Some witnesses to alleged incidents of research misconduct in Stanford President Marc Tessier-Lavigne’s lab would not talk to the committee investigating his research after being told their anonymity was not guaranteed, The Daily learned. The Daily also obtained email records showing that the committee was aware of additional allegations that it did not disclose in its report, released Wednesday morning.

The report, at 95 pages in length, contained a number of unflattering details about Tessier-Lavigne’s lab, including the conclusion that at least four papers with Tessier-Lavigne as principal author contained significant manipulation of research data and that Tessier-Lavigne had repeatedly failed to correct the scientific record for two decades. Its findings prompted Tessier-Lavigne’s resignation, who had been serving in his position since 2016. Still, the investigation had previously unreported limitations.

One person who spoke to the investigators said they asked for their identity not to be disclosed publicly or revealed to Tessier-Lavigne, telling investigators “the consequences of [recounting these events] could be enormous.” The witness said they were told investigators “couldn’t guarantee that.” As a result, they told The Daily that while they did participate in an interview, they withheld details from the investigators out of fear of retribution. 

Mark Filip, the former deputy attorney general who led the investigation, confirmed that sources were not guaranteed anonymity, saying that he did not believe it had hampered access to sources.

But another witness to internal Genentech discussions over potential fraud in Tessier-Lavigne’s lab, who was contacted by the investigators, said that they decided not to speak to the investigators at all after their concerns could not be assuaged. “There was zero possibility that my comments would be anonymous,” they said. Both provided The Daily with messages showing investigators’ requests to speak with them on the record.

The report did not ultimately name sources publicly. But the decision not to guarantee anonymity for potential sources who requested it on the front end concerned some outsiders, who worried about the investigators’ ability to obtain potentially sensitive information. Jeffrey Flier, who oversaw a number of research misconduct investigations as Dean of Harvard Medical School, called the move “extremely unusual” and said anonymity is an important tool “for the purposes of improving the access to information that is viewed as relevant.” Nancy Olivieri, a scientific whistleblower, viewed the decision as evidence “the senior administration wishes to limit the damage to Tessier-Lavigne” and avoid negative findings, a concern she has had since conflict-of-interest woes dogged the beginning of the inquiry.

The Stanford investigation, which was announced in a statement from board chair Jerry Yang that also praised Tessier-Lavigne’s “honor and integrity,” faced criticism from the start. Originally, it was to be led by a committee of five board members. The Daily revealed that Felix Baker, one of the members, maintained an $18 million stake in Denali Therapeutics, a biotech company co-founded by Tessier-Lavigne. After that disclosure, Baker stepped away and the board hired Filip to lead the review.

Filip and the scientists he recruited, including Randy Schekman, a Nobel laureate; Shirley Tilghman, a former Princeton president; Steve Hyman, a former Harvard provost and two other members of the National Academies have been tasked with investigating allegations against Tessier-Lavigne ranging from negligent oversight of papers bearing his name that appear to contain doctored images, to an alleged coverup of fabrication in Alzheimer’s research once thought to have upended prior theories about the cause of patients’ neurodegeneration. Tessier-Lavigne has adamantly denied any wrongdoing.

The report issued Wednesday admitted that “some individuals with knowledge or potential knowledge of matters pertaining to our work refused to speak with us,” but did not acknowledge that some refused to speak because of anonymity concerns.

The unwillingness of some to speak with the committee may have contributed to the exclusion of an allegation that Yang, who serves as a member of the special committee to investigate Tessier-Lavigne in addition to his role as board chair, learned about in a February email containing the account of a Genentech vice president. While two instances of alleged fraud in Tessier-Lavigne’s lab at Genentech have been reported publicly and were included in the report, this email contained an allegation about a third. “There was an earlier Cell paper that spawned a program and that data could also not be reproduced,” the email read. “That MTL postdoc was also fired.”

Filip declined to comment on what was left out of the report.

The two sources who did not provide their full accounts to the committee were in the position to possess knowledge about that allegation and a 2011 internal review inside Genentech that allegedly concluded there was fabrication in an Alzheimer’s study Tessier-Lavigne published in 2009. The paper, which Tessier-Lavigne described at the time as turning “our current understanding of Alzheimer’s on its head,” never turned into an Alzheimer’s treatment. Five senior leaders within the company have alleged that to be the fault of fabrication on the part of a postdoc in Tessier-Lavigne’s lab who left the company — and biotech — after the review concluded. 

Genentech confirms that Tessier-Lavigne knew the research was unreliable before he published it but says it has “no evidence of fraud”; Tessier-Lavigne denies any wrongdoing. Though Tessier-Lavigne ought to retract or heavily correct the paper, the Stanford report said, there was not evidence to suggest a finding of fraud.

“Certain allegations of ‘fraud’… are not accurate,” said the report. It also noted the conclusions reached were “necessarily based on the evidence and witnesses available to us.”

Elisabeth Bik, the prominent research misconduct investigator who first identified a number of the concerns that were verified as manipulation of research data by the committee, cautioned that not having guarantees of anonymity “would make several witnesses/sources very hesitant to speak.”

Bik, who has called for an independent investigation from the start, stressed that this approach may have allowed only one side of the story to be presented to the committee.

The Daily has spoken to seven people interviewed by the investigators, all of whom felt that the panel made good-faith efforts to extract their accounts. But some were confused that they were not asked questions about the third allegation of fraud in Tessier-Lavigne’s Genentech lab, despite being in a position to provide background.

The report did include information that had not been previously released, including new details about Tessier-Lavigne’s failure to correct the scientific record. This raises additional questions about why an allegation like the one that was sent in writing to the committee was not addressed and what else might not have been made public.

The committee has described its work as a “broad-based and thorough evaluation” that has required “hundreds of hours of meetings and witness interviews” and the review of thousands of documents.