Functional Genomics group

The Functional Genomics group at Estonian Genome Center is focused on understanding molecular function of human genome variation.  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). Group implements a range bioinformatics and genetic epidemiology techniques to map endophenotypes quantitative trait loci (QTL) and to annotate known disease associations with downstream molecular mechanisms.
Recently, the group co-lead the first large-scale study (eQTLgen) to identify genetic variants affecting blood gene expression levels using 5,300 samples (Westra, 2013). We identified causal local molecular mechanisms for 8,000 genes and these involved more than 25% of the genome variation. Furthermore, we showed that approximately 8% of disease-associated variants have downstream inter-chromosomal expression effects and enabled to prioritize causal biological candidates. Our group also demonstrated for the first time in human genetics the presence of global gene-gene interaction effects (epistasis) using gene expression (Hermani, 2014).  Human stature has been used as a model trait to understand the genetic architecture of highly polygenic trait. First, through close involvement in GIANT consortium, more than 700 genetic variants have found to contribute to growth regulation (Wood, 2014); and secondly, through co-leading ROHgen consortium, we first time demonstrated global adverse effect of distant parental relatedness (which enriches for deleterious recessive alleles) on human stature and cognitive function but not late on-set diseases (Joshi, 2015).
Group is lead by Dr Tõnu Esko, who has extensive experience in performing and implementing large-scale genetic association studies of international scale. Dr Esko, who next to being a senior scientist at University of Tartu spent the past 3 years as a postdoctoral research fellow at Boston Children’s Hospital and since Fall 2015 is part time employed by Broad Institute, Cambridge (Prof Eric Lander’s group).  This enables Functional Genomics group to access newly emerging state of the art computational tools, opens up fast computational resources and consults with world leading human geneticists.

Teaching and Research:
Tõnu Esko, PhD  (group leader)
Toomas Haller, PhD, Senior Researcher
Elin Org, PhD, Senior Researcher
Mari Nelis, PhD, Senior Researcher
Katrin Männik, PhD, Researcher
Maris Teder-Laving, MSc, Researcher
Markus Perola, PhD, Visiting Professor
Jaanika Kronberg-Guzman, MSc, Specialist 

PhD students:
Maris Alver, MSc
Timo Tõnis Sikka, MSc
Margit Nõukas, MSc
Anette Kalanapenkis, MSc

 MSc students:
Siim Kurvits, BSc
Mattis Jaama, BSc
Mirjam Tamme, BSc


back forward