WPI back on track?

The WPI has published its new research program. From its website (highlights are mine):

[Whittemore Peterson Institute] Current Research Program
http://www.wpinstitute.org/research/research_basic.html
Friday March 25th 2012

1. Pathophysiology of chronic fatigue syndrome

This National Institutes of Health (NIH) funded study proposes to identify pathogens associated with chronic fatigue syndrome (CFS). Initially, this study relied upon microarray technology to detect viruses potentially associated with CFS. However, now, under the direction of Dr. Vincent Lombardi, this study will instead utilize unbiased next generation sequencing technology. This state-of-the-art method is not subject to the limitations of viral microarrays. Not only does this technology have the capacity to identify any viruses, it also has the ability to identify any pathogens, associated with CFS. Additionally, it will allow us to perform transcriptome analysis, which has the ability to identify differences in the immune system when compared to those who do not suffer from CFS. Therefore, all of the original specific aims of the grant will be addressed; however, transcriptome analysis may provide additional knowledge that could not be obtained using originally proposed methods. This study also proposes to investigate dysregulation in the interferon response associated with CFS.

[From the PDF]
New Strategies to Decipher the Pathophysiology of Chronic Fatigue Syndrome

The original Aims of the National Institutes of Health (NIH) RO1 grant were to identify both novel viral infections and genetic susceptibility factors in European and American cohorts of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) patients. The principal investigator (PI), Dr. Vincent Lombardi, will pursue these Aims using more advance technology in order to discover pathogens (known or unknown infectious agents) and their associated immune responses in ME/CFS.

The overall goal of this research project is to define viral and host parameters that correlate with distinct disease phenotypes in European and American cohorts of ME/CFS patients with diagnoses fulfilling the Center for Disease Control (CDC) definition and Canadian Consensus Criteria for ME/CFS. To do this, we will obtain blood samples from ME/CFS patients and healthy control subjects from specific medical practices, with the recent approval from the University of Nevada, Reno Biomedical Institutional Review Board (IRB). We will utilize next generation sequencing by synthesis (SBS) technology to detect novel virus mRNA and evaluate transcriptome differences between ME/CFS subjects and healthy control subjects. Any pathogen infection will be confirmed with a combination of quantitative PCR (QPCR) and culture methods. Additionally, we will evaluate serum chemokine and cytokine profiles using multiplex suspension antibody arrays on a Luminex platform. Finally, we will evaluate HLA and KIR genotypes and investigate possible defects in the type I interferon signaling pathway.

At the conclusion of this study, we anticipate identifying any pathogens uniquely associated with ME/CFS. We also anticipate identifying differences in the lymphocyte transcriptome as well as any differences in HLA, KIR and interferon immune parameters.

Some observations from this:

• They are still looking for "knowns and unknown" "pathogens uniquely associated with ME/CFS".
• They are switching from an microarray-assay to next generation sequencing (next generation "sequencing by synthesis – SBS").
• They are doing a transcriptome analysis
• They are still focusing for cytokine differences

Sure sounds partially promising.

The question is: Will this yield once again results that are not based in reality, unreproducible by anybody else? After all, Dr. Lombardi worked together with Dr. Mikovits on her seminal work, and he is quite firmly rooted in Woo-Land. We'll see.

2. Pathogen and biomarker discovery in Gulf War illness

This Department of Defense (DOD) sponsored project will utilize next generation sequencing technology in order to identify differentially transcribed genes associated with Gulf War illness (GWI). This information will be used to better understand the pathophysiology of GWI. Additionally, this information will be used to identify potential biomarkers for diagnostic purposes and evaluation of treatment progress.

From the PDF:
Pathogen and Biomarker Discovery in Gulf War Illness

The goal of this study is to identify potential biomarkers, including pathogens, associated with Gulf War illness (GWI), which in turn will afford physicians the necessary tools to make more accurate diagnoses. This study will be conducted under the direction of Dr. Vincent Lombardi as the principal investigator (PI).

GWI is a chronic multi-­‐symptom disorder affecting approximately one third of the veterans and civilians who served during the Persian Gulf War (Desert Storm 1990-­‐ 1991). It is a syndrome primarily described by a spectrum of symptoms, innate immune abnormalities and opportunistic infections. A wide range of acute and chronic physical symptoms are associated with GWI including fatigue, musculoskeletal pain, gastrointestinal dysfunction and cognitive problems. Unfortunately, diagnosis of GWI is difficult in that no discrete biomarkers or etiological agents have been identified. A greater understanding of the innate immune system and the associated opportunistic pathogens may provide insight into the pathophysiology of this disease.

In order to explore this issue, we will recruit subjects diagnosed with GWI who served during the Persian Gulf War, whether or not actually deployed to Iraq and surrounding areas, along with healthy control subjects, following approval of the University of Nevada, Reno Institutional Review Board (IRB). We will conduct lymphocyte transcriptome analysis of GWI subjects and compare the results to the same analysis of healthy control subjects. The transcriptome is reflective of the genes that are being actively expressed at any given time; therefore, the lymphocyte transcriptome represents a window into the innate immune system, potentially leading to an understanding of GWI pathogenesis. Transcriptome analysis also has the ability to identify any pathogens present in the immune cells, potentially identifying an etiological trigger.

We look forward to commencing this important study after obtaining IRB approval of the study protocol.


3. Cytokine dysregulation in chronic fatigue syndrome

Cytokine and chemokine dysregulation is one of the most consistently reported observations in individuals with ME/CFS; nevertheless, the mechanism of this dysregulation remains unknown. The acute onset and epidemiological patterns of ME/CFS etiopathology support the involvement of a pathogenic trigger. Consistent with this observation, is the fact that the innate immune system responds to infection by producing proinflammatory cytokines and chemokines. The microbial pattern recognition receptors, Toll-like receptors (TLRs) 3 and 4, are activated by pathogen-derived dsRNA and LPS, respectively, to produce these proinflammatory cytokines. This system is tightly regulated; however, in patients with ME/CFS, it is constitutively active. The focus of this research project is to better understand the mechanism of this dysregulation.


4. Biomarker discovery in neuro-immune and inflammatory diseases

Previously, we identified a cytokine/chemokine signature with high specificity and sensitivity in diagnosing ME/CFS patients. Our project will extend this signature to other inflammatory and neuro-immune diseases, providing physicians with necessary tools to delineate closely related neuro-immune and inflammatory diseases.

"In Vitro Infidelium" on the WPI-RED-VIPdx-Connection and Conflict of Interest

"In Vitro Infidelium" on the WPI-RED-VIPdx-Connection and Conflict of Interest.

This looks like a rats-nest to me.

Digging for Dirt in Nevada

More interesting dirt from WPI/VIPdx/UNEVX:

Further email exchanges confirmed that “…XMRV testing is for both the culture and the serology tests…” and that “…ALL of the tests we run are validated and inspected by the State of Nevada,”

I asked to see the “validation data”, requested details about “the State of Nevada” and reiterated my question about why a “clinically validated” test (or tests) was withdrawn.

VIPdx replied that “The State does not “hold” this information. It is a proprietary record of the laboratory. They inspect but do not keep our records. Our validation records and test protocols are proprietary intellectual property of the laboratory.”

This is interesting too:

During the ensuing correspondence, and contrary to VIPdx’s statement to me, it emerged that “Vincent Lombardi is not the laboratory director, nor has he served in that regulatory capacity” and “they took this off their website today, it is incorrect.”

[The regulatory Laboratory Director (i.e. the person who represents the lab for regulatory purposes) was/is Sanford Barsky who, in February 2012, CFS Chronicles found to be accused of scientific fraud.
http://www.cfschronicles.com/1/post/2012/02/vote-of-no-confidence.html]

While I am pleased to see them digging up dirt on the WPI, it saddens me to at the same time that they ignore the contributions of our fine researcher and heroine at large Dr. Judy Mikovits. Just to reiterate:

January 22, 2009, Santa Barbara XMRV Seminar by Whittemore Peterson Research Director Dr. Judy Mikovits

Dr. Mikovits:
…
So you can be infected with retroviruses and be carriers and not be sick. And that’s one reason to be tested. If there is a genetic susceptibility, which we’re looking to, maybe a reason, an immune defect that was unknown as to why some people get sick and others don’t. You certainly want to know where the virus is, so if you’re a carrier you can protect your family.

Question:
Do you know how many have tested with VIP-Dx, and how many are positive?

Dr. Mikovits:
I don’t work with the company. They only take samples two days a week because it takes three days to do that, so they’ve done hundreds of samples in the last couple of months, and at least half of them are positive. Or 40 percent. And again, their doctors are looking at, the doctors who are well versed with CFS, so they’re immediately sending off. Dr. Cheney, Dr. Klimas, a doctor in Canada, Ellie Stein, maybe even Susan Levine in New York. I’m not sure, because it’s illegal for me to know those data because there’s confidentiality between the patient and the physician. But quite a number and, yes, it’s there.

…

Annette Whittemore: Earlier you said that 40% were positive [by VIP Dx]. So describe the fact that if you’re positive, you’re positive. But if you’re negative, you’re not necessarily so?

Dr. Mikovits: Yes, that’s correct. I answered that question based on the samples that came through there. Everyone who is positive is definitely positive for having the virus. But we don’t know what the people are, what the doctor is sending in, so the people might not have that disease. So it could be a clearly, distinguishing delineating marker – biomarker – or diagnostic at that point for various diseases. So a doctor might see a spectrum and say “I don’t know, maybe I’d better check.” Because the earlier you catch it, just like cancer. Early detection. Make sure the reservoir is (inaudible), make sure you don’t have that virus multiplying, and you can live a normal life. Don’t let it get (inaudible). You know the commercial out right now is “HIV doesn’t have to equal AIDS”; well XMRV doesn’t have to equal disease. If we keep it down, we keep the immune system strong.

Question: So what you’re saying is you may test negative but not be negative?

Dr. Mikovits: That’s correct. If you do it by the PCR. If you do it by VIP-Dx, at least right now, it’s running along the lines of (inaudible). We’ve got the antibody, and we’ve got three of the four tests. We’ll license it to anyone. We’re a non-profit institute, so everybody pays the same royalty, so any diagnostic company could do the gold standard. But right now, if you test negative, you’re not necessarily negative, even at VIP-Dx. Because we want to go do that serology test. Maybe we can’t find evidence of the virus. But you’ve been exposed, which would be a good thing because your levels are theoretically low, and you’ve just now made the antibodies, so you can prevent disease, as we did with Magic Johnson. But we don’t know anything about the immune response to the virus.

And this email from Dr. Judy Mikovits:

Email from Dr. Judy Mikovits on XMRV and ME
Posted by Birgitte on 14/03/2010
http://www.me-nyheter.info/?p=1191
(copy here: http://esme-eu.com/news/email-fra-dr-judy-mikovits-ang-xmrv-og-me-article304-7.html )

Dr. Judy Mikovits writes:
Regarding the ramifications of being XMRV negative. First of all the current diagnostic testing will define with essentially 100% accuracy XMRV infected patients. The negatives are more difficult as there are additional tests that can only be done in the research lab at this time and not in a clinical setting such as VIPDx. The most important test is to check your blood for an antibody to the virus. If you are positive in the serology test and have an antibody to the virus, you have evidence of infection but at the time your blood was drawn the amount of virus in your blood was below the limit that could be detected by the most sensitive test currently available clinically, which is the the one done at VIPDx. that means while you tested XMRV negative..it could be a false negative. …
…
But by definition if you have ME you must have XMRV. [????]
…
We will test everyone that tested negative to see if we can find antibodies in your blood and look for that variant that we describe..that is evidence of XMRV infection. …

Vincent Lombardi: We validated our XMRV tests ourselves

An old one again, sorry, I missed it.

So CLIA certified clinical labs need to validate their own tests by themselves. And that's what VIP Dx did. It comes down that the guy running the lab (which may or may not have been Vincent Lombardi) did sign a paper that VIP Dx did something to validate their tests by themselves, and that he swears that everything is A-Okay.

And that is what Dr. Mikovits was trying to tell us all the time: you need a lab that is validated by Vincent Lombardi! Doh.

A number of recent publications and individuals have mischaracterized the nature of certain clinical laboratory results reported by VIP Dx, a CLIA certified clinical laboratory. VIP Dx has met the required CLIA Program standards and is certified to offer and perform only clinically validated laboratory tests. The “XMRV test” offered by VIP Dx is clinically validated and performed under rigorous protocols to ensure the accuracy and reliability of the test results. XMRV testing was offered based upon the existing scientific knowledge at the time. The original assays for XMRV testing were based on the 2009 Science publication. Those assays, as well as all subsequent modifications, were internally validated prior to being used to process patients’ samples. WPI’s Research Director was instrumental in the decision to make such a test available to physicians. The interpretation of the XMRV test results, as with all laboratory tests, is the responsibility of the ordering physician.

Before offering any test to the public, VIP Dx established comprehensive performance specifications including accuracy, precision, analytical sensitivity, specificity, and others required for test performance.

http://niceguidelines.blogspot.com/2011/10/statement-by-vincent-lombardi.html

Patients with Cancer in Lombardi 2009?

A comment on ERVs blog:

1. "At the July workshop, Dr. Mikovits also presented preliminary data showing that 20 patients of the 101 in the study have lymphoma, a rare form of cancer. The link between XMRV and lymphoma is still being investigated, but it raised the possibility that XMRV may be associated with other cancers in addition to prostate cancer. NCI's Dr. Le Grice said studies will be launched to determine whether XMRV is associated with other diseases. At the Whittemore Peterson Institute, Dr. Mikovits said they also found XMRV in people with autism, atypical multiple sclerosis and fibromyalgia."

Cancer-Causing Virus Linked to Chronic Fatigue
BY AMY DOCKSER MARCUS
OCTOBER 12, 2009.

source- http://online.wsj.com/article/SB125501227713473525.html
-----------------------------------

2. "Since reliable, consistent information about the Science cohort has not been forthcoming, I have carefully analyzed data provided in the Science paper, its supplement and public presentations by two of the authors. The WPI investigators conducted a number of assays to detect XMRV DNA, protein, infectious virus and antibodies against XMRV. I used the patient ID numbers provided in the paper's figures to track results. Of the 101 CFS subjects reported in the paper, results for the various assays are shown for only 32 CFS subjects. Of the 32 CFS subjects whose results for any of the tests are displayed, 12 CFS subjects were positive for XMRV on more than one assay. The other 20 CFS subjects were documented as positive by just one testing method. Using information from a public presentation at the federal CFS Advisory Committee, four of the 12 CFS subjects (WPI 1118, 1150, 1199 and 1125) included in the Science paper were also reported to have cancer – either lymphoma, mantle cell lymphoma or myelodysplasia. The presentation reported that 17 WPI repository CFS subjects with cancer had tested positive for XMRV. This once again raises questions about the lack of detailed clinical characteristics of the CFS subjects included in the Science paper, and the differing public reports about where the samples originated."

Playing A Weak Hand Well
Suzanne D. Vernon, PhD
Scientific Director
The CFIDS Association of America

source- http://www.cfids.org/xmrv/070110study.asp
-------------------------------

3. Q: Were any patients with lymphoma mentioned in the XMRV study?

A: Blood samples from the WPI repository were chosen at random and there were no patients chosen with lymphoma or mention of lymphoma in this study. Another preliminary study was done at a later date that had nothing to do with the XMRV Science publication.

source- http://www.wpinstitute.org/research/research_biobank.html
--------------------------------

4. Q: Did any of the samples used in the original study come from patients who ultimately developed cancer?

A: Yes, one.

source- http://www.facebook.com/notes/whittemore-peterson-institute/xmrv-testing-facts/377139018025
------------------------------

5. From the NCI's Center for Cancer Research 2009 CCR Scientific Advances-

Detection of a retrovirus, XMRV, in blood products of patients with neurological diseases and cancer – submission by Francis Ruscetti, PhD
Reference(s): Science. 2009 Oct 23; 326(5952): 585-9

source- (webpage no longer online, a saved copy does exist)

(Note- Not sure what the exact import of the title is, since although the reference given is the WPI's XMRV/Science paper, Science was contacted and asked if the WPI/XMRV paper had ever had this or any other title than the one it was published with, which Science said it had no record of this. Given the above inconsistancies though, it kind of raises some questions)
----------------------------------

6. By comparing information in the 'XMRV Association with CFS' presentation given to the CFSAC on October 29-30, 2009, with Table 4- 'XMRV detection results of 101 patients' in 'Detection of an infectious retrovirus, XMRV, in blood cells of patients with chronic fatigue syndrome' in the Journal Virulence, at least 12 patients from the original XMRV/Science study had cancer, although its impossible to tell exactly due to only 93 patient numbers being listed in the table and not the full 101 stated. One more patient number which was listed as previously having had cancer in the CFSAC presentation, 1199, is included in Tables 1 and 2 but not Table 4. The cancer status of one of these patients, 1125, was known as far back as the year 2000.
sources-

6a. WPI patients w/ cancer, taken from pt. 5 of 'XMRV Association with CFS' presentation given on October 29-30, 2009-
pic- http://i54.tinypic.com/11aicyc.jpg

6b. 'XMRV Association with CFS' - Part 5- presentation given to the CFSAC on October 29-30, 2009- (see Slide 1)
http://www.hhs.gov/advcomcfs/meetings/presentations/peterson_1009_pt5.pptx

6c. 'Detection of an infectious retrovirus, XMRV, in blood cells of patients with chronic fatigue syndrome' Virulence 1:5, 386-390; September/October 2010- (see Table 4)
http://www.landesbioscience.com/journals/virulence/MikovitisVIRU1-5.pdf

6d. WPI 1125- http://i55.tinypic.com/2a8f495.jpg

Posted by: anonymous | October 7, 2011 3:59 AM

Sample Selection in Lombardi 2009

How were the samples chosen?

All of the patients/samples used in the study were chosen randomly on the basis of a CFS diagnosis from more than 200 patient samples stored in the WPI repository since 2006. No one knew the status of the patients as all samples were blinded. None of the samples came from the original repository of samples owned by Dr. Peterson.

Only 101 out of more than 200 patient samples were choosen. How were they chosen?

Study characteristic:
- 67% women, reflecting gender incidence of CFS
- Mean age: 55
- 320 control samples from same geographic locations

Only 218 out of 320 control samples were choosen. How were they chosen?

WPI's World of Woo – why anything from the WPI is suspect (2)

Cyrus Pourzan, M.D., H.M.D.
http://www.facebook.com/photo.php?fbid=10150613855074672&set=a.10150613854979672.407782.154801179671&type=3&permPage=1

Dr. Cyrus Pourzan is a rare find in the medical community. He is a Board Certified medical physician with a passion to find "medicine that works." [but does not seem to be passionate that the "medicine that works" was actually properly tested in clinical trials] In his practice, he combines his experience and knowledge of Western medicine with alternative therapies and natural medicines [for which no evidence of efficiency or safety exists – otherwise it would be called evidence-based medicine]. This allows him to tailor treatments to the individual. For the past 12 years of his 31 year medical career, he has been treating patients with neuro-immune disease and brings this experience to the Center for Translational Medicine.

Dr. Pourzan obtained his medical degree from the University of Cincinnati and went on to complete a residency at UCLA in Emergency Medicine. He has been Board Certified in Emergency Medicine since 1984. Aware of the limitations of Western medicine, he began to expand his education into complementary and alternative therapies [for which no evidence of efficiency or safety exists – otherwise it would be called evidence-based medicine]. He pursued this path by obtaining additional licensure in homeopathic medicine and medical acupuncture (UCLA) in 2002.

Living in the Reno-Tahoe region has provided Dr. Pourzan with the opportunity to work with some of the most eminent authorities in the fields of neuro-immune disorders, bio-identical hormone replacement, auricular acupuncture, and pain management. His current field of interest is the role of oxidative stress in illness. He finds [What? He "finds"? What a weasel word. Apparently he does not have evidence] that a balance between modern medicine and traditional therapies can successfully treat the cause of his patients' illnesses.

Dr. Pourzan's medical mission is to help people achieve the best quality of life. In his spare time, he likes to be outdoors cycling, hiking and skiing. He also enjoys music and art. His new practice location is the best of all worlds. It is an ideal environment for both his professional and personal pursuits.

The Center for Translational Medicine is proud to announce that Dr. Pourzan is now seeing patients.

Professor Plum and Colonel Mustard.

Lombardi made the contact to Silverman?

Vincent C. Lombardi, Ph.D. began his work in CFS, as an undergraduate in the field of Biostatistics, characterizing T-cell populations in CFS patients. He later continued to work in CFS-related research in the laboratory of Dr. Robert Suhadolnik at Temple University, studying the interferon regulated RNase L antiviral pathway and its involvement in CFS. Dr. Lombardi completed his graduate degree at the University of Nevada receiving his Ph.D. in Biochemistry in 2005. The primary focus of his Ph.D. thesis was the isolation and characterization of novel diuretic neuro-peptides. Prior to the completion of his graduate degree he co-founded the specialty clinical laboratory, Redlabs, U.S.A., Inc. This clinical laboratory, which later became VIPDx, was formed to serve doctors and their patients who suffer from CFS. Dr. Lombardi served as the Director of Operations as well as the leader of laboratory research and development for new diagnostics in the clinical laboratory.

Upon joining WPI July 1, 2007, Dr. Lombardi's research effort focused on the inflammatory component of CFS and its relationship to the development of lymphoma in CFS patients. It was at this time that Dr. Lombardi established his collaboration with Robert Silverman, Ph.D., of the Cleveland Clinic, the world's leading authority regarding the RNase L antiviral pathway. Dr. Silverman had recently made the discovery of XMRV in RNase L deficient cancer patients. Dr. Lombardi's research on the association of the RNase L pathway in CFS patients, and discussions with Dr. Silverman prompted him to begin the search for XMRV in CFS.

http://www.facebook.com/photo.php?fbid=10150613865384672&set=a.10150613854979672.407782.154801179671&type=3

Or met Mikovits first with Silverman?

In October 2007, Mikovits attended a prostate-cancer meeting near Lake Tahoe, Nevada, where she met Robert Silverman, a virologist at the Cleveland Clinic in Ohio. …At the meeting, Silverman was presenting research linking XMRV to deficiencies in a virus-defence pathway.

So who was it? Professor Vincent Plum or Colonel Judy Mustard?

The 100 NCI samples

Investigators at NCI received 100 samples from individuals without knowing their health status; furthermore, the samples were sent to NCI directly without passing through the WPI laboratory space. … NCI used plasma from all 100 samples they received in infection experiments with LNCaP cells.

This allows for different scenarios for the interpretation of the Ruscetti/NCI results:

1. Face Value: The above sentence is true and the results from NCI show the actual immune status of patients and controls.
2. It was the Phlebotomist: The above sentence is true, but the phlebotomists manipulated the samples.
3. It came from WPI space: The above sentence is not true and the samples came from WPI space.
4. Broken Code: The above sentence is not true and someone at NCI knew (or guessed) the code.
5. Changed Code: The above sentence is true, but the code was changed at WPI after the result came in from NCI.
6. Contaminated Phlebotomist Vials: The above sentence is true, but the way samples were collected allowed for contamination specifically of some of the patient samples.

(I think I cane safely rule out the "random contamination at NCI" scenario)

I think #2 (Phlebotomist) is unlikely. An "open" conspiracy like that would simply involve too many people.

I don't think #3 (WPI space) happened. Someone at NCI should have noticed that. But then again, it doesn't look like Ruscetti reads what is published in his name.

#4 (broken code) is interesting. If the samples arriving at NCI had numbers like 1103, 1104, 1105, etc. and then 2760, 2832, 2958, etc. a person at NCI who might have been under pressure to come up with positive results might have been able to successfully guess which sample is a patient sample and which's a control sample. Plus, if all control samples come from one place (like Maryland, maybe even in one shipment), while the patient samples came from different places, this would have been an easy task.

#5 (changed code) is possible as well, if one looks at how numbers coming from WPI seem to be in a state of flux.

#6 (contamination at the phlebotomist) is interesting as well. The patients were in Nevada, New York state and so on, while the controls were from one state (AFAIK Maryland). So if the phlebotomist for the control samples used clean vials, while one or two of the patient phlebotomists used contaminated vials… If this is the case, then this is one point were patients and controls were not treated the same, BTW.

So what about #1, that the reported results represent reality, or something close to it? After that many inconsistencies (and while I can not completely rule out that the NCI results represent reality) I can nevertheless safely say:

Falsus in uno, falsus in omnibus.

(And I think if one looks more closely, one could find more inconsistencies between Lombardi et al. 2009 and its addendum.)

Dr. Mikovits and the WPI published only VP62 sequences – even without Silverman

These are all the 27 sequences reported by Dr. Mikovits and the WPI since October 2009:
http://www.ncbi.nlm.nih.gov/nuccore?term=Whittemore%20AND%20Peterson

These are the 6 sequences reported between October 2009 and November 2009:
http://www.ncbi.nlm.nih.gov/nuccore?term=Mikovits

These are the 21 sequences reported by the WPI in June 2011 and August 2011:
http://www.ncbi.nlm.nih.gov/nuccore?term=Khaiboullina

These 21 sequences were done without the involvement of Dr. Silverman or his lab.

Go run BLAST on these 21 sequences for yourself:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&QUERY=JF907634.1%0DJF950033.1%0DJF950034.1%0DJF950032.1%0DJF907648.1%0DJF907642.1%0DJF907639.1%0DJF907637.1%0DJF907635.1%0DJF907631.1%0DJF907647.1%0DJF907640.1%0DJF907638.1%0DJF907636.1%0DJF907632.1%0DJF907646.1%0DJF907644.1%0DJF907641.1%0DJF907633.1%0DJF907645.1%0DJF907643.1&DATABASE=nr&MEGABLAST=on&BLAST_PROGRAMS=megaBlast&LINK_LOC=nuccore&PAGE_TYPE=BlastSearch

For all practical purposes, these 21 sequences are identical both to VP62 and anything else reported by the WPI since October 2009.

There is no HGRV.

Even without Silverman, the WPI only published VP62.

Harry Reid, Harvey Whittemore and Dark Clouds

Some members of the Nevada congressional delegation on Friday announced that they have given away campaign contributions they received from power broker Harvey Whittemore after FBI agents served subpoenas in an investigation into his campaign contribution activities.

Reports that the FBI was serving subpoenas as part of a federal grand jury investigation into claims that Whittemore funneled campaign contributions through his employees sparked a sharp response by some of the recipients of those funds, including U.S. Senate Majority Leader Harry Reid, D-Nev., a longtime Whittemore friend and supporter.

Kristen Orthman, a Reid spokeswoman, released a statement Friday saying Reid has given up all of Whittemore‘s contributions, but declined to say exactly when he did that or whether he was trying to distance himself from Whittemore and his current troubles.
…

The quality of research is the problem we should be concerned with

Maarten Maartensz about the Whittemores:

How could a grant be handed over to people willing to be involved with the Seenos? And how can patients ever again trust that they are handling money honestly? It is a clear waste of tax payer money to hand over $300K to the Whittemores.

Bullshit: It's a fallacy, guilt by association. Also, I am personally not so much concerned how they get money to invest in research into the disease that I have, nor concerned about their motives, if the research looks sound from a scientific point of view. And one just cannot know most or all about the persons one deals with, in virtually any case.

My problem with the Whittemores is that I don't believe the research looks sound, at present, though that is not their fault, nor indeed in their interest.

Las Vegas Review-Journal: FBI investigates campaign spending by Whittemore

Las Vegas Review-Journal: FBI investigates campaign spending by Whittemore

FBI agents fanned out across the state Thursday serving grand jury subpoenas in a criminal investigation into allegations longtime political power broker Harvey Whittemore was involved in funneling illegal campaign contributions to federal races in Nevada, the Las Vegas Review-Journal has learned.

About two dozen FBI agents served subpoenas on Whittemore business associates and others in some 30 locations in Northern and Southern Nevada, sources said.

Federal prosecutors expect to present evidence in the investigation to a federal grand jury in Reno at the end of the month, the sources said.

Whittemore, once a high-powered lobbyist who has many influential friends in Nevada politics, released a statement Thursday through a spokeswoman for a Las Vegas law firm.

"Understandably, based on the reckless accusations made in the civil lawsuit filed two weeks ago, law enforcement is requesting information from knowledgeable parties," said the statement from Elizabeth Trosper, spokeswoman for the Gordon Silver law firm.

Trosper was referring to a multimillion-dollar lawsuit filed against Whittemore by former business partners alleging embezzlement.

An FBI spokesman declined to confirm or deny the existence of the investigation.
…

FBI agents visited at least one location Thursday, the Whittemore Peterson Institute, a Reno research facility that focuses on neuro-immune diseases. The Whittemore family created the institute after one of their children who was diagnosed with chronic fatigue syndrome.

Annette Whittemore, in a brief conversation Thursday, confirmed that FBI agents had gone to the Whittemore Peterson Institute and "interviewed" an employee "involving a personal matter."

When asked whether the interview was in regards to a grand jury subpoena about campaign contribution violations, she said, "I am not at liberty to discuss that."

Annette Whittemore would not identify the employee.

Trosper said in her statement: "To be clear, the Whittemore Peterson Institute has not been raided and is cooperating in these inquiries."

Mikovits/WPI "UK study": At least one blood sample and consent form seems missing

After Judy Mikovits was dismissed by the WPI, I sought clarification from Annette Whittemore regarding the institute’s plans for the UK study so that I could decide whether or not to continue as a participant. It subsequently emerged that both my blood sample and consent form had been lost. Perhaps, predictably, the WPI blamed Dr Mikovits’ housekeeping and tried to ‘move me along’.
…

22nd November 2011
Kellen [Jones-Monick, WPI’s Office Manager] confirmed that the WPI holds the consent forms and that she could provide copies upon request.

I requested a copy of my consent form from Kellen (request sent again on 27th November 2011).

5th December 2011
Kellen confirmed that both my blood sample and consent form had been lost.

“After carefully reviewing our study records, I was unable to find a consent for you. I also checked with the lab to determine whether or not we have your blood sample and it appears we never received one. Therefore, according to our records you are not enrolled in the R01.”

Does Table Number 4 lie?

UPDATE: The questions that arise from table 4 can be found here.

At the end of this post is the table 4 from the addendum to Lombardi et al. 2009 (submitted in February 2010).

In this table we find:

• Only 93 of the 101 patients are reported (WTF?)
• 73/93 (78%) are positive by cDNA nested PCR
• 17/93 (18%) are positive by DNA nested PCR
• 34/45 (76%) are positive by LNCaP co-culture with PMCs 
• 35/46 (76%) are positive by Antibody in plasma
• 48/51 (94%) (!) are positive by LNCaP culture with plasma

Please note that PCR positive rate went up from 68/101 in Lombardi et al 2009 to 73/93 in the addendum.

When looking only at the 20 PCR negative patient samples, we find that:

• 12/20 (60%) PCR negative patient samples were not tested by other methods, only one PCR negative patient sample (the all negative 1139) was tested by all methods - this is at odds with the claims by Dr. Mikovits in her talks since October 2009 that all PCR negative samples were tested and that 31/33 PCR negative samples were positive by other methods 
• 1/2 (50%) are positive by LNCaP co-culture with PMCs 
• 3/4 (75%) are positive by Antibody in plasma
• 6/7 (86%) are positive by LNCaP culture with plasma
• Only one patient tested by all methods was negative by all methods (1139)

This is simply unbelievable sloppy work (only 93 patient samples reported, reports at odds with information given in talks). Why weren't they called out for this? This is a bad joke.


Here is the table, the rows are:

• Patient ID
• cDNA nested PCR
• DNA nested PCR
• LNCaP co-culture with PMCs 
• Antibody in plasma
• LNCaP culture with plasma

(With "nt" = not tested)

1103 + + + + +

1104 + + + + +

1105 + - + + +

1106 + + + + +

1107 + - - nt nt

1108 + - - - -

1109 + - nt nt nt

1110 + - + + +

1111 + + + - +

1112 + - nt nt nt

1113 + - + nt nt

1114 + - nt nt +

1115 + - + + +

1116 - - nt nt +

1117 - - nt nt nt

1118 + - + + +

1119 + - nt nt nt

1120 - - nt nt nt

1121 + - nt nt nt

1124 + - - - -

1125 + - + + +

1126 + - nt nt nt

1127 + - nt nt nt

1128 + - nt nt nt

1129 + - nt - nt

1130 + - nt nt nt

1131 + - nt nt nt

1132 + + + nt nt

1133 + + nt nt nt

1134 - - nt nt nt

1135 + + nt nt nt

1136 + + - + +

1137 + + - + +

1265 + - + + +

1138 + - nt nt nt

1335 + - nt + +

1139 - - - - -

1140 + - nt - +

1141 + - + + +

1142 - - nt nt +

1206 + - nt - +

1144 + - nt nt nt

1145 - - nt nt nt

1148 - - nt nt nt

1149 + - nt nt nt

1150 + + + + +

1151 + - nt nt nt

1230 + - + nt nt

1237 + - + nt nt

1154 - - nt nt nt

1155 - - nt nt nt

1156 - - nt nt +

1157 + + nt nt nt

1158 + - - + +

1159 + - nt nt nt

1231 + - + nt nt

1161 + - - + +

1220 + - + nt nt

1221 + - + nt +

1164 - - nt nt nt

1165 + - + + +

1166 + - - + +

1167 - - nt nt nt

1168 + - nt nt nt

1169 + - + + +

1170 - - nt nt nt

1235 - - + nt nt

1281 + - + + +

1172 + + + + +

1282 + - - - +

1173 + + + + +

1174 + - nt nt nt

1175 - - nt nt nt

1176 - - nt nt nt

1177 + - + + +

1178 + - + + +

1179 + - nt - +

1180 - - nt + +

1181 + - nt nt nt

1182 - - nt + +

1183 + - - - +

1236 + - + nt nt

1224 + - nt nt +

1186 + + + + +

1187 - - nt + +

1188 + - + + +

1189 + + + + +

1190 + - + + +

1191 + - + + +

1192 + + nt + +

1193 + + nt + +

1194 + - nt - +

1238 + - + + +

Please notice the "odd" numbers (like 1206 or 1238), and the two "missing" patient numbers (1122 and 1123).

Focusing only on the PCR negative, first we have 8 patients tested by other methods (7 positive by other methods, 1 negative by all methods):

1116 - - nt nt +

1142 - - nt nt +

1156 - - nt nt +

1180 - - nt + +

1182 - - nt + +

1187 - - nt + +

1139 - - - - -

1235 - - + nt nt

And twelve patients were PCR negative but not tested (WTF?):

1117 - - nt nt nt

1120 - - nt nt nt

1134 - - nt nt nt

1145 - - nt nt nt

1148 - - nt nt nt

1154 - - nt nt nt

1155 - - nt nt nt

1164 - - nt nt nt

1167 - - nt nt nt

1170 - - nt nt nt

1175 - - nt nt nt

1176 - - nt nt nt

(Sorry if the formatting of the table is garbled up, I can't post it any better; You can look up the table in the PDF)

Update: I uploaded the spreadsheet here.