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Article: Editorial: Can population health be personalized? Estonia and Finland as examples.

Kääriäinen, Helena / Metspalu, Andres / Perola, Markus

2022 Volume 13, Page(s) 1051085

Language	English
Publishing date	2022-10-24
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2022.1051085
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Article ; Online: Gut metagenome associations with extensive digital health data in a volunteer-based Estonian microbiome cohort.

Aasmets, Oliver / Krigul, Kertu Liis / Lüll, Kreete / Metspalu, Andres / Org, Elin

Nature communications

2022 Volume 13, Issue 1, Page(s) 869

Abstract: Microbiome research is starting to move beyond the exploratory phase towards interventional trials and therefore well-characterized cohorts will be instrumental for generating hypotheses and providing new knowledge. As part of the Estonian Biobank, we ... ...

Abstract	Microbiome research is starting to move beyond the exploratory phase towards interventional trials and therefore well-characterized cohorts will be instrumental for generating hypotheses and providing new knowledge. As part of the Estonian Biobank, we established the Estonian Microbiome Cohort which includes stool, oral and plasma samples from 2509 participants and is supplemented with multi-omic measurements, questionnaires, and regular linkages to national electronic health records. Here we analyze stool data from deep metagenomic sequencing together with rich phenotyping, including 71 diseases, 136 medications, 21 dietary questions, 5 medical procedures, and 19 other factors. We identify numerous relationships (n = 3262) with different microbiome features. In this study, we extend the understanding of microbiome-host interactions using electronic health data and show that long-term antibiotic usage, independent from recent administration, has a significant impact on the microbiome composition, partly explaining the common associations between diseases.
MeSH term(s)	Anti-Bacterial Agents/therapeutic use ; Databases, Factual ; Dysbiosis/chemically induced ; Dysbiosis/microbiology ; Electronic Health Records ; Estonia ; Feces/microbiology ; Gastrointestinal Microbiome/genetics ; Humans ; Metagenome/genetics ; Pharmaceutical Preparations ; Surveys and Questionnaires
Chemical Substances	Anti-Bacterial Agents ; Pharmaceutical Preparations
Language	English
Publishing date	2022-02-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-28464-9
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Article ; Online: Genome-wide meta-analysis identifies novel loci conferring risk of acne vulgaris.

Teder-Laving, Maris / Kals, Mart / Reigo, Anu / Ehin, Riin / Objärtel, Telver / Vaht, Mariliis / Nikopensius, Tiit / Metspalu, Andres / Kingo, Külli

European journal of human genetics : EJHG

2023

Abstract: Acne vulgaris is a common chronic skin disorder presenting with comedones, cystic structures forming within the distal hair follicle, and in most cases additionally with inflammatory skin lesions on the face and upper torso. We performed a genome-wide ... ...

Abstract	Acne vulgaris is a common chronic skin disorder presenting with comedones, cystic structures forming within the distal hair follicle, and in most cases additionally with inflammatory skin lesions on the face and upper torso. We performed a genome-wide association study and meta-analysis of data from 34,422 individuals with acne and 364,991 controls from three independent European-ancestry cohorts. We replicated 19 previously implicated genome-wide significant risk loci and identified four novel loci [11q12.2 (FADS2), 12q21.1 (LGR5), 17q25.3 (FASN), and 22q12.1 (ZNRF3-KREMEN1)], bringing the total number of reported acne risk loci to 50. Our meta-analysis results explain 9.4% of the phenotypic variance of acne. A polygenic model of acne risk variants showed that individuals in the top 5% of the risk percentiles had a 1.62-fold (95% CI 1.47-1.78) increased acne risk relative to individuals with average risk (20-80% on the polygenic risk score distribution). Our findings highlight the Wnt and MAPK pathways as key factors in the genetic predisposition to acne vulgaris, together with the effects of genetic variation on the structure and maintenance of the hair follicle and pilosebaceous unit. Two novel loci, 11q12.2 and 17q25.3, contain genes encoding key enzymes involved in lipid biosynthesis pathways.
Language	English
Publishing date	2023-03-16
Publishing country	England
Document type	Journal Article
ZDB-ID	1141470-4
ISSN	1476-5438 ; 1018-4813
ISSN (online)	1476-5438
ISSN	1018-4813
DOI	10.1038/s41431-023-01326-8
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Article ; Online: Correction: Genome-wide meta-analysis identifies novel loci conferring risk of acne vulgaris.

Teder-Laving, Maris / Kals, Mart / Reigo, Anu / Ehin, Riin / Objärtel, Telver / Vaht, Mariliis / Nikopensius, Tiit / Metspalu, Andres / Kingo, Külli

European journal of human genetics : EJHG

2023

Language	English
Publishing date	2023-04-20
Publishing country	England
Document type	Published Erratum
ZDB-ID	1141470-4
ISSN	1476-5438 ; 1018-4813
ISSN (online)	1476-5438
ISSN	1018-4813
DOI	10.1038/s41431-023-01366-0
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Article ; Online: Transcriptome analysis reveals involvement of thiopurine S-methyltransferase in oxidation-reduction processes.

Šmid, Alenka / Štajdohar, Miha / Milek, Miha / Urbančič, Dunja / Karas Kuželički, Nataša / Tamm, Riin / Metspalu, Andres / Mlinarič-Raščan, Irena

European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences

2023 Volume 192, Page(s) 106616

Abstract: Thiopurine S-methyltransferase (TPMT) is an important enzyme involved in the deactivation of thiopurines and represents a major determinant of thiopurine-related toxicities. Despite its well-known importance in thiopurine metabolism, the understanding of ...

Abstract	Thiopurine S-methyltransferase (TPMT) is an important enzyme involved in the deactivation of thiopurines and represents a major determinant of thiopurine-related toxicities. Despite its well-known importance in thiopurine metabolism, the understanding of its endogenous role is lacking. In the present study, we aimed to gain insight into the molecular processes involving TPMT by applying a data fusion approach to analyze whole-genome expression data. The RNA profiling was done on whole blood samples from 1017 adult male and female donors to the Estonian biobank using Illumina HTv3 arrays. Our results suggest that TPMT is closely related to genes involved in oxidoreductive processes. The in vitro experiments on different cell models confirmed that TPMT influences redox capacity of the cell by altering S-adenosylmethionine (SAM) consumption and consequently glutathione (GSH) synthesis. Furthermore, by comparing gene networks of subgroups of individuals, we identified genes, which could have a role in regulating TPMT activity. The biological relevance of identified genes and pathways will have to be further evaluated in molecular studies.
MeSH term(s)	Adult ; Female ; Humans ; Male ; Gene Expression Profiling ; Mercaptopurine/metabolism ; Methyltransferases/genetics ; Methyltransferases/metabolism ; Oxidation-Reduction ; Purines ; S-Adenosylmethionine/metabolism
Chemical Substances	2-mercaptopurine (81XK02929C) ; Mercaptopurine (E7WED276I5) ; Methyltransferases (EC 2.1.1.-) ; Purines ; S-Adenosylmethionine (7LP2MPO46S) ; thiopurine methyltransferase (EC 2.1.1.67) ; TPMT protein, human (EC 2.1.1.67)
Language	English
Publishing date	2023-10-19
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1154366-8
ISSN	1879-0720 ; 0928-0987
ISSN (online)	1879-0720
ISSN	0928-0987
DOI	10.1016/j.ejps.2023.106616
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Article ; Online: Manhattan Harvester and Cropper: a system for GWAS peak detection.

Haller, Toomas / Tasa, Tõnis / Metspalu, Andres

BMC bioinformatics

2019 Volume 20, Issue 1, Page(s) 22

Abstract: Background: Selection of interesting regions from genome wide association studies (GWAS) is typically performed by eyeballing of Manhattan Plots. This is no longer possible with thousands of different phenotypes. There is a need for tools that can ... ...

Abstract	Background: Selection of interesting regions from genome wide association studies (GWAS) is typically performed by eyeballing of Manhattan Plots. This is no longer possible with thousands of different phenotypes. There is a need for tools that can automatically detect genomic regions that correspond to what the experienced researcher perceives as peaks worthwhile of further study. Results: We developed Manhattan Harvester, a tool designed for "peak extraction" from GWAS summary files and computation of parameters characterizing various aspects of individual peaks. We present the algorithms used and a model for creating a general quality score that evaluates peaks similarly to that of a human researcher. Our tool Cropper utilizes a graphical interface for inspecting, cropping and subsetting Manhattan Plot regions. Cropper is used to validate and visualize the regions detected by Manhattan Harvester. Conclusions: We conclude that our tools fill the current void in automatically screening large number of GWAS output files in batch mode. The interesting regions are detected and quantified by various parameters by Manhattan Harvester. Cropper offers graphical tools for in-depth inspection of the regions. The tools are open source and freely available.
MeSH term(s)	Computer Graphics ; Data Interpretation, Statistical ; Data Mining/methods ; Genome-Wide Association Study/statistics & numerical data ; Genomics/methods ; Humans ; Phenotype ; Polymorphism, Single Nucleotide ; Software
Language	English
Publishing date	2019-01-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-019-2600-4
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Article ; Online: The PROPHET project paves the way for personalized prevention in the future healthcare.

Pastorino, Roberta / Pezzullo, Angelo Maria / Osti, Tommaso / Adany, Roza / Borry, Pascal / Barnhoorn, Floris / Fadil, Eva / Kroese, Mark / Metspalu, Andres / Perez-Gomez, Beatriz / Perola, Markus / Quaggia, Daniela / Scollen, Serena / Shabani, Mahsa / Swartling Peterson, Stefan / van El, Carla / Vicente, Astrid / Boccia, Stefania

European journal of cancer prevention : the official journal of the European Cancer Prevention Organisation (ECP)

2024

Language	English
Publishing date	2024-04-11
Publishing country	England
Document type	Journal Article
ZDB-ID	1137033-6
ISSN	1473-5709 ; 0959-8278
ISSN (online)	1473-5709
ISSN	0959-8278
DOI	10.1097/CEJ.0000000000000873
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Article: Advances in Genomic Discovery and Implications for Personalized Prevention and Medicine: Estonia as Example.

Prins, Bram Peter / Leitsalu, Liis / Pärna, Katri / Fischer, Krista / Metspalu, Andres / Haller, Toomas / Snieder, Harold

Journal of personalized medicine

2021 Volume 11, Issue 5

Abstract: The current paradigm of personalized medicine envisages the use of genomic data to provide predictive information on the health course of an individual with the aim of prevention and individualized care. However, substantial efforts are required to ... ...

Abstract	The current paradigm of personalized medicine envisages the use of genomic data to provide predictive information on the health course of an individual with the aim of prevention and individualized care. However, substantial efforts are required to realize the concept: enhanced genetic discoveries, translation into intervention strategies, and a systematic implementation in healthcare. Here we review how further genetic discoveries are improving personalized prediction and advance functional insights into the link between genetics and disease. In the second part we give our perspective on the way these advances in genomic research will transform the future of personalized prevention and medicine using Estonia as a primer.
Language	English
Publishing date	2021-04-29
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2662248-8
ISSN	2075-4426
ISSN	2075-4426
DOI	10.3390/jpm11050358
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Article: Mendelian Randomization Identifies the Potential Causal Impact of Dietary Patterns on Circulating Blood Metabolites.

Taba, Nele / Valge, Hanna-Kristel / Metspalu, Andres / Esko, Tõnu / Wilson, James F / Fischer, Krista / Pirastu, Nicola

Frontiers in genetics

2021 Volume 12, Page(s) 738265

Abstract: Nutrition plays an important role in the development and progress of several health conditions, but the exact mechanism is often still unclear. Blood metabolites are likely candidates to be mediating these relationships, as their levels are strongly ... ...

Abstract	Nutrition plays an important role in the development and progress of several health conditions, but the exact mechanism is often still unclear. Blood metabolites are likely candidates to be mediating these relationships, as their levels are strongly dependent on the frequency of consumption of several foods/drinks. Understanding the causal effect of food on metabolites is thus of extreme importance. To establish these effects, we utilized two-sample Mendelian randomization using the genetic variants associated with dietary traits as instrumental variables. The estimates of single-nucleotide polymorphisms' effects on exposures were obtained from a recent genome-wide association study (GWAS) of 25 individual and 15 principal-component dietary traits, whereas the ones for outcomes were obtained from a GWAS of 123 blood metabolites measured by nuclear magnetic resonance spectroscopy. We identified 413 potentially causal links between food and metabolites, replicating previous findings, such as the association between increased oily fish consumption and higher DHA, and highlighting several novel associations. Most of the associations were related to very-low-density, intermediate-density (IDL), and low-density lipoproteins (LDL). For example, we found that constituents of IDL particles and large LDL particles were raised by coffee and alcohol while lowered by an overall healthier diet and fruit consumption. Our findings provide a strong base of evidence for planning future RCTs aimed at understanding the role of diet in determining blood metabolite levels.
Language	English
Publishing date	2021-11-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2021.738265
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Article ; Online: Association analysis of juvenile idiopathic arthritis genetic susceptibility factors in Estonian patients.

Nikopensius, Tiit / Niibo, Priit / Haller, Toomas / Jagomägi, Triin / Voog-Oras, Ülle / Tõnisson, Neeme / Metspalu, Andres / Saag, Mare / Pruunsild, Chris

Clinical rheumatology

2021 Volume 40, Issue 10, Page(s) 4157–4165

Abstract: Background: Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic condition of childhood. Genetic association studies have revealed several JIA susceptibility loci with the strongest effect size observed in the human leukocyte antigen ...

Abstract	Background: Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic condition of childhood. Genetic association studies have revealed several JIA susceptibility loci with the strongest effect size observed in the human leukocyte antigen (HLA) region. Genome-wide association studies have augmented the number of JIA-associated loci, particularly for non-HLA genes. The aim of this study was to identify new associations at non-HLA loci predisposing to the risk of JIA development in Estonian patients. Methods: We performed genome-wide association analyses in an entire JIA case-control sample (All-JIA) and in a case-control sample for oligoarticular JIA, the most prevalent JIA subtype. The entire cohort was genotyped using the Illumina HumanOmniExpress BeadChip arrays. After imputation, 16,583,468 variants were analyzed in 263 cases and 6956 controls. Results: We demonstrated nominal evidence of association for 12 novel non-HLA loci not previously implicated in JIA predisposition. We replicated known JIA associations in CLEC16A and VCTN1 regions in the oligoarticular JIA sample. The strongest associations in the All-JIA analysis were identified at PRKG1 (P = 2,54 × 10 Conclusion: This study increases the number of known JIA risk loci and provides additional evidence for the existence of overlapping genetic risk loci between JIA and other autoimmune diseases, particularly rheumatoid arthritis. The reported loci are involved in molecular pathways of immunological relevance and likely represent genomic regions that confer susceptibility to JIA in Estonian patients. Key Points • Juvenile idiopathic arthritis (JIA) is the most common childhood rheumatic disease with heterogeneous presentation and genetic predisposition. • Present genome-wide association study for Estonian JIA patients is first of its kind in Northern and Northeastern Europe. • The results of the present study increase the knowledge about JIA risk loci replicating some previously described associations, so adding weight to their relevance and describing novel loci. • The study provides additional evidence for the existence of overlapping genetic risk loci between JIA and other autoimmune diseases, particularly rheumatoid arthritis.
MeSH term(s)	Arthritis, Juvenile/genetics ; Case-Control Studies ; Estonia ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2021-06-08
Publishing country	Germany
Document type	Journal Article
ZDB-ID	604755-5
ISSN	1434-9949 ; 0770-3198
ISSN (online)	1434-9949
ISSN	0770-3198
DOI	10.1007/s10067-021-05756-x
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