From Biobanking to Personalized Medicine: the journey of the Estonian Biobank

Milani, Lili; Alver, Maris; Laur, Sven; Reisberg, Sulev; Haller, Toomas; Aasmets, Oliver; Abner, Erik; Alavere, Helene; Allik, Annely; Annilo, Tarmo; Fischer, Krista; Hudjashov, Georgi; Jõeloo, Maarja; Kals, Mart; Karo-Astover, Liis; Kasela, Silva; Kolde, Anastassia; Krebs, Kristi; Krigul, Kertu Liis; Kronberg, Jaanika; Kruusmaa, Karoliina; Kukuškina, Viktorija; Kõiv, Kadri; Lehto, Kelli; Leitsalu, Liis; Lind, Sirje; Luitva, Laura Birgit; Läll, Kristi; Lüll, Kreete; Metsalu, Kristjan; Metspalu, Mait; Mõttus, René; Nelis, Mari; Nikopensius, Tiit; Nurm, Miriam; Nõukas, Margit; Oja, Marek; Org, Elin; Palover, Marili; Palta, Priit; Pankratov, Vasili; Pantiukh, Kateryna; Pervjakova, Natalia; Pujol-Gualdo, Natàlia; Reigo, Anu; Reimann, Ene; Smit, Steven; Sokurova, Diana; Taba, Nele; Talvik, Harry-Anton; Teder-Laving, Maris; Tõnisson, Neeme; Vaht, Mariliis; Vainik, Uku; Võsa, Urmo; Esko, Tõnu; Kolde, Raivo; Mägi, Reedik; Vilo, Jaak; Laisk, Triin; Metspalu, Andres

doi:10.1101/2024.09.22.24313964

2024

DOI: 10.1101/2024.09.22.24313964

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From Biobanking to Personalized Medicine: the journey of the Estonian Biobank

Lili Milani,

Maris Alver,

Sven Laur

et al.

Abstract: Large biobanks have set a new standard for research and innovation in human genomics and implementation of personalised medicine. The Estonian Biobank was founded a quarter of a century ago, and its biological specimens, clinical, health, omics, and lifestyle data have been included in over 800 publications to date. What makes the biobank unique internationally is its translational focus, with active efforts to conduct clinical studies based on genetic findings, and to explore the effects of return of results … Show more

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Cited by 2 publications

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Genome-wide association study for circulating metabolites in 619,372 individuals

Tambets,

Kronberg,

Abner

et al. 2024

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Examining the upstream molecular consequences of genetic variation significantly enhances our understanding of the heritable determinants of complex traits and disease predisposition. Metabolites serve as key indicators of various biological processes and disease states, playing a crucial role in this systematic mapping, also providing opportunities for the discovery of new biomarkers for disease diagnosis and prognosis. Here, we present a genome-wide association study for 249 circulating metabolite traits quantified by nuclear magnetic resonance spectroscopy across various genetic ancestry groups from the Estonian Biobank and the UK Biobank. We generated mixed model associations in the Estonian Biobank and six major genetic ancestry groups of the UK Biobank and performed two separate meta-analyses across the predominantly European genetic ancestry samples (n = 599,249) and across all samples (n = 619,372). In total, we identified 89,489 locus-metabolite pairs and 8,917 independent lead variants, out of which 4,184 appear to be novel associated loci. Moreover, 12.4% of the independent lead variants had a minor allele frequency of less than 1%, highlighting the importance of including low-frequency and rare variants in metabolic biomarker studies. Our publicly available results provide a valuable resource for future GWAS interpretation and drug target prioritisation studies.

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Genome-wide association study for circulating metabolites in 619,372 individuals

Tambets,

Kronberg,

Abner

et al. 2024

Preprint

View full text Add to dashboard Cite

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Parent-of-Origin inference and its role in the genetic architecture of complex traits: evidence from ∼220,000 individuals

Hofmeister,

Cavinato,

van der Graaf

et al. 2024

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Parent-of-origin effects (POEs) occur when the impact of a genetic variant depends on its parental origin. Traditionally linked to genomic imprinting, these effects are believed to have evolved from parental conflict over resource allocation to offspring, which results in opposing parental genetic influences. Despite their potential importance, POEs remain heavily understudied in complex traits, largely due to the lack of parental genomes.Here, we present a multi-step approach to infer the parent-of-origin of alleles without parental genomes, leveraging inter-chromosomal phasing, mitochondrial and chromosome X data, and sibling-based crossover inference. Applied to the UK Biobank (discovery cohort) and Estonian Biobank (replication cohort), this scalable approach enabled parent-of-origin inference for up to 221,062 individuals, representing the largest dataset of its kind.GWAS scans for more than 60 complex traits and over 2,400 protein levels contrasting maternal and paternal effects identified over 30 novel POEs and confirmed more than 50% of testable known associations. Notably, approximately half of our POEs exhibited a bipolar pattern, where maternal and paternal alleles exert conflicting effects. These effects were particularly prevalent for traits related to growth (e.g., IGF-1, height, fat-free mass) and metabolism (e.g., type 2 diabetes, triglycerides, glucose). Replication in the Estonian Biobank validated over 70% of testable associations.Overall, our findings shed new light on the influence of POEs on diverse complex traits and align with the parental conflict hypothesis, providing compelling evidence for this understudied evolutionary phenomenon.

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From Biobanking to Personalized Medicine: the journey of the Estonian Biobank

Cited by 2 publications

References 108 publications

Genome-wide association study for circulating metabolites in 619,372 individuals

Genome-wide association study for circulating metabolites in 619,372 individuals

Parent-of-Origin inference and its role in the genetic architecture of complex traits: evidence from ∼220,000 individuals

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