Estonian Genome Centre

The Estonian Genome Centre was established aside from Estonian Biobank to lead the genetic research related to human health and diseases.

 

Functional genomics, or the effect of DNA sequence variants on quantitative trait variability and disease risk expression in the population, has made EGC one of the most studied biobanks in the world, with EGC researchers participating in the work of numerous international consortiums and contributing to the discovery of more than 35,000 of the genetic variants associated with complex characteristics.

Lili Milani, the Head of the Estonian Genome Centre

Fields of research

In addition to functional genomics, as new fields of research, the Estonian Genome Centre has successfully launched systems biology, microbiome and pharmacogenetics, bringing to Estonia experts with an international background.

The research at the Estonian Genome Centre directly supports the activities of the Estonian National Personalized Medicine Program, both with the development of polygenic risk scores and with the improvement of genotyping chip data. As new directions, we see multi-level analysis of the health trajectories of biobank participants, analysis of molecular profiles at DNA, RNA, proteins, metabolites and cellular traits level, and hypothesis-free data mining using machine learning and AI techniques.

Research groups

Despite recent advances in pharmacogenomic research, interindividual variability in drug metabolism and sensitivity for drug toxicity persists as a major problem for drug treatment. Recent research has highlighted the large extent of rare variants in genes with importance for drug metabolism. The aim of this work is to discover and investigate the effect of common and rare genetic variants related to suboptimal drug metabolism and adverse drug reactions (ADRs) in the Estonian and other European populations. This will be achieved by using genome sequences of 5000 and genotype data of 200,000 individuals combined with extensive health records regarding drug prescriptions and ADR diagnoses. The identified gene-ADR associations will be tested using functional studies.

The results will serve as a basis for variants that can be included for preemptive pharmacogenomic testing, which could ultimately reduce the health and economic burden of low drug efficacy and unnecessary side effects caused by genetic variants.

The research group of pharmacogenetics is led by Professor Lili Milani, lili.milani@ut.ee

Studies the interactions between the genome and metabolome with regard to human diseases. This includes work with metabolomics data sets collected with NMR and mass spectrometry. We search for associations between genomic markers and metabolite levels as well as more complicated patterns in these data sets with the intent to understand and predict common diseases. This work requires creating new bioinformatics algorithms, scripts and tools (C++, Python) as well as conducting high-performance cluster computations.

The research group of metabolomics and systems is led by Associate Professor Toomas Haller, toomas.haller@ut.ee

It is known that the genome apparently healthy individuals actually harbors dozens of gene-disrupting variants (predicted to result in loss of function at the protein level). On the other hand, many phenotypic traits show inconsistent inheritance patterns due to penetrance and expressivity. The very first readout of genomic information is RNA, where cells have evolved several quality control mechanisms to minimize the impact of potentially harmful mutations. Our aim is to understand how mRNA regulation contributes to the buffering of such deleterious genetic variants.

The research group of mRNA is led by Associate Professor Tarmo Annilo, tarmo.annilo@ut.ee

The human intestinal tract is colonized by thousands of different species of microorganisms, collectively called the microbiota. The gut microbiome (collection of all microbial genes) encodes much more genes than the human genome and provides us with numerous complementary functions. The microbial community has a critical role in many aspects of health, including immunity and metabolism. Our group addresses questions about the relationships between microbiome and human host, where we currently focus on two major areas:
1) we explore the host-microbiome interactions in the development of type 2 diabetes and
2) elucidate the direct and indirect mechanisms through which the human microbiome shapes the efficacy and toxicity of commonly used drugs.

The research group of the microbiome is led by Associate Professor Elin Org, elin.org@ut.ee

Read more about the research group of microbiome

Research group of functional genomics is focused on understanding the molecular function of human genome variation. The group's broader scientific interest lies in understanding the genetic architecture of complex human phenotypes, focusing on intermediate molecular measurements (such as levels of gene expression in human tissues, cellular fractions and circulating small molecules) and human stature to estimate the role of both rare and common genetic variation of phenotypic outcomes through various models of inheritance (additive, recessive, epistatic and epigenetic). We implement a range of bioinformatics and genetic epidemiology techniques to map endophenotypes quantitive trait loci (QTL) and to annotate known disease associations with downstream molecular mechanisms.

The research group of functional genomics is led by Professor Tõnu Esko, tonu.esko@ut.ee

The bioinformatics research group handles the quality control and processing of multi-omics data and offers general bioinformatics support for all research groups within the Genome Centre. Method development plays an important role in the scientific activities of the group, including software for genome-wide association studies (GWAMA, MR-MEGA, SCOPA), as well as novel solutions for DNA copy number variant detection and analysis. In addition, the members of the group are involved in projects studying the genetic background of different traits and diseases related to metabolic health and female reproductive health.

The research group of functional genomics is led by Professor Reedik Mägi, reedik.magi@ut.ee

Mental health problems are extremely prevalent in modern societies, with every second individual affected during their lifetime. However, the causal mechanisms of such problems are not well understood. This is hindering advancements in novel prevention and treatment strategies to improve the quality of life of affected individuals and their family members. Our research team aims to advance the understanding of the causes and consequences of mental health problems across the lifespan and move towards better and personalized prevention and treatment strategies.

The research group of neuropsychiatric genomics is led by Associate Professor Kelli Lehto, kelli.lehto@ut.ee

Read more about the research group of neuropsychiatric genomics

The research group is focused on understanding the role of genetic variation in chronic diseases. We are developing novel computational tools and analytical methods to assess overall disease risks and combining the knowledge gained with other risk factors (e.g. age, gender, environmental factors and health behavior) to use this information to prevent and diagnose disease earlier and to identify potential therapeutic targets.

In 2022–2023 we are focusing on three phenotypes:

  1. Investigating the genetic basis of sebaceous gland diseases (acne, rosacea, perioral dermatitis) by performing GWAS (genome-wide association studies) and GRS (genetic risk score) analyses on the databases of Estonian Biobank and of Lifeline Biobank (Netherlands). Furthermore, we are analysing the links between co-morbidities and acne subtypes (in collaboration with Prof. K. Kingo, University of Tartu, Faculty of Medicine, Institute of Clinical Medicine and Tartu University Hospital, Dermatology Clinic).
  2. Performing GWAS and PRS (polygenic risk score) studies on Parkinson’s disease. We are investigating sonographically the change of Substantia nigra in density in people with high PRS to elaborate the calculation of early risk (in collaboration with Dr T Toomsoo, Head of the Center of Neurology, Confido Medical Center and Visiting Professor in School of Natural Sciences and Health, Tallinn University)
  3. Genetic basis of psoriatic arthritis (in collaboration with Prof. A. Märtson, Institute of Clinical Medicine, University of Tartu; and with Prof. E. Zeggini, the Technical University of Munich)
  4. In the framework of international cooperation (France, Germany, USA, Finland and others) we are also working on other phenotypes (venous diseases, the links between thromboembolism and hormone therapy, influenza, tricuspid aortic valve stenosis, panic disorder, etc.).
  5. Research Fellow of Human Genomics Mariliis Vaht started postdoctoral studies at the University of Helsinki in Prof. Samuli Ripatti’s research group and she is working on the Estonia-Finland cooperation project of genomic factors and associated harms for alcohol consumption.

Prof. Andres Metspalu is a member of the Coordination Group of the 1+ Million Genome initiative (“1 + MG Roadmap 2020-2022”), also the leader of WP10 (common complex disease genomics and PGx) and co-leader of WP12 Genome of Europe.

Ongoing research fundings where Prof. Andres Metspalu is the coordinator from Institute of Genomics or PI:

  1. B1MG grant no, 951724, 2019-2023
  2. OPTIMA grant no 101034347, 2021-2025 (in collaboration with the Institute of Computer Science, University of Tartu)
  3. Center of Excellence for Genomics and Translational Medicine  (until 01.03.2023)

Research group of human disease genomics is led by Professor Andres Metspalu, andres.metspalu@ut.ee.

Members of the research group:

  • Riin Ehin – PhD (Tallinn University of Technology)
  • Mart Kals – Research Fellow in Statistical Genomics (Institute of Genomics, University of Tartu)
  • Tiit Nikopensius – Research Fellow (Institute of Genomics, University of Tartu)
  • Telver Objärtel - BSc student (Genetic engineering, 3rd year)
  • Anu Reigo – Lead Specialist of Medical Genomics (Institute of Genomics, University of Tartu)
  • Ene Reimann – Research Fellow of Orthogenomics (Institute of Genomics, University of Tartu)
  • Maris Teder-Laving – Research Fellow of Human Genetics (Institute of Genomics, University of Tartu)
  • Mariliis Vaht – Research Fellow of Human Genomics (Institute of Genomics, University of Tartu), Postdoctoral researcher (University of Helsinki)

In collaboration with:

  • Külli Kingo – Professor in Dermatology and Venereology (Faculty of Medicine, University of Tartu), head physician (Dermatology Clinic, Tartu University Hospital), Head of the Clinic (Tartu University Hospital), Project manager of Estonian Doctoral School of Clinical Medicine (University of Tartu)
  • Toomas Toomsoo – Head of the Center of Neurology (Center of Neurology, Confido Medical Center), Visiting professor (School of Natural Sciences and Health, Tallinn University)
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Ilustratsioon inimese evolutsioonist

Prestigious grant helps the University of Tartu study the development of the human immune system over its long history

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Annual Conference of the Institute of Molecular and Cell Biology and the Institute of Genomics

The traditional annual conference uniting the Institute of Molecular and Cell Biology and the Institute of Genomics of the University of Tartu will take place on 19-20 January 2023.
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Elutööpreemiaga tunnustatud Andres Metspalu Ene Ergma ja Tõnis Lukasega_autor Maanus Kullamaa

Geneticist Andres Metspalu received lifetime achievement award for popularisation of science