the CAA, it seems, are moving to make these samples 'gold standard', to ensure they will be used in future studies. This means that if a study chooses not to use these samples it may be viewed as irrelevant. If there is a problem with this cohort, it will corrupt and skew me/cfs findings for many years to come.

The CAA has never been behind retroviral findings, even before the negative studies came pouring in. The CAA has actively campaigned against HGRVs. It could be strongly argued that a retroviral discovery as the cause for me/cfs would make the CAA irrelevant.

http://www.occupycfs.com/2012/09/22/thos...n-samples/
There are several sample repositories in the works. There's the Lipkin study samples. There's the CFI biobank. I think there is substantial overlap with the Lipkin cohort there, although I am not positive about that. And then there's the CFIDS Association's SolveCFS Biobank which is larger and different from the Lipkin cohort.

I appreciate your link to my blog post on the Lipkin samples. I was disappointed to hear that NIH will not make funding available for work on that cohort, after what Lipkin said on TWiV.

As far as the Association actively campaigning against HGRVs or that a retroviral cause would make the Association irrelevant, this is not the case. This has been hashed and rehashed on other threads. I'm no longer on the Association's Board, but I do know that they have a pathogen discovery project ongoing, plus a treatment screening study and more.