A collaboration launched today by Illumina and the Lundbeck Foundation GeoGenetics Centre at the University of Copenhagen plans to generate and analyze one of the largest sets of ancient human and pathogen genome panels ever created—with the goal of underpinning new approaches to developing treatments for mental and neurological conditions.
Illumina and the center said they plan to base those approaches on the insights they glean as they study the role of microbes in the pathogenesis of neuropsychiatric illnesses, such as Alzheimer’s disease and schizophrenia.
The value of the collaboration was not disclosed.
The partners aim to learn more about the medical and biological understanding of special factors underlying the development of human neuropsychiatric diseases through the ages. Understanding those factors is expected to help the research team advance understanding of the evolution of disease variance and its interaction with the human genome and pathogen pressure.
To that end, Prof. Eske Willerslev, DSc, Lundbeck Foundation Professor at the University of Copenhagen, and colleagues plan to build one of the largest sets of ancient human and pathogen genomic reference panels ever created, through complete DNA mapping of thousands of ancient Eurasian human remains.
Data will be obtained from bones and teeth, with the oldest remains dating back 10,000 years, Illumina and the center said.
Willerslev, an evolutionary geneticist, spent his early adult life as a fur trapper discovering the remote rawness of northeastern Siberia. His explorations brought him to Arctic shorelines strewn with mammalian remains, like seashells lapping against the seashore. Exploring that wilderness was a childhood dream, he said, adding: “but I can see now that back then, it was not just the adventure, I was trying to understand the environment.”
In the collaboration with Illumina, Willerslev will lead an international, multi-disciplinary team of scientists that plans to focus on creating two unique subsets of genomic data—a panel of 5,000 ancient human genomes, and a panel to consist of ancient pathogen DNA that is associated with human diseases. Both panels will be made publicly available.
“Over the past 10,000 years, mankind has experienced some of the greatest lifestyle changes in the history of our species,” Willerslev, who is also Prince Philip Professor at the University of Cambridge and a research associate at Wellcome Trust Sanger Institute, said in a statement. “Our diet changed as we developed from hunter-gatherers into farmers, our settlement patterns changed, and there have been changes in pressure of infection from the pathogenic micro-organisms to which we were exposed due to altered living conditions.
Creating Public Reference Sets
“We also know that chronic viral, bacterial and fungal infections might be causative factors in neuropsychiatric diseases, so there is every reason to believe that the analyses of DNA from this period will show significant trends, giving us the ability to create new, publicly available reference sets, to enhance both the scientific and healthcare communities’ understanding of disease evolution,” Willerslev added.
Willerslev and his team will use Illumina’s NovaSeq™ 6000 Sequencing System, and leverage Illumina’s S4 flow cell to sequence up to 20 billion ancient DNA fragments every two days.
NovaSeq is Illumina’s current top-of-the-line sequencer, reaching $1 billion in revenues in 2018, some two years since its launch, making it Illumina’s fastest revenue ramp-up of any product. NovaSeqs have sequenced more than 600,000 whole genomes, with some 30% of NovaSeq customers being new to Illumina or converting from benchtop sequencers, and about 25% being HiSeq customers, CEO Francis deSouza said in January at the J.P. Morgan 37th Healthcare Conference.
“While we conceived this project to explore the evolutionary origins of genetic disorders years ago, it was simply impossible to realize before Illumina’s NovaSeq System came on the market,” Willerslev said. “We are delighted that Lundbeck Foundation had the foresight to see the importance of our project and that Illumina’s technology will make the research possible.”
Lundbeck Foundation GeoGenetics Centre for Brain, Disease & Evolution specializes in ancient DNA research in humans, pathogens and environmental DNA. The center explores human migration, disease evolution, adaptations to lifestyle changes and language development. The center says its goals are to increase our mutual appreciation for what it means to be human as well as to decrease suffering through understanding disease etiologies and respecting our diversity.
The center was founded in 2009 as a Danish National Research Foundation Centre of excellence, and continues its work through funding from Lundbeck Foundation, Carlsberg Foundation, Novo Nordisk Foundation, and the Wellcome Trust.
“It will be extremely valuable, if by going back 10,000 years, we can acquire new information about when, and under which environmental conditions, a brain disorder may have been introduced into human DNA,” added Paula Dowdy, Senior Vice President and General Manager for Europe, Middle East and Africa at Illumina. “This project has the potential to influence future product developments in genetics and precision medicine by providing invaluable insights to those affected by mental health issues.”