Gene-Guided Chemotherapy Research Questioned as 3 NCI Trials Are Halted

Zosia Chustecka

July 27, 2010

July 27, 2010 — Three ongoing cancer trials funded by the National Cancer Institute have been suspended after the validity of the technology being used was called into question by a large group of US scientists.

Developed at Duke University, the technology now under question uses gene signatures to predict responses to chemotherapy. Two of the trials involve patients with non-small cell lung cancer (NCT00545948 and NCT00509366), and the third is in patients with breast cancer (NCT00636441).

The trials were suspended on July 22 and 23.

The move was made after a group of 31 scientists called on the National Cancer Institute to suspend the trials because of concerns over the prediction models that were being used. The models were developed on the basis of research reported by Anil Potti, MD, and Joseph Nevins, PhD, from Duke University, Durham, North Carolina, but the validity of those models has been questioned by peer-reviewed reanalyses of their work, the scientists note.

In a letter dated July 19 and addressed to the new National Cancer Institute director, Harold Varmus, MD, the group of researchers called for the trials to be suspended until a "fully independent review is conducted of both the clinical trials and of the evidence and predictive models being used to make cancer treatment decisions."

At the same time, one of the Duke scientists involved in developing the technology has been suspended from his place of work. Dr. Potti was placed on administration leave while the university investigates allegations that he had falsely claimed to be Rhodes scholar, according to a report in the New York Times.

In addition, one of the published papers that reported this technology has now come under scrutiny. The Lancet Oncology has issued an "expression of concern" over a paper published in the journal in 2007, which described the validation of gene signatures to predict the response of breast cancer to neoadjuvant chemotherapy (Lancet Oncol. 2007;8:1071-1078).

That research was praised by an independent expert contacted by Medscape Medical News at the time, as it showed for the first time that gene signatures could predict responses to individual chemotherapy regimens.

However, since its publication in 2007, the methodology used to generate the response predictions has been questioned by statisticians from the M.D. Anderson Cancer Center in Houston, Texas, the journal notes.

The Lancet Oncology was contacted by senior author Richard Iggo, PhD, from the Swiss Institute for Experimental Cancer Research in Epalinges, Switzerland, and first author Hervé Bonnefoi, MD, from the Institut Bergonié, University of Bordeaux, France. They "expressed grave concerns about the validity of their report in light of evolving events," and said they had repeatedly tried to contact their coauthors at Duke University (including Dr. Potti) without success.

The journal notes that the 15 European coauthors of the paper concur with the "expression of concern" notice that the journal has posted online and said that the 4 coauthors from Duke University have been contacted separately.

Controversy Surrounding Dr. Anil Potti and Duke University

The controversy surrounding Dr. Potti and his team's research at Duke University is outlined in exhaustive detail in a report published in the July 16 issue of The Cancer Letter. This publication found Dr. Potti's false claim of being Rhodes scholar in multiple grant applications submitted by him, and notes that the claim was also featured in a Duke newsletter in January 2007. However, this credential "disappeared" from Dr. Potti's biography later in 2007. The publication also found mentions of 2 other awards that it was unable to verify.

In addition to questions about Dr. Potti's credentials, The Cancer Letter notes that research coming out of his group has been "marred by corrections and even corrections of corrections," and points out that "errors in genomics research could have direct implications for patients."

Dr. Potti is considered to be a pioneer of personalized medicine because of his team's work on using gene signatures to predict responses to chemotherapy, and he has been featured in Duke University commercials aimed at the general public, the publication notes.

However, this work has been questioned by other scientists, it points out.

Two biostatisticians at the M.D. Anderson Cancer Center, Keith Baggerley, PhD, and Kevin Coombes, PhD, attempted to verify this work but found a series of errors, including mislabeling and mismatching of gene probe identifiers. They published their findings in November 2009 in the Annals of Applied Statistics (2009;3:1309-1334) and concluded: "Unfortunately, poor documentation can shift from an inconvenience to an active danger when it obscures not just methods but errors."

The biostaticians also suggested that the errors they found in the technology — which was being used in ongoing clinical trials to allocate patients to treatment group — may be putting patients at risk.

The Cancer Letter reports that as a result of that publication, Duke University temporarily suspended 3 clinical trials that were using gene signatures to assign patients to treatment — these are the same 3 trials that were suspended again a just few days ago.

However, even though Duke suspended those trials in October 2009, they were restarted again in January 2010 after an internal investigation by Duke's Institutional Review Board confirmed the research and concluded that this approach was "viable and likely to succeed."

When contacted by The Cancer Letter and shown documents obtained under the Freedom of Information Act, the 2 statisticians from M.D. Anderson who had questioned the technology said they were not satisfied by the internal review. "Duke's statement implies that other members of the scientific community should be able to replicate the reported results with the data available," they told the publication. "Having tried, we can confidently state that this is not yet true."

The letter to the National Cancer Institute from the group of 31 scientists, which comprises many professors of statistics and biostatistics from prestigious US universities, including Johns Hopkins, Harvard, and Princeton, refers both to the Annals of Applied Statistics paper and The Cancer Letter reports.

"It is absolutely premature to use these prediction models to influence the therapeutic options open to cancer patients," the letter says, as independent experts have been unable to substantiate the researchers' claims using the researchers' own data. If the data and analysis can be validated, then it would be appropriate to reinitiate the trials, but until then, suspension of the ongoing trials is necessary, "given the potential of patients being assigned to improper treatment arms...[and] the associated potential risk posed to these patients."

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