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May 2009
ENGAGE Young Investigator

Tõnu Esko
M.Sc. student, supervisor Prof. Andres Metspalu, University of Tartu, Estonia

Tõnu is interested in understanding the genetic architecture of complex phenotypes.His main interest is to find out the genetic basis of longevity and personality traits.
He is the primary analyst for Estonian Genome Project genotype data and therefore involved in many ENGAGE collaborative meta-analyzes.
Currently he is involved in collaborative project with genotyping centers over Europe (in large part ENGAGE members) performing between-population stratification analyses and characterization of the patterns of various genetic features (like SNP, CNV, ROH and micro deletions) in the 17 European populations (22 cohorts and about 4000 samples). The first stage of that work was published recently in PLoS ONE.

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Genetic Structure of Europeans: a view from the North-East

When designing a genetic association study, it is important to avoid confounding caused by structure of the population. Moreover, current GWAS which are using common SNP markers should be very large in order to find statistically significantly associated markers and often it is not possible to get thousands (or even tens of thousands) of cases and controls from one population. This is especially true for the smaller countries. In this study we have analyzed 19 different population based samples from 16 European countries - from Finland to Italy and from Russia to Spain - and describe three different and basic measures (inflation factor λ, Fst and PC), which are used to estimate how closely (or distantly) are populations related. The results of the principal component analysis demonstrated that 19 European populations form a genetic map where four major areas could be identified: 1) Central and Western Europe, 2) the Baltic countries, Poland and Western Russia, 3) Finland, and 4) Italy. Results presented here will help to choose the populations for the genetic studies and if intra-population study or replication analysis is planned, loss of the power can be estimated from the presented data.

Paper:
Genetic Structure of Europeans: a view from the North-East

Mari Nelis*, Tõnu Esko*, Reedik Mägi, Fritz Zimprich, Alexander Zimprich, Draga Toncheva, Sena Karachanak, Tereza Piskáčková, Ivan Balaščák, Leena Peltonen, Eveliina Jakkula, Karola Rehnström, Mark Lathrop, Simon Heath, Pilar Galan, Stefan Schreiber, Thomas Meitinger, Arne Pfeufer, H-Erich Wichmann, Béla Melegh, Noémi Polgár, Daniela Toniolo, Paolo Gasparini, Pio D'Adamo, Janis Klovins, Liene Nikitina-Zake, Vaidutis Kučinskas, Jūratė Kasnauskienė, Jan Lubinski, Tadeusz Debniak, Svetlana Limborska, Andrey Khrunin, Xavier Estivill, Raquel Rabionet, Sara Marsal, Antonio Julià, Stylianos E. Antonarakis, Samuel Deutsch, Christelle Borel, Homa Attar, Maryline Gagnebin, Milan Macek, Michael Krawczak, Maido Remm, Andres Metspalu

PLoS ONE 4(5): e5472

http://dx.plos.org/10.1371/journal.pone.0005472

*These authors contributed equally to this work.


 

 

May 2009
ENGAGE Young Investigator

Mari Nelis



Ph.D. student, supervisor Prof. Andres Metspalu, University of Tartu, Estonia; Manager of the Genotyping Core Facility, Estonian Biocentre

Mari’s main interest has been population genetics – genetic variation in human genome and how phenotypes are influenced by it. She has been coordinating the whole-genome genotyping of thousands of samples representing Estonia and different other European populations with the Illumina genotyping platform, and also performed the statistical analysis. In addition, before she was responsible for the genotyping part of the large FP5 project ARCAGE (“Alcohol-related cancers and genetic susceptibility in Europe”), where 5000 cases and controls were genotyped on APEX platform in our Tartu Lab. Mari is participating in several other studies, but now her main task is to write up Ph.D. dissertation and defend it in October 2009.