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As Russia's War in Ukraine Continues, Genomics Research May Become Another Casualty


NEW YORK – As Russia's invasion of Ukraine moves into its second month, the war has not only caused unimaginable hardship for millions of Ukrainians and sparked the largest refugee crisis in Europe since World War II, but it has also profoundly affected the lives and work of genomics researchers in both countries, and their relationships with colleagues in the US and elsewhere.

While Ukrainian scientists in cities under attack by the Russian army are merely trying to stay alive as their institutes, homes, and infrastructure are being destroyed, a number of researchers in Russia who don't agree with their government's actions no longer see a professional future at home, while others have voiced their opposition to the war in the face of a regime that does not tolerate dissent.

In the meantime, scientists in the US, some with Ukrainian or Russian backgrounds, have been scrambling to support their colleagues and to keep existing projects and collaborations going.

The war has also created deep divides between Russia and Ukraine that might be difficult to repair once the immediate attacks subside. One medical geneticist from Kyiv, for example, who had originally agreed to be interviewed for this article, withdrew her participation when she heard that it would cover researchers from both countries, who are arguably very unequally affected. "Russia is waging a brutal war against Ukraine," she wrote in an email. "Being at constant risk of losing your life and home is incomparable with the financial difficulties that Russian scientists may have experienced."

Taras Oleksyk, a professor in the Department of Biological Sciences at Oakland University in Michigan whose research focuses on human population genetics and evolutionary genomics, grew up in Ukraine and still has family there, many of whom he said are either fighting against the Russian invaders right now or hosting refugees. "I am trying to help them as much as I can," he wrote in an email.

Oleksyk holds another faculty appointment at Uzhhorod National University, located in Western Ukraine by the Carpathian Mountains, not far from the Slovakian border, where he continues to teach an online course in genomics for graduate students. "Most of them were logging in from bomb shelters during my last lecture" a week ago, he said.

In early March, Oleksyk made impassioned appeals on Facebook — recently banned in Russia — that were also posted on UzhNU's website, one asking Russian friends to speak out against the war and not believe in government propaganda, the other appealing to the international community to support Ukraine.

But despite the horrors of the war, Oleksyk does not stop thinking about the future of genomics research in Ukraine. Around 2018, he helped initiate the Genome Diversity in Ukraine project, which seeks to generate genome-wide data from Ukrainians across the country. A year ago, the project published its first results in GigaScience, an analysis of sequencing and genotyping data from 97 DNA samples from volunteers recruited in different parts of Ukraine. "We are working on a much larger project and hope to be able to start it as soon as this war is over," Oleksyk said.

Involving researchers from UzhNU, Oakland University, the University of Michigan, BGI, and hospitals and companies in different regions of Ukraine, the initial study represents "the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population," according to the authors. Funding came from BGI, UzhNU, the US National Cancer Institute, and Oakland University, according to the paper.

But the study did not remain free of politics. Oleksyk said there were objections from Saint Petersburg State University against the publication of a preprint of the results in BioRxiv in August 2020 because the analysis drew on previously published data from another effort, the Genome Russia project, that had been removed from the public domain. After replacing the contested data with data from a Russian population from the Human Genome Diversity Project (HGDP), Oleksyk's team withdrew the original preprint and reposted a new version in November 2020.

Still, even the journal publication that followed a few months later ran into objections from Russia, with "a security officer from Russia even harassing (unsuccessfully) the editor of GigaScience," Oleksyk said. That paper has remained somewhat obscure, receiving its first citation only last week, he said, more than a year after it came out, but all data remains publicly available.

That was not the case for the Genome Russia project, an effort originally spearheaded by Oleksyk; Vladimir Brukhin, a Russian biologist and bioinformatician; and US geneticist Stephen O'Brien, a former lab director at the National Cancer Institute. O'Brien, who retired from the NCI after 25 years in 2011, took up a post at Saint Petersburg State University (also known as St. Petersburg University, or SPbU) in early 2012, where he helped create the Theodosius Dobzhansky Center for Genome Bioinformatics and served as its CSO. In 2013, he also took a faculty position at Nova Southeastern University in Florida, which he still holds.

O'Brien said the position in Russia — funded by a generous grant from the Russian government under the so-called mega-grant program, in part designed to recruit Russian expats back home — was attractive to him because he knew his field needed more bioinformaticians, and good programmers were plentiful in Russia. Indeed, the programmers he recruited and trained at his new center were among the best he had ever worked with, he said. "They were just good and smart and capable."

The idea for the Genome Russia project was borne out of a realization that many other nations — including the US and China — had started their own population genomics projects to better understand their population history as well as population-specific disease risks, but "the gaping hole was Russia," O'Brien said. Initially, the project was met with great enthusiasm, he recalled, as well as with funding.

In 2015, he and his two co-organizers described an outline of the Genome Russia project in GigaScience and in Science, writing that it "promises to fill one of the largest gaps [in human population genetics], the expansive regions across the Russian Federation, informing not just medical genomics of the territories, but also the migration settlements of historic and prehistoric Eurasian peoples."

The project was endorsed by both the Russian Academy of Sciences and the Russian Ministry of Education and Science, they wrote, and "while political diplomacies continue, the Genome Russia Project can and should become an example of international collaboration on the common ground and with the common goal of improving human health and betterment."

According to the project's website, available in Russian and English, the aim was to generate a database with whole-genome sequencing data for at least 3,000 Russians from different regions of the country.

By that time, however, Russia had invaded Crimea. "I was disgusted with the Russian policy towards Ukraine, and while continuing to work with my colleagues that contributed to the project, could not make myself come to Russia again," Oleksyk said.

The Genome Russia project did manage to publish an initial analysis of the genomes of 264 Russian individuals, including 60 newly sequenced samples from Western Russia and Eastern Siberia, in the journal Genomics in March 2019. The study included authors affiliated with institutions in Russia, the US, the Netherlands, and Puerto Rico, and listed funding from various Russian institutions and agencies.

But while the data generated for the project was initially publicly available, SPbU later removed it, leaving the paper with a broken link. "I am still pretty upset about the incident and the data that was earned so hard and completely wasted as it cannot be used by the community," Oleksyk said.

Also, by then, the Genome Russia project had fallen out of favor with Russian authorities and some Russian scientists who were not involved with it, O'Brien said, and he ended up dissolving his group at SPbU. In 2019, he took up a new position at ITMO University, also in St. Petersburg, taking many of his students with him, where he remains a professor and CSO of the Laboratory of Genomics Diversity at the Center for Computer Technologies.

Around the same time, "reports started coming out from Russia about Putin being convinced that the US is developing genetics-based weapons against Russia," and authorities were "organizing a different Genome Russia project, now headed by Putin's daughter," Oleksyk said. That project, according to media reports, is led by Maria Vorontsova, a pediatric oncologist who is the daughter of President Vladimir Putin.

"All of a sudden, the enthusiasm about myself and the Dobzhansky Center went sour about the time she announced this, and about the time the newspapers were complaining about having an American leader, and about the time we published our first data paper," O'Brien said.

At ITMO University, his group continued to work on evolutionary and comparative genomics, mainly of animal species, for which data were freely and openly available. "I was happy to do it, even projects that I thought were boring, because I wanted the kids to get on their feet, wanted them to get the practice, wanted them to be competitive when it came to looking around in the West for a postdoc job," he said. Many of his former students in Russia did end up with positions abroad, including in the US, UK, France, Japan, and South America, he said. When the pandemic hit in 2020, things turned more difficult, but the research continued.

However, on Feb. 24 of this year, "everything changed," he said. With the Western world unanimously condemning Russia's invasion of Ukraine, imposing sanctions on Russia, and journals suggesting they may stop publishing research from Russian scientists, O'Brien said, many members of his group at ITMO University — at last count, about a dozen — as well as other colleagues in Russia decided they wanted to leave the country.

While Western social media networks, like Facebook and Twitter, are shut down in Russia, "the internet is still working and people in the university have VPNs [virtual private networks]," he said, allowing them to stay informed about the war in Ukraine.

"I'm trying to comfort them and advising them to stay out of demonstrations, because they will arrest them," he said, possibly resulting in long prison sentences. He has also been trying to secure positions for them abroad. One of his former colleagues was able to obtain a four-month Fulbright scholarship at a university in Florida, for instance. "He left on one of the last flights to the US," O'Brien said, and is now pondering how he will be able to meet with his wife again, who is still in St. Petersburg. "The truth is, all of us feel helpless."

"I thought that genomics [in Russia] had a future, it was moving along OK, but after Feb. 24, I don't count on it anymore," O'Brien said.

The Center for Algorithmic Biotechnology at SPbU's Institute of Translational Biomedicine is another place that has long been collaborating with Western scientists. Established in 2014 under Russia's mega-grant program, it is currently directed by Alla Lapidus, a Russian bioinformatician who worked in the US for more than a decade, including as group leader at the Joint Genome Institute for seven years. It was formerly headed by Pavel Pevzner, a professor of computer science and engineering at the University of California, San Diego who is originally from Russia.

Since 2017, researchers at the center have organized an annual conference in St. Petersburg, called "Bioinformatics: From Algorithms to Applications" (BiATA), that has attracted a roster of notable overseas speakers, including from the US, the UK, and Canada. After two years in a virtual format, the meeting was supposed to be hybrid this July, with invited speakers from the US and Germany, but it is unclear whether it will be able to proceed as planned. BiATA organizers did not respond to a request for comment, and two of the invited speakers had not heard about any planned changes as of last week.

Pevzner, who is not involved with organizing the meeting, said he expects the sanctions against Russia "will soon bring experimental genomics research in Russia to a complete stop."

"More importantly, the invasion has triggered an enormous brain drain of educated people (including biologists and bioinformaticians) who recently fled to Tbilisi, Yerevan, Istanbul, and a few other cities that still have flights from Russia," he said in an email earlier this month. "The next step for all these people is to search for positions in the West. … Never in my life have I seen so many Russian bioinformaticians trying to find positions in the West."

D. is among the Russian bioinformaticians who left their country at the beginning of the war, with no certain future. He asked to remain anonymous because his current whereabouts in Armenia are unknown to his institution, where he recently defended his doctoral thesis.

He was already interested in doing a postdoc abroad, either in the US or France, but when the war started, he was not sure whether that would remain an option. "There was always a kind of informal convention in Russia, 'If you don't like it, you can always leave,'" he said. "This convention worked with a possibly bad but sane government. Now, I'm not sure it's sane."

While he thinks it's unlikely Russia will prohibit its scientists from leaving the country going forward, "the probability is not zero, it's not negligible," he said. As such, he is keeping his options open — returning to Russia for a while or directly moving on to a postdoctoral position abroad — and is working remotely from his current location. "I feel safe now, I have some emergency plans if my postdoc options won't work," he said.

For now, his team's collaborations with scientists in the US and France are still ongoing, D. said, though he believes funding from a US grant will soon stop. Gmail and YouTube were still working in Russia as of a week ago, and his colleagues in Russia were using VPNs to stay on top of the news.

"It's really nice that the scientists understand that Russian scientists are mostly against the war, even if the heads of the institutions have to sign something" in support of the military actions, he said. "I'm not even sure they want to sign, but they have to sign." D. himself has put his signature on several petitions against the war, he said, but he does not consider himself a political activist.

As for his immediate future, he is not sure yet. "It's hard to predict anything," he said. "First the bombs have to stop falling, then you can just look around and try to understand the situation."

Other researchers in Russia have been more vocal about their opposition to the war, often at great personal risk. The Russian government has detained thousands of protesters and has threatened those who call the Russian military action in Ukraine a "war" with up to 15 years in prison.

At the beginning of the invasion, Mikhail Gelfand, a bioinformatician and professor at the Skolkovo Institute of Science and Technology (Skoltech), helped organize an open letter by Russian scientists protesting the war.

In an email, he said many scientists he knows have left Russia, including some of his students, who are now working remotely from countries such as the US, Turkey, Georgia, Israel, Montenegro, Serbia, and the Czech Republic. "They have different reasons for that, and in most cases, this was not considered as a one-way trip," he noted, though that situation may change. "The motives were diverse, but as it were the first days [of the conflict], for the most part they were emotional, personal, or political."

Gelfand said it is too early to speculate on the medium- or long-term consequences of the war for science in Russia, but he is sure there will be no return to what it was like before the invasion. "What will be there instead, nobody knows," he said.