Cort
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Original Science Cohort Questions
- Thread starter Cort
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misskoji
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Another?
moved to XMRV Replication thread.
moved to XMRV Replication thread.
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Katie
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moved to XMRV Replication thread.
A
ABarker
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Xmrv
After the initial Science publication came out on October 8th, many with ties to WPI stated that the 101 CFS cohort included samples from Dr. Peterson's Bio Bank repository. About 3 weeks ago, the WPI changed their website, now stating that none of the original 101 samples came from Peterson's Bio Bank, and that they all were collected between 2006-2009. It states:
"Dr. Daniel Peterson understood the promise that a historical bio bank could bring to scientific understanding thus he began collecting and storing patient samples in the early 1980's. However, it is important to note that no samples from this historical bio bank were used in the Institute's XMRV studies." http://www.wpinstitute.org/research/research_biobank.html
So they clearly state that none of the 101 samples from the original Science punlication were from earlier than 2006. But sample "WPI-1125" clearly shows that it is from as early as 1988. In addition to this, on the same page of the WPI website, there is a section entitled "FAQs about the Whittemore Peterson Institute Bio Bank". It states that for the original XMRV study:
"All samples were collected from 2006-2009, under the WPI's research department with signed patient consent forms."
They also address the issue of lymphoma, stating that:
"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."
http://www.wpinstitute.org/research/research_biobank.html
Peterson's slide-show from his October 29th CFSAC presentation was available in paper format; it is 5 pages long, with 5 slides per page.
On page 5 of the original XMRV Science study published on October 8th, 11 samples representative of the CFS patients that were assayed for the GAG are marked as group "A", and appear on the left of the page. Of theses 11 patients, the 7th from the left is represented as "WPI-1125". In Peterson's presentation, page 1, slide 5 is similar to the GAG assay results from the original Science study, marked group "A". It is difficult to read, but on this slide, the 7th from the left in group "A" is also identified as "WPI-1125" -- the same patient as the Science article. On this slide, it also clearly indicates that these 11 samples are part of the 101 patient CFS cohort. This is represented at the bottom of the slide, by the "68/101 (67%)".
On page 5 of Peterson's presentation, the 2nd slide of the page (22nd overall), is titled, "WPI-1125 CFS Diagnosis One Decade Prior to MCL". In this slide, patient "WPI-1125" is again identified as part of the CFS cohort. Furthermore, it includes a timeline of his illness:
During his presentation, Peterson stated that they had went back and looked at samples from his Bio Bank since the original Science publication, and I don't doubt this. However, the initial Science publication clearly shows that patient "WPI-1125" was included in the original 101 CFS cohort. In addition, it was clearly known since at least 2000 that patient "WPI-1125" had lymphoma. The statement on WPI's website about all of the 101 original samples being from 2006-2009 was only posted to their website approximately 2-3 weeks ago. At that time, the statement that none of the original 101 samples had lymphoma was posted to the WPI site as well.
The WPI site states that: "Another preliminary study was done at a later date that had nothing to do with the (original) XMRV Science publication." -- however this clearly contradicts the inclusion of patient "WPI-1125" in the original study. Like I said, I don't doubt further sampling has been done, but it is blatantly obvious that something is not right here...
"WPI-1125" is also mentioned in the "Supporting Online Material" published by Science on October 23rd, but the same sample WITH lymphoma, and FROM Peterson's repository WAS included in the original 101 cohort...
This is the only patient that I have spent time looking into -- I don't know if other samples from the original 101 CFS cohort had lymphoma, or if they were from Peterson's Bio Bank, and not from 2006-2009, as WPI claims...
After the initial Science publication came out on October 8th, many with ties to WPI stated that the 101 CFS cohort included samples from Dr. Peterson's Bio Bank repository. About 3 weeks ago, the WPI changed their website, now stating that none of the original 101 samples came from Peterson's Bio Bank, and that they all were collected between 2006-2009. It states:
"Dr. Daniel Peterson understood the promise that a historical bio bank could bring to scientific understanding thus he began collecting and storing patient samples in the early 1980's. However, it is important to note that no samples from this historical bio bank were used in the Institute's XMRV studies." http://www.wpinstitute.org/research/research_biobank.html
So they clearly state that none of the 101 samples from the original Science punlication were from earlier than 2006. But sample "WPI-1125" clearly shows that it is from as early as 1988. In addition to this, on the same page of the WPI website, there is a section entitled "FAQs about the Whittemore Peterson Institute Bio Bank". It states that for the original XMRV study:
"All samples were collected from 2006-2009, under the WPI's research department with signed patient consent forms."
They also address the issue of lymphoma, stating that:
"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."
http://www.wpinstitute.org/research/research_biobank.html
Peterson's slide-show from his October 29th CFSAC presentation was available in paper format; it is 5 pages long, with 5 slides per page.
On page 5 of the original XMRV Science study published on October 8th, 11 samples representative of the CFS patients that were assayed for the GAG are marked as group "A", and appear on the left of the page. Of theses 11 patients, the 7th from the left is represented as "WPI-1125". In Peterson's presentation, page 1, slide 5 is similar to the GAG assay results from the original Science study, marked group "A". It is difficult to read, but on this slide, the 7th from the left in group "A" is also identified as "WPI-1125" -- the same patient as the Science article. On this slide, it also clearly indicates that these 11 samples are part of the 101 patient CFS cohort. This is represented at the bottom of the slide, by the "68/101 (67%)".
On page 5 of Peterson's presentation, the 2nd slide of the page (22nd overall), is titled, "WPI-1125 CFS Diagnosis One Decade Prior to MCL". In this slide, patient "WPI-1125" is again identified as part of the CFS cohort. Furthermore, it includes a timeline of his illness:
- 1988 -- Seen at NIH for CFS
- 1998 -- Splenectomy to decrease aggressiveness
- 2000 -- Seen at NIH for mantle cell lymphoma. Given Rituxan and Velcade.
- 2004 -- BMT with adult stem cells
- 2008 -- Blast crisis MCL ... death
During his presentation, Peterson stated that they had went back and looked at samples from his Bio Bank since the original Science publication, and I don't doubt this. However, the initial Science publication clearly shows that patient "WPI-1125" was included in the original 101 CFS cohort. In addition, it was clearly known since at least 2000 that patient "WPI-1125" had lymphoma. The statement on WPI's website about all of the 101 original samples being from 2006-2009 was only posted to their website approximately 2-3 weeks ago. At that time, the statement that none of the original 101 samples had lymphoma was posted to the WPI site as well.
The WPI site states that: "Another preliminary study was done at a later date that had nothing to do with the (original) XMRV Science publication." -- however this clearly contradicts the inclusion of patient "WPI-1125" in the original study. Like I said, I don't doubt further sampling has been done, but it is blatantly obvious that something is not right here...
"WPI-1125" is also mentioned in the "Supporting Online Material" published by Science on October 23rd, but the same sample WITH lymphoma, and FROM Peterson's repository WAS included in the original 101 cohort...
This is the only patient that I have spent time looking into -- I don't know if other samples from the original 101 CFS cohort had lymphoma, or if they were from Peterson's Bio Bank, and not from 2006-2009, as WPI claims...
dipic
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moved to XMRV replication thread
Cort
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Whoops! - Removed post
A
ABarker
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Peterson's slide-show
Dr. Peterson's slide-show presentation from the CFSAC is available to the public -- I tried to upload it here, but the file is too large.
Dr. Peterson's slide-show presentation from the CFSAC is available to the public -- I tried to upload it here, but the file is too large.
Cort
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A.Barker has obviously taken a very close look at the study. In the kind of circles the WPI is engaged with now we should assume, I would think, that everything is being given a very close look.
That Science cohort has been something of a problem; the Science paper stated that they all had immunological abnormalities and other problems; it later followed by a statement that not all of them did immunological abnormalities. A reporter apparently got Dr. Mikovits statement wrong that 20 of the CFS patients had lymphoma. The WPI later put out a clarifying statement that none of the patients had lymphoma.
Dr. Peterson's old BioBank he'd collected over 25 years was, according to A. Barker, not used in the study (presumably because the samples may not have been in the greatest shape).
If A. Barker is right then at least one of the patients did have lymphoma and his sample may have come from the original BioBank. (I would think that he probably had his sample done from 2006-2008 and inserted into the new biobank(?))
That patient had had a rough time; they removed his spleen, it looks like, to try and turn down his immune system (?), was diagnosed with lymphoma, got chemotherapy and stem cell therapy and later died.
This is not the type of patient that you'd want in a representative study - his case was far too severe to be representative. Of course it does bring up questions if there was anyone else like him in the study.
That Science cohort has been something of a problem; the Science paper stated that they all had immunological abnormalities and other problems; it later followed by a statement that not all of them did immunological abnormalities. A reporter apparently got Dr. Mikovits statement wrong that 20 of the CFS patients had lymphoma. The WPI later put out a clarifying statement that none of the patients had lymphoma.
Dr. Peterson's old BioBank he'd collected over 25 years was, according to A. Barker, not used in the study (presumably because the samples may not have been in the greatest shape).
If A. Barker is right then at least one of the patients did have lymphoma and his sample may have come from the original BioBank. (I would think that he probably had his sample done from 2006-2008 and inserted into the new biobank(?))
That patient had had a rough time; they removed his spleen, it looks like, to try and turn down his immune system (?), was diagnosed with lymphoma, got chemotherapy and stem cell therapy and later died.
This is not the type of patient that you'd want in a representative study - his case was far too severe to be representative. Of course it does bring up questions if there was anyone else like him in the study.
Eric Johnson from I&I
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Why are you saying the supplement was put out Oct 23? It was put out with the main paper, I downloaded them both on the same night. Just curious how you got that impression, since you have such an nose for detail otherwise (I'm being earnest, not backhandedly sarcastic).
Anyway, those are worthwhile points for sure. But wasnt WPI-1125 sort of Peterson's "favorite" case, which he sent to NIH to be studied as a paradigmatic case? Isnt it possible that Peterson put him (and only him) in out of curiosity, because of his fascination with this case, and that this detail slipped mind of the person making the categorical statements about lymphoma and the date of blood/tissue sampling?
WPI-1125's procedures with Rituxan and immunoablation with stem cell rescue which is probably what is meant by BMT, bone marrow transplant) are of overwhelming theoretical interest for the mechanisms of CFS, so Peterson's interest in him is not misplaced. If you like I can show you posts I made years ago, begging anyone to come up with any info on CFS patients that have had immunoablation done (for cancer), and explaining why it matters.
> But sample "WPI-1125" clearly shows that it is from as early as 1988.
What is it exactly that you say clearly shows this; where can I read it? NVLLIVS IN VERBA!, as momma always said when you were just a lad.
And do you have a source for your statements about people tied to WPI saying stuff about samples from the Peterson stash, or about WPI changing its website?
At any rate, WPI was already judged by Coffin et al; they can take this thing no further themselves. Whether this thing is true or false will now be decided by other labs.
Anyway, those are worthwhile points for sure. But wasnt WPI-1125 sort of Peterson's "favorite" case, which he sent to NIH to be studied as a paradigmatic case? Isnt it possible that Peterson put him (and only him) in out of curiosity, because of his fascination with this case, and that this detail slipped mind of the person making the categorical statements about lymphoma and the date of blood/tissue sampling?
WPI-1125's procedures with Rituxan and immunoablation with stem cell rescue which is probably what is meant by BMT, bone marrow transplant) are of overwhelming theoretical interest for the mechanisms of CFS, so Peterson's interest in him is not misplaced. If you like I can show you posts I made years ago, begging anyone to come up with any info on CFS patients that have had immunoablation done (for cancer), and explaining why it matters.
> But sample "WPI-1125" clearly shows that it is from as early as 1988.
What is it exactly that you say clearly shows this; where can I read it? NVLLIVS IN VERBA!, as momma always said when you were just a lad.
And do you have a source for your statements about people tied to WPI saying stuff about samples from the Peterson stash, or about WPI changing its website?
At any rate, WPI was already judged by Coffin et al; they can take this thing no further themselves. Whether this thing is true or false will now be decided by other labs.
Chris
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XMRV replication
Cort, there is also Dr. Paul Jolicoeur at L'Institute de recherche attached to the University of Montreal in Montreal; he is a retroviral specialist, and has advertised for 50 CFS patients to come forward--wish I were still in Montreal! Chris
Cort, there is also Dr. Paul Jolicoeur at L'Institute de recherche attached to the University of Montreal in Montreal; he is a retroviral specialist, and has advertised for 50 CFS patients to come forward--wish I were still in Montreal! Chris
Cort
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Its just a problem. Its not necessarily a big problem. Its not just Dr. Peterson's slides - thats understandable that he would want to highlight that patient but if I understand the post right - and it is complicated - then that patient was a member of the Science cohort and he did have lymphoma - and the WPI said that no patients in the study had lymphoma.
Its messy and it shouldn't happen in a research paper. I'm sure it does probably more than we wish. Its a little thing, not a big thing.
It doesn't negate the science in the paper at all. That is the most important part and that's the thing to focus on but it does bring up questions about the original cohort.
Of course over time we'll know all we need to know about who these findings apply to.
Its messy and it shouldn't happen in a research paper. I'm sure it does probably more than we wish. Its a little thing, not a big thing.
It doesn't negate the science in the paper at all. That is the most important part and that's the thing to focus on but it does bring up questions about the original cohort.
Of course over time we'll know all we need to know about who these findings apply to.
Andrew
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We haven't established a lymphoma discrepancy in the research. The paper doesn't even mention lymphoma, one way or the other. Someone else will have to check the supplement because I don't have it.
ABarker is talking about a difference between the slide and the website. It might just be an error on the part of the webmaster, or the slide might be of a test that was not included in the study, or who knows what. But were it my data, I'd like someone to notify me.
A
ABarker
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You might be right about the publication date of the Supplemental Materials. For some reason, I thought it was October 23rd, but either way, it doesn't matter with regard to the discrepancy between what the WPI is claiming, and what was published in the Science study, and in Peterson's slide-show.
"WPI-1125" may have been of special interest to Peterson. All I'm pointing out is that the WPI categorically denies that any of their samples used in the original XMRV study were from Peterson's Bio Bank, and that none of the samples had lymphoma. According to Peterson's CFSAC testimony, and the original Science publication, sample "WPI-1125" did have lymphoma, and was from Peterson's Bio Bank.
My source for WPI changing its website? Well, the information about the XMRV samples being from 2006-2009, and not from Peterson's Bio Bank was not there about 3 weeks ago. The statement about no patients from the original 101 cohort having lymphoma was not there about 3 weeks ago. Now they both are there.
Peterson's CFSAC presentation shows that "WPI-1125" was from as early as 1988. The original Science publication shows that "WPI-1125" was part of the 101 patient cohort.
Peterson's slide-show was available to the public at the CFSAC meeting. I tried to upload it here, but the file is too large.
"WPI-1125" may have been of special interest to Peterson. All I'm pointing out is that the WPI categorically denies that any of their samples used in the original XMRV study were from Peterson's Bio Bank, and that none of the samples had lymphoma. According to Peterson's CFSAC testimony, and the original Science publication, sample "WPI-1125" did have lymphoma, and was from Peterson's Bio Bank.
My source for WPI changing its website? Well, the information about the XMRV samples being from 2006-2009, and not from Peterson's Bio Bank was not there about 3 weeks ago. The statement about no patients from the original 101 cohort having lymphoma was not there about 3 weeks ago. Now they both are there.
Peterson's CFSAC presentation shows that "WPI-1125" was from as early as 1988. The original Science publication shows that "WPI-1125" was part of the 101 patient cohort.
Peterson's slide-show was available to the public at the CFSAC meeting. I tried to upload it here, but the file is too large.
Eric Johnson from I&I
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Cort, I think you may be mistaken about the immune abnormalities. All I find is this, from the supplement, which doesnt imply that all of them had immune abnormalities. (At least not to my ear.)
A
ABarker
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I'm pointing out a discrepancy between this: the WPI claims on their website that no samples in the Science publication were from Peterson's Bio Bank, and no samples had lymphoma. However, in Peterson's CFSAC presentation states that "WPI-1125" was included in the original Science publication, amd had lymphoma. The original Science publication also includes patient "WPI-1125". So there is discrepancy because a patient with lymphoma and from Peterson's Bio Bank was included in the original XMRV study, however the WPI states that no patients from the study had lymphoma, and no patients were from Peterson's Bio Bank.
Peterson's slide-show was public, so maybe someone else has it. I have it, but it went let me upload it...
Peterson's slide-show was public, so maybe someone else has it. I have it, but it went let me upload it...
Eric Johnson from I&I
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> Peterson's CFSAC presentation shows that "WPI-1125" was from as early as 1988.
It's not clear why this is a problem; "as early as 1988" includes the years 1988, 1989, 2005, 3453, and 30467234, but not 1987. But it does include 2006-8 just as Cort says. Since the man perished in '08, he was alive for most of '06-08.
> Well, the information about the XMRV samples being from 2006-2009, and not from Peterson's Bio Bank was not there about 3 weeks ago. The statement about no patients from the original 101 cohort having lymphoma was not there about 3 weeks ago. Now they both are there.
Adding stuff to your website is pretty blase, ho-hum. If it contradicts past statements thats another story, but there will only be a contradiction, I think, if you have a source for this:
> After the initial Science publication came out on October 8th, many with ties to WPI stated that the 101 CFS cohort included samples from Dr. Peterson's Bio Bank repository.
Other than that I dont dispute you on the facts, clearly it seems that at least one patient had cancer, contrary to whats been said. Even though the guy has been known to Peterson for a long time, its not clear that the man was not sampled in 2006-8 with the others; you seem to be wrong on that.
I think it could have just been an oversight about one guy having cancer -- especially since it seems to be one of the most interesting of all cases to Peterson. Because of his interest he might have added the guy in after the other samples were all taken, which would make it easy for someone to forget about the guy and the fact of his cancer. I agree with you completely that I cant prove this, its basically rank speculation.
It's not clear why this is a problem; "as early as 1988" includes the years 1988, 1989, 2005, 3453, and 30467234, but not 1987. But it does include 2006-8 just as Cort says. Since the man perished in '08, he was alive for most of '06-08.
> Well, the information about the XMRV samples being from 2006-2009, and not from Peterson's Bio Bank was not there about 3 weeks ago. The statement about no patients from the original 101 cohort having lymphoma was not there about 3 weeks ago. Now they both are there.
Adding stuff to your website is pretty blase, ho-hum. If it contradicts past statements thats another story, but there will only be a contradiction, I think, if you have a source for this:
> After the initial Science publication came out on October 8th, many with ties to WPI stated that the 101 CFS cohort included samples from Dr. Peterson's Bio Bank repository.
Other than that I dont dispute you on the facts, clearly it seems that at least one patient had cancer, contrary to whats been said. Even though the guy has been known to Peterson for a long time, its not clear that the man was not sampled in 2006-8 with the others; you seem to be wrong on that.
I think it could have just been an oversight about one guy having cancer -- especially since it seems to be one of the most interesting of all cases to Peterson. Because of his interest he might have added the guy in after the other samples were all taken, which would make it easy for someone to forget about the guy and the fact of his cancer. I agree with you completely that I cant prove this, its basically rank speculation.
Eric Johnson from I&I
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> So there is discrepancy because a patient with lymphoma and from Peterson's Bio Bank was included in the original XMRV study
Lymphoma yes, Peterson's private stash, I dont agree -- since theres no indication that he wasnt re-sampled WPI in 06-08.
> Peterson's slide-show was public, so maybe someone else has it. I have it, but it went let me upload it...
I looked at the video on youtube. Definitely 1125. Its also possible though not particularly likely, that he wrote 1125 on the slide when he meant some other number.
Lymphoma yes, Peterson's private stash, I dont agree -- since theres no indication that he wasnt re-sampled WPI in 06-08.
> Peterson's slide-show was public, so maybe someone else has it. I have it, but it went let me upload it...
I looked at the video on youtube. Definitely 1125. Its also possible though not particularly likely, that he wrote 1125 on the slide when he meant some other number.
A
ABarker
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Maybe "WPI-1125" was sampled between 2006-2008. But it was known from at least 2000 that the patient had lymphoma. Either way, its a discrepancy with what the WPI is now claiming.
A
ABarker
Guest
In the paper copy of Peterson's slide-show, the image on the 5th slide, page 1 is identical to page 5 of the original Science publication. The only difference is that at the bottom of Peterson's slide it states:
"68/101 (67%)" and "These results are representative of the 101 patients tested. They reflect the presence of virus (DNA PCR)."
"68/101 (67%)" and "These results are representative of the 101 patients tested. They reflect the presence of virus (DNA PCR)."
Andrew
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Where can I find the paper copy of his slide show? And where can I see the medical information you quote for WPI-1125.