Advocates for genomic research in Africa are worried about fallout from a dispute that has roiled the Wellcome Sanger Institute, a major genome research center in Hinxton, U.K. Last year, whistleblowers privately accused Sanger of commercializing a gene chip without proper legal agreements with partner institutions and the consent of the hundreds of African people whose donated DNA was used to develop the chip. “What happened at Sanger was clearly unethical. Full stop,” says Jantina de Vries, a bioethicist at the University of Cape Town in South Africa, who has followed the dispute.
Sanger’s troubles have mounted since the beginning of the dispute, which was first made public last month. The institute says it did not commercialize the chips or profit from them, but admits in a statement that its relationship with some African partners has been “disrupted.” Stellenbosch University in South Africa has demanded that Sanger return samples. In addition, one whistleblower says she was fired because of the controversy, and a large research team has left the institute and ended a plan to study the genomes of 100,000 Africans.
More broadly, Sanger’s mishandling of the matter could erode trust between researchers and African people, setting back genomic research that could benefit them, de Vries says. “The tragedy and the scandal is that the people who will pay the price are Africans.”
Genome sequencing can reveal the genetic roots of diseases and offer clues for new drugs and personalized medicine. But whole genome sequencing costs $800 to $1200 per person. Researchers use gene chips as a cheaper shortcut to look at key spots in a person’s genome where variation might be expected. The chips can lower the cost to less than $100 per sample, but first they need to be designed based on entire genomes from a given population.
In a $2.2 million deal inked in 2017, Thermo Fisher Scientific made 75,000 gene chips, or microarrays, for Sanger based on African genomic data gathered through several collaborations. Working with a unit of the Medical Research Council in Entebbe, Uganda, researchers at Sanger sequenced nearly 2100 genomes of Ugandan people. To capture more of the variation on the continent, they partnered with other institutions in Africa to sequence the genomes of about 400 more people.
Sanger planned to use the new chips to study the genomes of up to 100,000 Africans, looking for genetic insights into conditions such as heart disease, diabetes, and high blood pressure. The data could benefit Africans, and because populations in Africa are more diverse than other populations, they also might contain genetic variants—rare or missing elsewhere in the world—that could help researchers understand the mechanisms behind common diseases.
The problems started when some Sanger scientists questioned the financial arrangements with their partner institutions, according to a whistleblower who was involved in the project. Thermo Fisher planned to pay $384,000 cash back on Sanger’s $2.2 million order, which would be distributed among the other partners. Sanger initially agreed not to take a share, according to internal emails seen by Science, as it was getting a discount on the chips. But the emails indicate that later in the process, administrators wanted Sanger to get a share of the payment. In early 2018, partners objected that they hadn’t been fully consulted.
Four scientists made a formal complaint in April 2018 to the Wellcome Trust, which provides the bulk of Sanger’s funding. They were also concerned that Sanger had developed the chips without the necessary legal agreements and consent. Some of the material transfer agreements (MTAs) Sanger had signed with African universities did not allow for commercialization. Sanger administrators agreed they would need to gain permission from their partners, according to the emails. But these records also indicate that Sanger was eager to buy the arrays before Thermo Fisher’s price guarantee expired at the end of 2018. In October 2017, Sanger and Thermo Fisher went ahead with a press release announcing the commercial launch of the gene chips, and Sanger ordered its chips in December 2017 without permission from all its partners. “The way it was done, we were in breach with ethics and many of these legal agreements,” says one whistleblower, who wishes to remain anonymous for fear of retribution in her career. The institute planned to consult with partners and get the required permissions if Thermo Fisher were to publicly sell any of the chips, spokesperson Steve Palmer says.
In March of this year, Stellenbosch University demanded Sanger return about 100 samples donated by the Nama people, as its MTA did not permit commercialization. “This conduct of the Wellcome Sanger Institute raises serious legal and ethical consequences,” wrote Vice-Rector Eugene Cloete. The University of KwaZulu-Natal in South Africa, which had gathered DNA from 100 people of Zulu descent, has also expressed concerns.
Ciara Staunton, an expert in the governance of genomic data at Middlesex University in London, says manufacturing and purchasing the chips, even for internal use, is commercial and should be consistent with MTAs and participant consent. “To do otherwise is hugely concerning, and legally and ethically questionable,” she says.
Sanger disputes the whistleblower allegations, which were first reported by The Times on 14 October. The institute says intellectual property lawyers who reviewed the whistleblowers’ complaint found no breach of contract or infringement of intellectual property. “There was no commercialization of the arrays,” Palmer says, adding that the institute never sold the arrays and has not received any payments in connection with them. Ron O’Brien, a spokesperson for Thermo Fisher in Waltham, Massachusetts, also claims the company did not commercialize the array.
The Thermo Fisher chip would have been cheaper than another gene chip created for African populations in 2017 by Illumina, researchers say. Researchers involved in Human Heredity and Health in Africa (H3Africa), a collaboration funded since 2010 by the U.S. National Institutes of Health (NIH) and the Wellcome Trust, have already used the “H3A” chip to screen 60,000 Africans to find gene variants linked to disease. Ambroise Wonkam, a medical geneticist at the University of Cape Town, is using them to study 2000 people with sickle cell anemia to learn about genes that favor survival. “The H3A chip is already helping a lot,” he says.
That chip was developed with a different set of African donor DNA. The donors’ consent did not restrict commercial use, says de Vries, who chaired the H3Africa ethics committee. She and others worry the Sanger affair could jeopardize the trust the collaboration has built with African institutions and people. “I do not want the fallout to start to have effects on H3Africa,” says Charles Rotimi, a member of the H3Africa steering committee and a genetic epidemiologist at NIH’s National Human Genome Research Institute in Bethesda, Maryland. “We are just gaining traction with genomics on the African continent.”
After the whistleblowers filed their complaint, the Wellcome Trust’s subsidiary that oversees Sanger asked an external lawyer to investigate. A summary of the lawyer’s report, which Sanger released in October 2018, addressed a separate complaint about alleged bullying by senior Sanger management, concluding that no wrongdoing took place. Regarding the gene chip work, it found there was “no wrongful exploitation of scientific work.”
All four whistleblowers have since left Sanger. One says she was fired in June for bringing Sanger “into disrepute” for writing emails to colleagues about the issue. Sanger declined to comment on personnel. The 75,000 gene arrays, stored at Sanger, have not been used and will expire in December.
With additional reporting by Sarah Wild.
*Correction, 30 October, 12:30 p.m.: An earlier version of this story stated that the Wellcome Trust asked an external lawyer to investigate whistleblower allegations. The request was made by the board of Genome Research Limited, a wholly owned subsidiary of the Wellcome Trust that oversees the Wellcome Sanger Institute. Also, a description of the source of the DNA samples used by H3Africa to design its array was attributed to de Vries, but she was not responsible for this aspect of the project.