Karoliina Kruusmaa

New technology to help sequence whole genomes from 10,000 gene donors

The Core Facility of Genomics at the Institute of Genomics of the University of Tartu received new PacBio HiFi RevioTM sequencers. These will soon be used to analyse the whole genomes of 10,000 gene donors to the Estonian Biobank.

The three new sequencers were acquired as part of the large-scale TeamPerMed project, the main aim of which is to establish Estonia as the leading research and development centre for personalised medicine in the region. The project is funded by the European Commission and the Estonian government with a total of €30 million.

"Sequencing is a method of analysis that sequences the whole human genome, or 3.2 billion nucleotides. 10,000 new whole genomes will significantly diversify the existing Estonian Biobank, enhancing its value compared to other biobanks across the world,” said Mait Metspalu, Director of the Institute of Genomics and head of the supervisory board of the personalised medicine research and development centre. So far, with the support of Estonian state funding, the genome of nearly 200,000 gene donors has been genotyped or partially analysed and 3,000 DNA samples from the gene pool have been sequenced or completely analysed.

According to Metspalu, based on the whole genome data, it is possible to study the genetic background of various diseases in even more detail, search for new drug targets and more accurately assess the reaction of the human organism to different active substances.

While the whole genomic sequences of the previously analysed 3,000 gene donors have been sequenced using short-sequence technology (sequences 150 nucleotides long), the new sequencers allow sequencing genomes in sequences up to 25,000 nucleotides long. "Sequencing long reads allows better coverage of the whole genome so that longer and more complex repetitive regions and pseudogenes are also sequenced. Analysing long reads also helps to distinguish between two strands of human genomic DNA, and sometimes it is important to know whether DNA variants are located side by side on one strand or come from different strands,” said Paula Ann Kivistik, Vice Manager of Sequencing Core Facility.

The central goal of sequencing 10,000 genomes in the Teaming project is to create the best possible reference map of the variability of Estonian genomes, i.e. the imputation panel. "Such a panel makes it possible to derive, or impute, the missing data to people whose DNA samples have been analysed with much cheaper genotyping technology. This way we can fill in the gaps that are missing and use the data obtained in the provision of personal medicine services,” Metspalu explained.

In addition to sequencing all genomic DNA, according to Kivistik, the PacBio Revio sequencer also provides information about the methylation pattern of DNA strands, or the epigenome. "Methylation plays an important role in human gene regulation and development. Thus, aberrant changes in the methylation status can lead to various diseases and anomalies, including the triggering of tumor processes,” explained Kivistik.

The acquisition of the sequencers is supported by the Ministry of Education and Research in connection with the Teaming for Excellence action under the ‘Widening participation and spreading excellence’ of Horizon Europe.

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