The team behind Russia's biggest genome project to date, Genome Russia, is holding a “bake off” of genome sequencing centres to determine which centre would handle the crucial task most efficiently. There's just one problem: if the winner of the five labs taking part is not the single one located in Russia, the DNA samples cannot be sent abroad to be processed anyway.
From right to left: Yuri Nikolsky, Tatiana Tatarinova and Stephen O'Brien at the Genome Russia conference. Photo: Sk.ru.
Under Russian law, biological samples cannot be taken out of the country. But U.S. professor Dr. Stephen O'Brien, the project's supervisor, wants to ensure the important task is carried out with maximum efficiency and accuracy.
“We have developed what I call a bake off – a competition among sequencing centres to compare quality,” O'Brien told participants of the Genome Russia conference devoted to genomics and held at the Skolkovo Innovation Centre on Thursday.
The Genome Russia project, coordinated by St. Petersburg State University’s Dobzhansky Centre for Genome Bioinformatics, aims to collect a nationwide database of Russian genomes that will help to discover new gene variants that may affect the frequency of diseases among Russians, as well as to trace historical migration routes.
“It’s important to know the distribution and frequency of various genes in order to know what varieties of illnesses are widespread among the population, how to treat them, how they will react to various medicines,” Yuri Nikolsky, science director of the Skolkovo Foundation’s biomedicine cluster and the co-chair of the conference, told Sk.ru ahead of the event.
Genome studies also help to establish the history of a country’s people and their origins – a particularly relevant topic in Russia, which is home to nearly 200 different ethnicities.
“The [international] 1000 Genomes project has a big hole in it in Russia … and Genome Russia is meant to help try to fill in that gap as well as complement the studies that are already going on,” O’Brien told the conference.
Five contenders
The sequencing centres being tested within the bake off are BGI in China, Illumina in the U.K., Macrogen in South Korea; Pacific Biosciences in California; and one Russian centre in Peterhof, a satellite town of St. Petersburg.
But four of those centres are banned under Russian law from working on the Genome Russia project: Russia’s Federal Customs Service imposed restrictions on the export of human biological materials in 2007, reportedly as a result of a warning issued by the Federal Security Service of genetic biological weapons being developed against Russia. Andrei Belianinov, head of the Customs Service, was quoted at the time as saying that an export ban was necessary for the prevention of crime.
“It [the law] is a result of certain structures viewing DNA as an object of state security,” Nikolsky told Sk.ru.
Because of that law, the scientists working on Genome Russia cannot provide the foreign labs with Russian samples to work on in order for the quality of their sequencing to be assessed, so instead the centres have all been sent DNA from a separate study into Autoimmune Hepatitis, O'Brien said.
The results are expected within two months, and will be delivered to the rector and vice rectors of St. Petersburg State University – which is funding and coordinating the project – as well as its other partners, “so that they can understand why we are recommending where it be done,” says O'Brien.
“We have been told that we have no choice but to do the sequencing in Russia, but we will still deliver those results and recommendations. I'm hoping that the Peterhof facility or another facility in Russia will be just as good,” he said.
“The restriction [on sending biological materials abroad] has already slowed down the process appreciably, but I remain optimistic that this can be reversed with proper leadership and authority,” O’Brien told Sk.ru following the conference.
“The accuracy will be optimum if the leadership is scientifically qualified and attentive and not bureaucratic and politically driven,” he added.
Dr. Stephen O'Brien speaking at the conference. Photo: Sk.ru
Home improvement?
In the event that the bake off results indicate that the Peterhof facility does not have the most efficient sequencing facilities, one way to solve the problem without contravening the Russian law on sending samples abroad would be to improve the equipment and conditions in domestic labs.
“I do believe that Russia can develop state of the art capacity, but it will be more expensive, nearly twice the original budget,” O’Brien told Sk.ru. “But it can be done here and with ideal quality … with proper funding and scientific leadership.”
Nikolsky of Skolkovo’s biomed cluster said there were already plenty of sequencing centres in Russia that could do the work satisfactorily, but that it would be more expensive than in other countries.
“There are at least 10 decent DNA sequencing centres in Russia – there’s an excellent centre in Kazan, for example,” he told Sk.ru.
“It’s more expensive here because of customs rules,” he explained. “The sequencing machines cost up to twice as much, like any biological equipment, unfortunately.”
On the other hand, Nikolsky said that most of Russia’s sequencing centres have plenty of resources available to work on the Genome Russia project, as currently there are simply not enough existing projects – or enough money for those projects – for them to be working to their maximum capacity.
More cash needed
The Genome Russia team has already collected data from 900 people, and aims to increase that figure to between 2,000 and 2,500 during the next two years, said Vladimir Brukhin, coordinator of the Genome Russia project at the Dobzhansky Centre.
While the project will identify national gene variations that could eventually lead to the development of precision medicine used to increase the effectiveness of treatment by adjusting it according to a person’s genetic makeup, for now, the Genome Russia project does not entail clinical genetics.
“This is unusual for genome projects, because they usually try to use precision medicine to discover mutations that affect complex diseases that we don’t know the cause of,” O’Brien told the conference.
He said that studying clinical data would be much more expensive, and that the team at the Dobzhansky Centre was currently learning how to mine the genomes for DNA sequences, and that neither it nor the genomics community at large was ready to do justice to the task.
“I would recommend that we add clinical genetics and clinical phenotypes [disease attributes] in future, but right now, I think it’s the wrong time,” he said.
“When we do that, the funding agencies that will be providing it will need to put up the kind of money that’s coming out the other big projects [in other countries such as the U.S. and U.K.], which is not tens of millions of U.S. dollars, but hundreds of millions of U.S. dollars,” he added.
The Genome Russia project is currently being funded by St. Petersburg State University.
“Carrying out a project on this scale using just the resources of the university would be impossible, and we’re pleased to say that we are now working with colleagues from almost every region of Russia,” the university’s vice rector for science, Sergei Tunik, told the conference.
“I hope that in the near future, we will manage to get full financing for its implementation,” Tunik said, adding that the project has the support of President Vladimir Putin.