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Original XMRV/Prostate Cancer study retracted

RRM

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94
http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.0020025

Sorry for the multiple threads but I thought this deserved its own thread.

In light of the findings from a recent study “In-Depth Investigation of Archival and Prospectively Collected Samples Reveals No Evidence for XMRV Infection in Prostate Cancer” (http://dx.plos.org/10.137...) and others in the field, the editors of PLOS Pathogens have issued a retraction of this study. The association of XMRV with prostate cancer has now been thoroughly refuted. Although the original finding of a novel gammaretrovirus, XMRV, with the use of a pan-viral detection microarray is valid, and sequencing and phylogenetic characterization of the virus still stands, the editors agree that it is clear that XMRV found in this study is laboratory-derived and there is no association of XMRV with prostate cancer. As a result the paper was retracted from PLOS Pathogens on September 18th, 2012.
 

Firestormm

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Looks like this editors retraction is proving a tad controversial after all - with Silverman at least:

Retraction of First Paper on XMRV Takes Authors by Surprise

The journal PLoS Pathogens yesterday retracted the first ever paper about XMRV, the virus that has become notorious for its reported—and now firmly refuted—link to chronic fatigue syndrome (CFS). The retraction, issued by the journal's editors, surprised the authors of the 2006 study, which reported a different link between XMRV and prostate cancer. The authors didn't think the paper needed to be retracted and weren't consulted by the journal or informed that the retraction would happen.

The retraction follows the publication of a new study yesterday in PLoS ONE, in which the authors of the retracted paper—along with others—conclude that the 2006 results don't hold up and report on an in-depth investigation on what went wrong in their labs. "But the discovery of XMRV, a new virus, still stands," says one of the authors, Robert Silverman of the Cleveland Clinic in Ohio, and an erratum to withdraw the prostate cancer link would have sufficed. "Why retract results that are valid?" Silverman asks.

Silverman's work on XMRV had started much earlier, around 2004. His group suspected that a virus might be involved in some cases of prostate cancer cases because men with mutations in the gene for RNase L, which is involved in innate immunity, have a higher risk for the disease. A collaboration with UCSF researchers Joseph DeRisi and Donald Ganem, who had developed a virus discovery microarray called the ViroChip, then turned up XMRV.

When the CFS study unraveled, Silverman says he realized that his results, too, might be in trouble. A series of papers published in 2010 and 2011—most notably, a study by Vinay Pathak and John Coffin of the National Cancer Institute in Frederick, Maryland—convinced him that the study was wrong and that XMRV had accidentally infected samples in the lab. From then on, "I felt I couldn't rest until I figured out how it happened," he says. "I wanted to get some closure."

Further studies—some using techniques unavailable at the time of the study—revealed that the virus originated in LNCaP, a cell line infected with XMRV that Silverman's lab used for other studies. The LNCaP cells, in turn, had become contaminated by 22Rv1, another widely used cell line that is now known to harbor XMRV.

The new study wins praise for its meticulous effort to set the record straight. "This paper made me feel proud of the authors and of our profession," Pathak says. "These scientists put their egos aside and aggressively and relentlessly pursued several lines of investigation to get to the truth." The team "deserves a medal," adds Kim McCleary, head of the CFIDS Association of America, an advocacy group for CFS patients. In the long history of pathogens falsely blamed for CFS, McCleary says she's never seen scientists retrace their steps so scrupulously.

In the paper, the group writes that XMRV is still a "genuine infectious agent" with "as-yet undefined pathogenic potential"; they point out that the virus is able to infect mice and two primate species and that several research groups have discovered interesting biological properties that could be useful, for instance, in cancer research. That's why an erratum to the original study would have been enough, Silverman says. "We've corrected the literature," he says.

A spokesperson for PLoS Pathogens couldn't answer questions about the retraction this morning but said the journal would respond later today or tomorrow. The retraction acknowledges that "the original finding of a novel gammaretrovirus, XMRV, with the use of a pan-viral detection microarray is valid, and sequencing and phylogenetic characterization of the virus still stands." It doesn't explain why the entire paper was nonetheless retracted.

http://news.sciencemag.org/sciencenow/2012/09/retraction-of-first-paper-on-xmr.html?ref=hp
 

Firestormm

Senior Member
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5,055
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Cornwall England
Retraction Watch have posted an update following their pursuit of this also:

Update, 5:45 pm Eastern, 9/19/12: Kasturi Haldar, the editor of PLoS Pathogens, tells us the journal acted after not hearing back from the authors:
PLOS Pathogens is a member of the Committee on Publication Ethics (COPE: http://publicationethics.org) and we follow their guidelines in reviewing any situation in which the literature may need to be corrected. The decision to retract the original 2006 paper was made in consultation with a large group of PLOS Pathogens’ senior editors. The authors were contacted by email on August 27th regarding our decision, and were asked to comment on the retraction text and suggest changes. We did not receive a reply, and decided to move forward with the retraction in conjunction with the PLOS ONE publication yesterday, September 18th.​

http://retractionwatch.wordpress.co...os-pathogens-prostate-cancer-study-retracted/
 

Firestormm

Senior Member
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5,055
Location
Cornwall England
Journal Apologizes for Retracting XMRV Paper Without Contacting Author

1 October 2012: http://news.sciencemag.org/scienceinsider/2012/10/journal-apologizes-for-retractin.html



In another unusual twist in the tumultuous history of XMRV, the journal PLoS Pathogens has apologized to a corresponding author for retracting the first paper on the virus without contacting him beforehand. In a statement posted on PLoS Blogs on Friday, Editor-in-Chief Kasturi Haldar acknowledged that the 2006 paper should not have been pulled without consulting Robert Silverman of the Cleveland Clinic in Ohio, one of two corresponding authors. But Haldar defended the editorial decision to retract the paper, which has been the subject of an intense online debate for the past week.

PLoS Pathogens retracted the paper, which reported the discovery of XMRV and its putative link to prostate cancer, on 18 September after a new study, co-authored by Silverman and published in PLoS ONE, had shown that the 2006 findings were the result of an accidental lab contamination. Silverman says he was "completely blindsided" by the retraction; he felt a correction would have been enough because the discovery of XMRV as a new virus still stands and other papers have corrected the erroneous link to prostate cancer.

PLoS Pathogens says it did notify the other corresponding author, Joseph DeRisi of the University of California, San Francisco—with whom editors had corresponded during the submission and review of the paper -- about the impending retraction in a 27 August e-mail; when DeRisi didn't reply, the editors retracted on their own. Since then, "We have apologized for not contacting the second corresponding author," Haldar's statement says. "Our expectation was that the first would discharge responsibilities to all remaining authors. We have since corresponded with all authors."

On Saturday, DeRisi posted a response to the retraction, in which he said he agreed with it. But whether he received the 27 August e-mail, and if so, why he failed to respond or to alert his co-authors, remains unclear. (DeRisi did not respond to multiple emails and voice messages from ScienceInsider.)

Silverman says he cannot comment on DeRisi's inaction; "Suffice it to say we have not been in contact for a long time," he says. As to the journal's apology, "I accept it, and I really appreciate it," he says.

Retraction guidelines from the Committee on Publication Ethics (COPE) say that editors should negotiate with authors on how to phrase a retraction, but not whether a journal should contact all of the authors, or what it should do when they don't respond to an e-mail.

The XMRV paper may well lead to more specific guidelines in the future, says COPE Chair Virginia Barbour, who's also PLoS medicine editorial director.

Meanwhile, a vigorous debate has erupted on whether the paper by DeRisi and Silverman needed to be retracted in the first place. Readers of PLoS Blogs and the Web site Retraction Watch have argued that there is no need to retract papers with honest mistakes in them, and that the word retraction carries the connotation of scientific misconduct.

Haldar stands by the decision to retract, on which "six senior PLoS Pathogens editors unanimously agreed," given that its key findings were wrong.

But in a post following her statement, Barbour acknowledges that there is "a clear need to have a discussion about how to annotate the literature post publication," and invites readers to chime in.

"Specifically, it is clear that somehow 'retraction' implies 'malfeasance' and although we at PLOS don't share that view, we understand that it is others' perception," Barbour writes.

Clear as mud :)