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Next generation sequencing is not to be used to find the ME retroviruses

Given that it is now undeniable that next generation sequencing (deep sequencing) must be used for detecting MLVs (1), it is astounding that this superior technology is not to be used in the Government multi lab study which Dr W Ian Lipkin has been asked to head up. 

You may have heard however that Dr Lipkin is to use next generation sequencing (2) in his work for the hurriedly established Chronic Fatigue Initiative (3). An organization funded by the Hutchins family foundation (2). Glenn Hutchins himself is extremely well connected with many financial organizations (4), and has served as a White House special advisor on economic and health-care policy (5).


“Dr. Ian Lipkin and Dr. Mady Hornig, Use Deep Sequencing and Proteomics to Hunt CFS Viruses” (2)

Shockingly next generation sequencing (NGS) is not to be used by Dr Lipkin to look for XMRV in his work for the Chronic fatigue Initiative. They are not looking for these viruses at all.

“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.” (6)

We have to assume this also means the XMRV-like/PreXMRV-2-like viruses that were detected in ME patients by Lombardi et al., 2009 (7), Lo et al., 2010 (8), and Lee et al., 2012 (9), as Dr Lipkin has never acknowledge that Dr Mikovits and Dr Ruscetti discovered these viruses in ME patients.

As MLVs cannot be detected using antiquated PCR it makes every sense that next generation sequencing should have been included in the Governments “Lipkin” study, as this is the best technology.  Dr Lipkin obviously does recognize that this technology can discover new pathogens, but has deliberately selected to not use it for confirming the presence of XMRV-like/PreXMRV-2-like or similar retroviruses in ME patients.  

Please note, that as Dr Lipkin has said he is looking for infectious agents already implicated in ME, he must be using sequence dependent amplification with next generation sequencing technology.  To identify unknown novel retroviruses however he would need to be using sequence independent amplification with next generation sequencing.

MLVs cause horribly diseases in mice and other animals, to suggest that not using this technology is sensible should horrify every patient out there. With the Governments “Lipkin” study also not having used a recognized diagnostic criteria for patient selection (10), we should heed the words used by the CFIDS Association of America in response to the CDCs faux attempt to detect the same viruses.   


“So the explanation for not finding XMRV in these samples is simple – this was a study designed to not detect XMRV using a hodge-podge sample set.” (11)

Dr Mikovits and Dr Ruscetti may have assays that detect these viruses, but those assays are very easily undermined if the correct procedures are not followed by those who have been tasked with the collection and processing of the samples for the “Lipkin” study. Alter the separation times, get the storage temperatures wrong, use repeated freeze thaw cycles, wrong aliquot volumes, refreezing samples, wrong tubes, wrong centrifugation times, poor storage, and the antibody antigen binding will not occur nor will they be able to amplify the viral sequences from degraded RNA that will result.

Dr Mikovits and Dr Ruscetti should have been allowed to use this superior technology themselves. They should be funded through Government grants to use NGS to study ME patients.

 

CHRONIC FATIGUE INITITIVE (CFI) COHORTHROTH

It is also concerning that the CFI may share the same ideological flaws regarding the nature of ME/CFS versus fatigue that the CDC and other Government organizations continue to advertise to the world, because the cohort of the Hutchins’ funded initiative could be highly inappropriate for studying ME/CFS. 

“The CFI-sponsored cohort recruitment protocol uses the updated CDC definition and the Canadian Consensus Criteria to identify well-characterized subjects.” (12)

The updated CDC definition is the Reeves (2005) empirical definition of fatigue (13). If it is the first barrier used to screen persons to be included in research then there should be few if any patients present who meet the Canadian Consensus Criteria (CCC), because the Reeves definition does not require any person to have the cardinal feature of ME, which is PEM, more accurately termed post activity relapse (PAR). This criteria establishes a very broad cohort of fatigued people without any evidence of having the neuro-immune disease ME. You can find more on this criteria as it relates to research in our article, ‘Chaos in the cohort’.

How the CFI has applied these criteria should be described in detail within any published study. There should in fact be no reason for them to not state at this time what they are really intending to do and no reason for them to be using the Reeves definition of fatigue (13). If they do not state that the CCC was used separately to select patients or used as the initial screening tool, then we must assume that they are filtering people from the study. If this occurs then they should not be claiming there are any patients present in the study who meet only the CCC. 


It is more than disappointing that any of these issues have to be pointed out to any person who calls themselves a scientist. Next generation sequencing (NGS) should now be used to study these viruses in patients confirmed as meeting the Canadian consensus criteria alone and with proven objective signs of having the neuro-immune disease ME. 


REFERENCES

  1. Mayer et al. 2012. Comparing PreXMRV-2 gag sequence diversity in laboratory and wild mice using deep sequencing. Virus Res.
  2. Kate Benson. 2011. Dr. Ian Lipkin and Dr. Mady Hornig, Use Deep Sequencing and Proteomics to Hunt CFS Viruses. Cure Talk. 
  3. Chronic Fatigue Initiative 
  4. Glenn H. Hutchins. 2012. NNBD. 
  5. Glenn H. Hutchins, Co-Founder & Managing Director, Silver Lake. 2012. NASDAQ OMX. 
  6. Amy Dockser Marcus. 2011. Applying Venture Philanthropy to Chronic Fatigue Syndrome. WSJ.
  7. Lombardi et al. 2009. Detection of an Infectious Retrovirus, XMRV, in Blood Cells of Patients with Chronic Fatigue Syndrome. Science. 326, 585-589.
  8. Lo et al. 2010. Detection of MLV-related virus gene sequences in blood of patients with chronic fatigue syndrome and healthy blood donors. PNAS. 107, 15874-15879. 
  9. Lee et al. 2012. Sensitivity of PCR Assays for Murine Gammaretroviruses and Mouse Contamination in Human Blood Samples. PLoS ONE. 7(5): e37482. DOI:10.1371/journal.pone.0037482 
  10. W. Ian Lpkin. 28 December 2011. A Message from CII Director W. Ian Lipkin Regarding the XMRV/MLV CFS/ME Study. Columbia University.
  11. Suzanne Vernon. 2010. Blood from a stone. CAA. 
  12. Mindy Kitei. 2011. Q & A with Scott Carlson of Chronic Fatigue Initiative. CFS Central. 
  13. Reeves et al. (2005) Chronic Fatigue Syndrome – A clinically empirical approach to its definition and study. BMC Medicine. 3:19. 

18 July 2012 
ME Advocacy © 2012   The material on this site is for informational purposes only, and is not a substitute for medical advice, diagnosis or treatment provided by a qualified health care provider.
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