04.06.2026
research

Metabolomics and Systems Research Group

The Estonian Biobank has accumulated extensive metabolomics datasets, including hundreds of plasma biomarkers measured using nuclear magnetic resonance, mass spectrometry, and standard biochemical methods. In addition, clinical blood measurements from hospitals are increasingly available through database linkage.

Metabolic biomarkers are among the most informative tools for studying, predicting, and helping to prevent human diseases. They represent an intermediate phenotypic layer that is closer to clinical disease than the genome and can be measured with high accuracy.

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Principal Investigator: Associate Professor Toomas Haller, PhD

Research Focus

Our research focuses on common diseases, with increasing emphasis on kidney diseases—particularly chronic kidney disease—as well as Wilson’s disease and hemochromatosis. Our work has three main aims:

  1. To identify associations between metabolic and genetic markers and link them to clinically relevant outcomes.
  2. To use metabolic markers to improve disease understanding, prediction, and prevention, with particular interest in disease subtypes and trajectories.
  3. To develop new methods and tools for extracting health-related information from metabolomics data.

Current Directions

A central research direction is the development of a novel computational framework for constructing metabolic aging trees, in which normal aging trajectories form the main branches and disease-associated trajectories form side branches. This approach allows us to quantify disease paths, study interactions between related disease states, and map the landscape of common disease development. Our ultimate goal is to predict individual disease risk based on early, subclinical metabolic signatures and to assess the potential for returning to a normal aging trajectory.

Research Group

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Toomas Haller

PhD
Institute of Genomics
Estonian Genome Centre
Associate Professor in Genomic-Metabolomic

[email protected]

A

Aigar Ottas

PhD (Medicine)
Institute of Genomics
Estonian Genome Centre
Research Fellow of Medical Metabolomics

[email protected]

Miriam

Miriam Nurm

MSc (biotehnika)
Institute of Genomics
Estonian Genome Centre
Junior Research Fellow of Genetics

[email protected]

A
Ainika Harro
MSc (Computer Science)
Institute of Genomics
Estonian Genome Centre
Junior Research Fellow

[email protected]

leelo
Leelo Järv
Institute of Clinical Medicine
Department of Internal Medicine
Assistant in Nephrology,
Institute of Genomics
Estonian Genome Centre
Consultant

[email protected]

Funding

PRG2585: A New Methodology for Predicting the Onset of Chronic Kidney Disease, Its Subtypes, and Disease Trajectories

Selected publications

Nurm M, Annilo T, May-Wilson S, Reigo A, Mägi, R, Võsa U; Estonian Biobank Research Team; Haller T. Unraveling Genotype–Phenotype Relationships in Hereditary Hemochromatosis Through Integrated Biobank Data Analysis. BMC Genomics. Accepted for publication 2026

Oja KT, et al. Front Neurol. 2025 Dec 1;16:1684456. doi: 10.3389/fneur.2025.1684456. PMID: 41404459; PMCID: PMC12703977.

Milani L, et al. The Estonian Biobank's journey from biobanking to personalized medicine. Nat Commun. 2025 Apr 5;16(1):3270. doi: 10.1038/s41467-025-58465-3. PMID: 40188112; PMCID: PMC11972354.

Nurm M, Reigo A, Annilo T, Toomsoo T, Nõukas M, Nikopensius T, Pankratov V, Reisberg T, Hudjashov G; Estonian Biobank Research Team; Haller T, Tõnisson N. Use of Estonian Biobank data and participant recall to improve Wilson's disease management. Eur J Hum Genet. 2025 Nov;33(11):1499-1508. doi: 10.1038/s41431-024-01767-9. Epub 2024 Dec 14. PMID: 39674827; PMCID: PMC12583600.

Figuerêdo J et al. Uncovering the shared genetic components of thyroid disorders and reproductive health. Eur J Endocrinol. 2024 Aug 5;191(2):211-222. doi: 10.1093/ejendo/lvae094. PMID: 39067062.

Karjalainen MK et al. Genome-wide characterization of circulating metabolic biomarkers. Nature. 2024 Apr;628(8006):130-138. doi: 10.1038/s41586-024-07148-y. Epub 2024 Mar 6. PMID: 38448586; PMCID: PMC10990933.

Kurvits S, Harro A, Reigo A, Ott A, Laur S, Särg D, Tampuu A; Estonian Biobank Research Team; Alasoo K, Vilo J, Milani L, Haller T; PRECISE4Q consortium. Common clinical blood and urine biomarkers for ischemic stroke: an Estonian Electronic Health Records database study. Eur J Med Res. 2023 Mar 25;28(1):133. doi: 10.1186/s40001-023-01087-6. PMID: 36966315; PMCID: PMC10039346.

Sadegh S, et al. Lacking mechanistic disease definitions and corresponding association data hamper progress in network medicine and beyond. Nat Commun. 2023 Mar 25;14(1):1662. doi: 10.1038/s41467-023-37349-4. PMID: 36966134; PMCID: PMC10039912.

Winkler, TW et al. Differential and shared genetic effects on kidney function between diabetic and non-diabetic individuals. Commun Biol. 2022 Jun 13;5(1):580. doi: 10.1038/s42003-022-03448-z. PMID:35697829; PMCID: PMC9192715.

Guida, F et al. The blood metabolome of incident kidney cancer: A case-control study nested within the MetKid consortium. PLoS Med. 2021 Sep 20;18(9):e1003786. doi: 10.1371/journal.pmed.1003786. PMID: 34543281; PMCID: PMC8496779.

Nikopensius, T et al. Association analysis of juvenile idiopathic arthritis genetic susceptibility factors in Estonian patients. Clin Rheumatol. 2021 Oct;40(10):4157-4165. doi: 10.1007/s10067-021-05756-x. Epub 2021 Jun 8. PMID: 34101054; PMCID: PMC8463396.

Prins, BP et al. Discovery and Implications for Personalized Prevention and Medicine: Estonia as Example. J Pers Med. 2021 Apr 29;11(5):358. doi: 10.3390/jpm11050358. PMID: 33946982; PMCID: PMC8145318.