A retraction in the Potti case?

In our very first post, we noted the case of Anil Potti,

a Duke researcher who posed as a Rhodes Scholar and appears to have invented key statistical analyses in a study of how breast cancer responds to chemotherapy[.The case] has sent ripples of angst through the cancer community. Potti’s antics prompted editors of The Lancet Oncology to issue an “expression of concern” — a Britishism that might be better expressed as “Holy Shit!” — about the validity of a 2007 paper in their journal by Potti and others.

There hasn’t been any further movement on The Lancet Oncology study, as far as we know, but on Friday the Raleigh News & Observer reported that one of Potti’s co-authors on a 2007 Journal of Clinical Oncology (JCO) paper had requested a retraction:

The work, which claims to establish a genetic basis for predicting which cancer patients will respond best to different treatments, has been questioned for at least a year, when scientists elsewhere tried to reproduce it and could not. In addition, the other scientists found numerous errors, requiring published corrections.

It’s not clear which paper the story is referring to. [See update at end.] Potti and Nevins co-authored two JCO studies in 2007, along with a slew of co-authors. One, “An integrated genomic-based approach to individualized treatment of patients with advanced-stage ovarian cancer,” has been cited 86 times, according to the Thomson Scientific Web of Knowledge.

We were unable to reproduce the results reported, and the structure that we did find appears driven far more by run date than by clinical response.

In other words, there was a large amount of variation in the results, depending on what day they were obtained.

The Nevins-Potti’s team responses to the letter are worth a read in light of recent events. At one point, they write:

…we believe it is incumbent on those who question the accuracy and reproducibility of scientific studies, and thus the value of these studies, to base their accusations with the same level of rigor that they claim to address.

A Saturday story in the News & Observer quoted Baggerly as “a biostatistician at MD Anderson Cancer Center in Texas who was among the first to question Potti’s research when it couldn’t be replicated.”

That suggests it’s the ovarian cancer paper that Nevins is requesting be retracted [see update below], which also squares with this passage from the Nevins-Potti team’s response to Baggerly:

While it is certainly important to present all information as accurately as possible, and we do regret the errors that were introduced when we generated several of the tables containing supplementary information, these errors do not affect the conclusions of the study.

The other paper co-authored by Nevins and Potti in the JCO in 2007 was “Pharmacogenomic Strategies Provide a Rational Approach to the Treatment of Cisplatin-Resistant Patients With Advanced Cancer.” It was cited 49 times, and was already the subject of a correction in the June 1, 2010 issue of the journal:

The October 1, 2007, article by Hsu et al, entitled “Pharmacogenomic Strategies Provide a Rational Approach to the Treatment of Cisplatin-Resistant Patients With Advanced Cancer” (J Clin Oncol 25:4350-4357, 2007), contained errors.

In Figure 1B, the labels for resistant and sensitive cell lines were inadvertently transposed.

In the legend of Figure2A,the reference to“bottom,lung” as well as the corresponding P value (P = .03) should have been omitted.

Journal of Clinical Oncology apologizes to the authors and readers for the mistakes.

We’ve contacted the JCO to confirm which paper is under review, and will update this post when we find out.

Update, 12:15 p.m. Eastern, 11/1/10: We’ve just received this response from the JCO, and the retraction request was for the second paper discussed here, “Pharmacogenomic Strategies Provide a Rational Approach to the Treatment of Cisplatin-Resistant Patients With Advanced Cancer:”

JCO only received notification from Dr. Joseph Nevins on Friday that says the paper is to be retracted. JCO has begun the process of looking in to this request, following the Committee on Publication Ethics (COPE) guidelines and JCO’s internal procedures.

When the Journal of Clinical Oncology (JCO) retracts a paper, notification of the retraction is immediately added to the online version of the article. Anyone coming to the site to view the article will see that it has been retracted. The article remains on the site in keeping with the standard of practice in publishing, which says that the history of an article should not be violated. In addition to the online notification, JCO will publish in the most immediately available print issue notification of the retraction. The notification appears prominently at the beginning of the table of contents and at the end along with the page number in the issue on which the retraction appears. Prior to retracting any paper, JCO must receive a signed statement from each author saying that he or she agrees that the article should be retracted and that the wording of the retraction is satisfactory to him or her.

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