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Beuchel C, Dittrich J, Becker S, Kirsten H, Tönjes A, Kovacs P, Stumvoll M, Loeffler M, Teren A, Thiery J, Isermann B, Ceglarek U, Scholz M. An atlas of genome-wide gene expression and metabolite associations and possible mediation effects towards body mass index. J Mol Med (Berl) 2023; 101:1305-1321. [PMID: 37672078 PMCID: PMC10560167 DOI: 10.1007/s00109-023-02362-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 08/07/2023] [Accepted: 08/15/2023] [Indexed: 09/07/2023]
Abstract
Investigating the cross talk of different omics layers is crucial to understand molecular pathomechanisms of metabolic diseases like obesity. Here, we present a large-scale association meta-analysis of genome-wide whole blood and peripheral blood mononuclear cell (PBMC) gene expressions profiled with Illumina HT12v4 microarrays and metabolite measurements from dried blood spots (DBS) characterized by targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) in three large German cohort studies with up to 7706 samples. We found 37,295 associations comprising 72 amino acids (AA) and acylcarnitine (AC) metabolites (including ratios) and 8579 transcripts. We applied this catalogue of associations to investigate the impact of associating transcript-metabolite pairs on body mass index (BMI) as an example metabolic trait. This is achieved by conducting a comprehensive mediation analysis considering metabolites as mediators of gene expression effects and vice versa. We discovered large mediation networks comprising 27,023 potential mediation effects within 20,507 transcript-metabolite pairs. Resulting networks of highly connected (hub) transcripts and metabolites were leveraged to gain mechanistic insights into metabolic signaling pathways. In conclusion, here, we present the largest available multi-omics integration of genome-wide transcriptome data and metabolite data of amino acid and fatty acid metabolism and further leverage these findings to characterize potential mediation effects towards BMI proposing candidate mechanisms of obesity and related metabolic diseases. KEY MESSAGES: Thousands of associations of 72 amino acid and acylcarnitine metabolites and 8579 genes expand the knowledge of metabolome-transcriptome associations. A mediation analysis of effects on body mass index revealed large mediation networks of thousands of obesity-related gene-metabolite pairs. Highly connected, potentially mediating hub genes and metabolites enabled insight into obesity and related metabolic disease pathomechanisms.
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Affiliation(s)
- Carl Beuchel
- Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
| | - Julia Dittrich
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany
| | - Susen Becker
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany
- Department of Forensic Toxicology, Institute of Legal Medicine, University Leipzig, Leipzig, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
- LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Anke Tönjes
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University Hospital Leipzig, Leipzig, Germany
- Deutsches Zentrum für Diabetesforschung, Neuherberg, Germany
| | - Michael Stumvoll
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
- LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | | | - Joachim Thiery
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany
- LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany
- LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Uta Ceglarek
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany
- LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany.
- LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany.
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2
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Hammel MC, Stein R, Kratzsch J, Vogel M, Eckert AJ, Triatin RD, Colombo M, Meigen C, Baber R, Stanik J, Spielau U, Stoltze A, Wirkner K, Tönjes A, Snieder H, Holl RW, Stumvoll M, Blüher M, Kiess W, Körner A. Fasting indices of glucose-insulin-metabolism across life span and prediction of glycemic deterioration in children with obesity from new diagnostic cut-offs. THE LANCET REGIONAL HEALTH. EUROPE 2023; 30:100652. [PMID: 37465325 PMCID: PMC10350850 DOI: 10.1016/j.lanepe.2023.100652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 07/20/2023]
Abstract
Background Fasting indices of glucose-insulin-metabolism are an easy and affordable tool to assess insulin resistance. We aimed to establish reference ranges for fasting insulin indices that reflect age-dependent variation over the entire life span and subsequently test their clinical application regarding the prediction of glycemic deterioration in children. Methods We calculated age- and puberty-dependent reference values for HOMA-IR, HOMA2-IR, HOMA-β, McAuley index, fasting insulin, and fasting glucose from 6994 observations of 5512 non-obese healthy subjects aged 5-80 years. Applying those references, we determined the prevalence of insulin resistance among 2538 subjects with obesity. Furthermore, we investigated the intraindividual stability and the predictive values for future dysglycemia of these fasting indices in 516 children and adolescents with obesity up to 19 years of follow-up. We validated the results in three independent cohorts. Findings There was a strong age-dependent variation of all indices throughout the life span, including prolonged recovery of pubertal insulin resistance and a subsequent continuous increase throughout adulthood. Already from age 5 years onwards, >40% of children with obesity presented with elevated parameters of insulin resistance. Applying newly developed reference ranges, insulin resistance among children with obesity doubled the risk for future glycemic deterioration (HOMA-IR HR 1.88 (95% CI 1.1-3.21)), fasting insulin HR 1.89 (95% CI 1.11-3.23). In contrast, fasting glucose alone was not predictive for emerging dysglycemia in children with obesity (HR 1.03 (95% CI 0.62-1.71)). The new insulin-based thresholds were superior to fasting glucose and HbA1c in detecting children eventually manifesting with dysglycemia in prospective analyses. Interpretation The variation of fasting glucose-insulin-metabolism across the life span necessitates age-specific reference ranges. The improved prediction of future glycemic deterioration by indices based on fasting insulin beyond simple glucose measures alone could help to stratify risk characteristics of children with obesity in order to guide patient-tailored prevention and intervention approaches. Funding German Research Foundation (DFG)-through SFB 1052, project number 209933838, subproject C5; Federal Ministry of Education and Research, Germany; European Union-European Regional Development Fund; Free State of Saxony. The German Diabetes Association, the CarbHealth consortium (01EA1908B). EU-IMI2-Consortium SOPHIA (grant agreement No 875534), German Center for Diabetes Research (DZD), grant number 82DZD14E03.
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Affiliation(s)
- Maximiliane Chiara Hammel
- Medical Faculty, University Hospital for Children and Adolescents, Center for Pediatric Research, University of Leipzig, Leipzig, Germany
| | - Robert Stein
- Medical Faculty, University Hospital for Children and Adolescents, Center for Pediatric Research, University of Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Germany
| | - Jürgen Kratzsch
- Medical Faculty, Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnosis, University of Leipzig, Leipzig, Germany
| | - Mandy Vogel
- LIFE Child Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Alexander J. Eckert
- University of Ulm, Institute of Epidemiology and Medical Biometry, ZIBMT, Ulm, Germany
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Rima Destya Triatin
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marco Colombo
- Medical Faculty, University Hospital for Children and Adolescents, Center for Pediatric Research, University of Leipzig, Leipzig, Germany
| | - Christof Meigen
- LIFE Child Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Ronny Baber
- Medical Faculty, Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnosis, University of Leipzig, Leipzig, Germany
- LIFE Child Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Juraj Stanik
- Medical Faculty, University Hospital for Children and Adolescents, Center for Pediatric Research, University of Leipzig, Leipzig, Germany
- Medical Faculty, Department of Pediatrics, and DIABGENE Laboratory, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Comenius University, Bratislava, Slovakia
| | - Ulrike Spielau
- Medical Faculty, University Hospital for Children and Adolescents, Center for Pediatric Research, University of Leipzig, Leipzig, Germany
| | - Anette Stoltze
- Medical Faculty, University Hospital for Children and Adolescents, Center for Pediatric Research, University of Leipzig, Leipzig, Germany
| | - Kerstin Wirkner
- LIFE Child Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute for Medical Informatics, Statistics and Epidemiology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Anke Tönjes
- Department of Endocrinology, Nephrology und Rheumatic Diseases, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Reinhard W. Holl
- University of Ulm, Institute of Epidemiology and Medical Biometry, ZIBMT, Ulm, Germany
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Michael Stumvoll
- Department of Endocrinology, Nephrology und Rheumatic Diseases, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Matthias Blüher
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Germany
- Department of Endocrinology, Nephrology und Rheumatic Diseases, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Wieland Kiess
- Medical Faculty, University Hospital for Children and Adolescents, Center for Pediatric Research, University of Leipzig, Leipzig, Germany
- LIFE Child Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Antje Körner
- Medical Faculty, University Hospital for Children and Adolescents, Center for Pediatric Research, University of Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Germany
- LIFE Child Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
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Genome-wide meta-analysis of phytosterols reveals five novel loci and a detrimental effect on coronary atherosclerosis. Nat Commun 2022; 13:143. [PMID: 35013273 PMCID: PMC8748632 DOI: 10.1038/s41467-021-27706-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 11/22/2021] [Indexed: 12/29/2022] Open
Abstract
Phytosterol serum concentrations are under tight genetic control. The relationship between phytosterols and coronary artery disease (CAD) is controversially discussed. We perform a genome-wide meta-analysis of 32 phytosterol traits reflecting resorption, cholesterol synthesis and esterification in six studies with up to 9758 subjects and detect ten independent genome-wide significant SNPs at seven genomic loci. We confirm previously established associations at ABCG5/8 and ABO and demonstrate an extended locus heterogeneity at ABCG5/8 with different functional mechanisms. New loci comprise HMGCR, NPC1L1, PNLIPRP2, SCARB1 and APOE. Based on these results, we perform Mendelian Randomization analyses (MR) revealing a risk-increasing causal relationship of sitosterol serum concentrations and CAD, which is partly mediated by cholesterol. Here we report that phytosterols are polygenic traits. MR add evidence of both, direct and indirect causal effects of sitosterol on CAD.
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Long runs of homozygosity are associated with Alzheimer's disease. Transl Psychiatry 2021; 11:142. [PMID: 33627629 PMCID: PMC7904832 DOI: 10.1038/s41398-020-01145-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/27/2020] [Accepted: 12/04/2020] [Indexed: 11/12/2022] Open
Abstract
Long runs of homozygosity (ROH) are contiguous stretches of homozygous genotypes, which are a footprint of inbreeding and recessive inheritance. The presence of recessive loci is suggested for Alzheimer's disease (AD); however, their search has been poorly assessed to date. To investigate homozygosity in AD, here we performed a fine-scale ROH analysis using 10 independent cohorts of European ancestry (11,919 AD cases and 9181 controls.) We detected an increase of homozygosity in AD cases compared to controls [βAVROH (CI 95%) = 0.070 (0.037-0.104); P = 3.91 × 10-5; βFROH (CI95%) = 0.043 (0.009-0.076); P = 0.013]. ROHs increasing the risk of AD (OR > 1) were significantly overrepresented compared to ROHs increasing protection (p < 2.20 × 10-16). A significant ROH association with AD risk was detected upstream the HS3ST1 locus (chr4:11,189,482‒11,305,456), (β (CI 95%) = 1.09 (0.48 ‒ 1.48), p value = 9.03 × 10-4), previously related to AD. Next, to search for recessive candidate variants in ROHs, we constructed a homozygosity map of inbred AD cases extracted from an outbred population and explored ROH regions in whole-exome sequencing data (N = 1449). We detected a candidate marker, rs117458494, mapped in the SPON1 locus, which has been previously associated with amyloid metabolism. Here, we provide a research framework to look for recessive variants in AD using outbred populations. Our results showed that AD cases have enriched homozygosity, suggesting that recessive effects may explain a proportion of AD heritability.
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Jacobi T, Massier L, Klöting N, Horn K, Schuch A, Ahnert P, Engel C, Löffler M, Burkhardt R, Thiery J, Tönjes A, Stumvoll M, Blüher M, Doxiadis I, Scholz M, Kovacs P. HLA Class II Allele Analyses Implicate Common Genetic Components in Type 1 and Non-Insulin-Treated Type 2 Diabetes. J Clin Endocrinol Metab 2020; 105:5715056. [PMID: 31974565 DOI: 10.1210/clinem/dgaa027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/15/2020] [Indexed: 12/20/2022]
Abstract
CONTEXT Common genetic susceptibility may underlie the frequently observed co-occurrence of type 1 and type 2 diabetes in families. Given the role of HLA class II genes in the pathophysiology of type 1 diabetes, the aim of the present study was to test the association of high density imputed human leukocyte antigen (HLA) genotypes with type 2 diabetes. OBJECTIVES AND DESIGN Three cohorts (Ntotal = 10 413) from Leipzig, Germany were included in this study: LIFE-Adult (N = 4649), LIFE-Heart (N = 4815) and the Sorbs (N = 949) cohort. Detailed metabolic phenotyping and genome-wide single nucleotide polymorphism (SNP) data were available for all subjects. Using 1000 Genome imputation data, HLA genotypes were imputed on 4-digit level and association tests for type 2 diabetes, and related metabolic traits were conducted. RESULTS In a meta-analysis including all 3 cohorts, the absence of HLA-DRB5 was associated with increased risk of type 2 diabetes (P = 0.001). In contrast, HLA-DQB*06:02 and HLA-DQA*01:02 had a protective effect on type 2 diabetes (P = 0.005 and 0.003, respectively). Both alleles are part of the well-established type 1 diabetes protective haplotype DRB1*15:01~DQA1*01:02~DQB1*06:02, which was also associated with reduced risk of type 2 diabetes (OR 0.84; P = 0.005). On the contrary, the DRB1*07:01~DQA1*02:01~DQB1*03:03 was identified as a risk haplotype in non-insulin-treated diabetes (OR 1.37; P = 0.002). CONCLUSIONS Genetic variation in the HLA class II locus exerts risk and protective effects on non-insulin-treated type 2 diabetes. Our data suggest that the genetic architecture of type 1 diabetes and type 2 diabetes might share common components on the HLA class II locus.
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Affiliation(s)
- Thomas Jacobi
- University of Leipzig Medical Center, IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Lucas Massier
- University of Leipzig Medical Center, IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Nora Klöting
- University of Leipzig Medical Center, IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Katrin Horn
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Alexander Schuch
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Peter Ahnert
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Markus Löffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Ralph Burkhardt
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Joachim Thiery
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine and Clinical Chemistry, University of Leipzig, Leipzig, Germany
| | - Anke Tönjes
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Michael Stumvoll
- University of Leipzig Medical Center, IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Matthias Blüher
- University of Leipzig Medical Center, IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Ilias Doxiadis
- Institute for Transfusion Medicine, University Hospital of Leipzig, Leipzig, Germany
| | - Markus Scholz
- University of Leipzig Medical Center, IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Peter Kovacs
- University of Leipzig Medical Center, IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
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Weingarten MFJ, Scholz M, Wohland T, Horn K, Stumvoll M, Kovacs P, Tönjes A. Circulating Oxytocin Is Genetically Determined and Associated With Obesity and Impaired Glucose Tolerance. J Clin Endocrinol Metab 2019; 104:5621-5632. [PMID: 31361301 DOI: 10.1210/jc.2019-00643] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 07/22/2019] [Indexed: 01/01/2023]
Abstract
CONTEXT Despite the emerging evidence on the role of oxytocin (OXT) in metabolic diseases, there is a lack of well-powered studies addressing the relationship of circulating OXT with obesity and diabetes. OBJECTIVES AND DESIGN Here, we measured OXT in a study cohort (n = 721; 396 women, 325 men; mean age ± SD, 47.7 ± 15.2 years) with subphenotypes related to obesity, including anthropometric traits such as body mass index [BMI (mean ± SD), 26.8 ± 4.6 kg/m2], waist-to-hip ratio (WHR; 0.88 ± 0.09), blood parameters (glucose, 5.32 ± 0.50 mmol/L; insulin, 5.3 ± 3.3 µU/mL), and oral glucose tolerance test to clarify the association with OXT. We also tested in a genome-wide association study (GWAS) whether the interindividual variation in OXT serum levels might be explained by genetic variation. RESULTS The OXT concentration was increased in subjects with elevated BMI and positively correlated with WHR, waist circumference, and triglyceride levels. The OXT concentration in subjects with BMI <25 kg/m2 was significantly lower (n = 256; 78.6 pg/mL) than in subjects with a BMI between 25 and 30 kg/m2 (n = 314; 98.5 pg/mL, P = 6 × 10-6) and with BMI >30 kg/m2 (n = 137; 106.4 pg/mL, P = 8 × 10-6). OXT levels were also positively correlated with plasma glucose and insulin and were elevated in subjects with impaired glucose tolerance (P = 4.6 × 10-3). Heritability of OXT was estimated at 12.8%. In a GWAS, two hits in linkage disequilibrium close (19 kb) to the OXT reached genome-wide significant association (top-hit rs12625893, P = 3.1 × 10-8, explained variance 3%). CONCLUSIONS Our data show that OXT is genetically affected by a variant near OXT and is associated with obesity and impaired glucose tolerance.
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Affiliation(s)
| | - Markus Scholz
- Institute for Medical Informatics, Statistics, and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center, University of Leipzig, Leipzig, Germany
| | - Tobias Wohland
- IFB Adiposity Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Katrin Horn
- Institute for Medical Informatics, Statistics, and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center, University of Leipzig, Leipzig, Germany
| | - Michael Stumvoll
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Peter Kovacs
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Anke Tönjes
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
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Beuchel C, Becker S, Dittrich J, Kirsten H, Toenjes A, Stumvoll M, Loeffler M, Thiele H, Beutner F, Thiery J, Ceglarek U, Scholz M. Clinical and lifestyle related factors influencing whole blood metabolite levels - A comparative analysis of three large cohorts. Mol Metab 2019; 29:76-85. [PMID: 31668394 PMCID: PMC6734104 DOI: 10.1016/j.molmet.2019.08.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 12/31/2022] Open
Abstract
Objective Human blood metabolites are influenced by a number of lifestyle and environmental factors. Identification of these factors and the proper quantification of their relevance provides insights into human biological and metabolic disease processes, is key for standardized translation of metabolite biomarkers into clinical applications, and is a prerequisite for comparability of data between studies. However, so far only limited data exist from large and well-phenotyped human cohorts and current methods for analysis do not fully account for the characteristics of these data. The primary aim of this study was to identify, quantify and compare the impact of a comprehensive set of clinical and lifestyle related factors on metabolite levels in three large human cohorts. To achieve this goal, we improve current methodology by developing a principled analysis approach, which could be translated to other cohorts and metabolite panels. Methods 63 Metabolites (amino acids, acylcarnitines) were quantified by liquid chromatography tandem mass spectrometry in three cohorts (total N = 16,222). Supported by a simulation study evaluating various analytical approaches, we developed an analysis pipeline including preprocessing, identification, and quantification of factors affecting metabolite levels. We comprehensively identified uni- and multivariable metabolite associations considering 29 environmental and clinical factors and performed metabolic pathway enrichment and network analyses. Results Inverse normal transformation of batch corrected and outlier removed metabolite levels accompanied by linear regression analysis proved to be the best suited method to deal with the metabolite data. Association analyses revealed numerous uni- and multivariable significant associations. 15 of the analyzed 29 factors explained >1% of variance for at least one of the metabolites. Strongest factors are application of steroid hormones, reticulocytes, waist-to-hip ratio, sex, haematocrit, and age. Effect sizes of factors are comparable across studies. Conclusions We introduced a principled approach for the analysis of MS data allowing identification, and quantification of effects of clinical and lifestyle factors with metabolite levels. We detected a number of known and novel associations broadening our understanding of the regulation of the human metabolome. The large heterogeneity observed between cohorts could almost completely be explained by differences in the distribution of influencing factors emphasizing the necessity of a proper confounder analysis when interpreting metabolite associations. Amino-acids and acylcarnitines analyzed in three studies with >16,000 individuals. Develop a generic and adaptable bioinformatics workflow. Analysis of the impact of 29 clinical and life-style factors on blood metabolites. Analysis of network between factors and metabolites. Comparison of results between studies.
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Affiliation(s)
- Carl Beuchel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Susen Becker
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany; Department of Pediatric Surgery, University of Leipzig, Leipzig, Germany
| | - Julia Dittrich
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany; LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Anke Toenjes
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Michael Stumvoll
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany; LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | | | | | - Joachim Thiery
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany; LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Uta Ceglarek
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany; LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany; LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany; IFB Adiposity Diseases, University Hospital Leipzig, Leipzig, Germany.
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8
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Breitfeld J, Wiele N, Gutsmann B, Stumvoll M, Blüher M, Scholz M, Kovacs P, Tönjes A. Circulating Adipokine
VASPIN
Is Associated with Serum Lipid Profiles in Humans. Lipids 2019; 54:203-210. [DOI: 10.1002/lipd.12139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Jana Breitfeld
- IFB Adiposity DiseasesUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
| | - Norman Wiele
- Department of Medicine, Division of Endocrinology and NephrologyUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
| | - Beate Gutsmann
- Department of Medicine, Division of Endocrinology and NephrologyUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
| | - Michael Stumvoll
- IFB Adiposity DiseasesUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
- Department of Medicine, Division of Endocrinology and NephrologyUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
| | - Matthias Blüher
- IFB Adiposity DiseasesUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
- Department of Medicine, Division of Endocrinology and NephrologyUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of Leipzig Härtelstrasse 16‐18, 04103, Leipzig Germany
- LIFE Research CenterUniversity of Leipzig Philipp‐Rosenthal‐Straβe 27, 04103, Leipzig Germany
| | - Peter Kovacs
- Department of Medicine, Division of Endocrinology and NephrologyUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
| | - Anke Tönjes
- Department of Medicine, Division of Endocrinology and NephrologyUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
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9
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Tönjes A, Scholz M, Krüger J, Krause K, Schleinitz D, Kirsten H, Gebhardt C, Marzi C, Grallert H, Ladenvall C, Heyne H, Laurila E, Kriebel J, Meisinger C, Rathmann W, Gieger C, Groop L, Prokopenko I, Isomaa B, Beutner F, Kratzsch J, Fischer-Rosinsky A, Pfeiffer A, Krohn K, Spranger J, Thiery J, Blüher M, Stumvoll M, Kovacs P. Genome-wide meta-analysis identifies novel determinants of circulating serum progranulin. Hum Mol Genet 2019; 27:546-558. [PMID: 29186428 DOI: 10.1093/hmg/ddx413] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 11/22/2017] [Indexed: 11/14/2022] Open
Abstract
Progranulin is a secreted protein with important functions in processes including immune and inflammatory response, metabolism and embryonic development. The present study aimed at identification of genetic factors determining progranulin concentrations. We conducted a genome-wide association meta-analysis for serum progranulin in three independent cohorts from Europe: Sorbs (N = 848) and KORA (N = 1628) from Germany and PPP-Botnia (N = 335) from Finland (total N = 2811). Single nucleotide polymorphisms (SNPs) associated with progranulin levels were replicated in two additional German cohorts: LIFE-Heart Study (Leipzig; N = 967) and Metabolic Syndrome Berlin Potsdam (Berlin cohort; N = 833). We measured mRNA expression of genes in peripheral blood mononuclear cells (PBMC) by micro-arrays and performed mRNA expression quantitative trait and expression-progranulin association studies to functionally substantiate identified loci. Finally, we conducted siRNA silencing experiments in vitro to validate potential candidate genes within the associated loci. Heritability of circulating progranulin levels was estimated at 31.8% and 26.1% in the Sorbs and LIFE-Heart cohort, respectively. SNPs at three loci reached study-wide significance (rs660240 in CELSR2-PSRC1-MYBPHL-SORT1, rs4747197 in CDH23-PSAP and rs5848 in GRN) explaining 19.4%/15.0% of the variance and 61%/57% of total heritability in the Sorbs/LIFE-Heart Study. The strongest evidence for association was at rs660240 (P = 5.75 × 10-50), which was also associated with mRNA expression of PSRC1 in PBMC (P = 1.51 × 10-21). Psrc1 knockdown in murine preadipocytes led to a consecutive 30% reduction in progranulin secretion. In conclusion, the present meta-GWAS combined with mRNA expression identified three loci associated with progranulin and supports the role of PSRC1 in the regulation of progranulin secretion.
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Affiliation(s)
- Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig 04103, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig 04107, Germany.,LIFE Research Center, University of Leipzig, Leipzig 04103, Germany
| | - Jacqueline Krüger
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig 04103, Germany
| | - Kerstin Krause
- Department of Medicine, University of Leipzig, Leipzig 04103, Germany
| | - Dorit Schleinitz
- Department of Medicine, University of Leipzig, Leipzig 04103, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig 04107, Germany.,LIFE Research Center, University of Leipzig, Leipzig 04103, Germany
| | - Claudia Gebhardt
- Department of Medicine, University of Leipzig, Leipzig 04103, Germany
| | - Carola Marzi
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg 85764, Germany.,German Research Center for Environmental Health, Institute of Epidemiology II, Helmholtz Center Munich, Neuherberg 85764, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg 85764, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg 85764, Germany.,German Research Center for Environmental Health, Institute of Epidemiology II, Helmholtz Center Munich, Neuherberg 85764, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg 85764, Germany
| | - Claes Ladenvall
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University and Lund University Diabetes Centre, CRC at Skåne University Hospital, Malmö 20502, Sweden
| | - Henrike Heyne
- Institute of Human Genetics, University of Leipzig, Leipzig 04103, Germany
| | - Esa Laurila
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University and Lund University Diabetes Centre, CRC at Skåne University Hospital, Malmö 20502, Sweden
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg 85764, Germany.,German Research Center for Environmental Health, Institute of Epidemiology II, Helmholtz Center Munich, Neuherberg 85764, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg 85764, Germany
| | - Christa Meisinger
- German Research Center for Environmental Health, Institute of Epidemiology II, Helmholtz Center Munich, Neuherberg 85764, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg 85764, Germany
| | - Wolfgang Rathmann
- German Diabetes Center, Institute of Biometrics and Epidemiology, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg 85764, Germany.,German Research Center for Environmental Health, Institute of Epidemiology II, Helmholtz Center Munich, Neuherberg 85764, Germany
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University and Lund University Diabetes Centre, CRC at Skåne University Hospital, Malmö 20502, Sweden
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LE, UK.,Department of Genomics of Common Diseases, Imperial College London, London SW7 2AZ, UK
| | - Bo Isomaa
- Department of Social Services and Healthcare, Jakobstad 68601, Finland.,Folkhälsan Research Centre, Helsinki 00290, Finland
| | - Frank Beutner
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig 04103, Germany
| | - Jürgen Kratzsch
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig 04103, Germany
| | - Antje Fischer-Rosinsky
- Department of Endocrinology, Diabetes and Nutrition, Charité-Universitätsmedizin, Berlin 10117, Germany
| | - Andreas Pfeiffer
- Department of Endocrinology, Diabetes and Nutrition, Charité-Universitätsmedizin, Berlin 10117, Germany.,Department of Clinical Nutrition, German Institute of Human Nutrition, Nuthetal 14558, Germany
| | - Knut Krohn
- Interdisciplinary Centre for Clinical Research, University of Leipzig, Leipzig 04103, Germany
| | - Joachim Spranger
- Department of Endocrinology, Diabetes and Nutrition, Charité-Universitätsmedizin, Berlin 10117, Germany
| | - Joachim Thiery
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig 04103, Germany
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig 04103, Germany.,Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig 04103, Germany
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig, Leipzig 04103, Germany.,Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig 04103, Germany
| | - Peter Kovacs
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig 04103, Germany
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10
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Gross A, Tönjes A, Scholz M. On the impact of relatedness on SNP association analysis. BMC Genet 2017; 18:104. [PMID: 29212447 PMCID: PMC5719591 DOI: 10.1186/s12863-017-0571-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/23/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND When testing for SNP (single nucleotide polymorphism) associations in related individuals, observations are not independent. Simple linear regression assuming independent normally distributed residuals results in an increased type I error and the power of the test is also affected in a more complicate manner. Inflation of type I error is often successfully corrected by genomic control. However, this reduces the power of the test when relatedness is of concern. In the present paper, we derive explicit formulae to investigate how heritability and strength of relatedness contribute to variance inflation of the effect estimate of the linear model. Further, we study the consequences of variance inflation on hypothesis testing and compare the results with those of genomic control correction. We apply the developed theory to the publicly available HapMap trio data (N=129), the Sorbs (a self-contained population with N=977 characterised by a cryptic relatedness structure) and synthetic family studies with different sample sizes (ranging from N=129 to N=999) and different degrees of relatedness. RESULTS We derive explicit and easily to apply approximation formulae to estimate the impact of relatedness on the variance of the effect estimate of the linear regression model. Variance inflation increases with increasing heritability. Relatedness structure also impacts the degree of variance inflation as shown for example family structures. Variance inflation is smallest for HapMap trios, followed by a synthetic family study corresponding to the trio data but with larger sample size than HapMap. Next strongest inflation is observed for the Sorbs, and finally, for a synthetic family study with a more extreme relatedness structure but with similar sample size as the Sorbs. Type I error increases rapidly with increasing inflation. However, for smaller significance levels, power increases with increasing inflation while the opposite holds for larger significance levels. When genomic control is applied, type I error is preserved while power decreases rapidly with increasing variance inflation. CONCLUSIONS Stronger relatedness as well as higher heritability result in increased variance of the effect estimate of simple linear regression analysis. While type I error rates are generally inflated, the behaviour of power is more complex since power can be increased or reduced in dependence on relatedness and the heritability of the phenotype. Genomic control cannot be recommended to deal with inflation due to relatedness. Although it preserves type I error, the loss in power can be considerable. We provide a simple formula for estimating variance inflation given the relatedness structure and the heritability of a trait of interest. As a rule of thumb, variance inflation below 1.05 does not require correction and simple linear regression analysis is still appropriate.
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Affiliation(s)
- Arnd Gross
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, Leipzig, 04107, Germany. .,LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, Philipp-Rosenthal-Strasse 27, Leipzig, 04103, Germany.
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Liebigstrasse 18, Leipzig, 04103, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, Leipzig, 04107, Germany.,LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, Philipp-Rosenthal-Strasse 27, Leipzig, 04103, Germany
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11
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Blant A, Kwong M, Szpiech ZA, Pemberton TJ. Weighted likelihood inference of genomic autozygosity patterns in dense genotype data. BMC Genomics 2017; 18:928. [PMID: 29191164 PMCID: PMC5709839 DOI: 10.1186/s12864-017-4312-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/16/2017] [Indexed: 12/14/2022] Open
Abstract
Background Genomic regions of autozygosity (ROA) arise when an individual is homozygous for haplotypes inherited identical-by-descent from ancestors shared by both parents. Over the past decade, they have gained importance for understanding evolutionary history and the genetic basis of complex diseases and traits. However, methods to infer ROA in dense genotype data have not evolved in step with advances in genome technology that now enable us to rapidly create large high-resolution genotype datasets, limiting our ability to investigate their constituent ROA patterns. Methods We report a weighted likelihood approach for inferring ROA in dense genotype data that accounts for autocorrelation among genotyped positions and the possibilities of unobserved mutation and recombination events, and variability in the confidence of individual genotype calls in whole genome sequence (WGS) data. Results Forward-time genetic simulations under two demographic scenarios that reflect situations where inbreeding and its effect on fitness are of interest suggest this approach is better powered than existing state-of-the-art methods to infer ROA at marker densities consistent with WGS and popular microarray genotyping platforms used in human and non-human studies. Moreover, we present evidence that suggests this approach is able to distinguish ROA arising via consanguinity from ROA arising via endogamy. Using subsets of The 1000 Genomes Project Phase 3 data we show that, relative to WGS, intermediate and long ROA are captured robustly with popular microarray platforms, while detection of short ROA is more variable and improves with marker density. Worldwide ROA patterns inferred from WGS data are found to accord well with those previously reported on the basis of microarray genotype data. Finally, we highlight the potential of this approach to detect genomic regions enriched for autozygosity signals in one group relative to another based upon comparisons of per-individual autozygosity likelihoods instead of inferred ROA frequencies. Conclusions This weighted likelihood ROA inference approach can assist population- and disease-geneticists working with a wide variety of data types and species to explore ROA patterns and to identify genomic regions with differential ROA signals among groups, thereby advancing our understanding of evolutionary history and the role of recessive variation in phenotypic variation and disease. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4312-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexandra Blant
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Michelle Kwong
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Zachary A Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Trevor J Pemberton
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada.
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12
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Ehler E, Vanek D. Forensic genetic analyses in isolated populations with examples of central European Valachs and Roma. J Forensic Leg Med 2017; 48:46-52. [PMID: 28454050 DOI: 10.1016/j.jflm.2017.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 03/22/2017] [Accepted: 04/09/2017] [Indexed: 01/27/2023]
Abstract
Isolated populations present a constant threat to the correctness of forensic genetic casework. In this review article we present several examples of how analyzing samples from isolated populations can bias the results of the forensic statistics and analyses. We select our examples from isolated populations from central and southeastern Europe, namely the Valachs and the European Roma. We also provide the reader with general strategies and principles to improve the laboratory practice (best practice) and reporting of samples from supposedly isolated populations. These include reporting the precise population data used for computing the forensic statistics, using the appropriate θ correction factor for calculating allele frequencies, typing ancestry informative markers in samples of unknown or uncertain ethnicity and establishing ethnic-specific forensic databases.
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Affiliation(s)
- Edvard Ehler
- Department of Biology and Environmental Studies, Charles University in Prague, Faculty of Education, Magdaleny Rettigove 4, Prague, 116 39, Czech Republic; Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland.
| | - Daniel Vanek
- Forensic DNA Service, Janovskeho 18, Prague 7, 170 00, Czech Republic; Charles University in Prague, 2nd Faculty of Medicine, V Uvalu 84, Prague, 150 06, Czech Republic; Nemocnice Na Bulovce, Institute of Legal Medicine, Budinova 2, Prague, 180 81, Czech Republic.
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13
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Cho S, Seo HJ, Lee J, Yu HJ, Lee SD. Kinship Testing Based on SNPs Using Microarray System. Transfus Med Hemother 2016; 43:429-432. [PMID: 27994531 DOI: 10.1159/000446322] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/15/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Kinship testing using biallelic SNP markers has been demonstrated to be a promising approach as a supplement to standard STR typing, and several systems, such as pyrosequencing and microarray, have been introduced and utilized in real forensic cases. The Affymetrix microarray containing 169 autosomal SNPs developed for forensic application was applied to our practical case for kinship analysis that had remained inconclusive due to partial STR profiles of degraded DNA and possibility of inbreeding within the population. CASE REPORT 169 autosomal SNPs were typed on array with severely degraded DNA of two bone samples, and the kinship compared to genotypes in a reference database of their putative family members. RESULTS Two bone samples remained unidentified through traditional STR typing with partial profiles of 10 or 14 of 16 alleles. Because these samples originated from a geographically isolated population, a cautious approach was required when analyzing and declaring true paternity only based on PI values. In a supplementary SNP typing, 106 and 78 SNPs were obtained, and the match candidates were found in each case with improved PI values than using only STRs and with no discrepant SNPs in comparison. CONCLUSION Our case showed that the utility of multiple SNPs on array is expected in practical forensic caseworks with an establishment of reference database.
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Affiliation(s)
- Sohee Cho
- Department of Forensic Medicine, Seoul National University, College of Medicine, Seoul, South Korea
| | - Hee Jin Seo
- Department of Forensic Medicine, Seoul National University, College of Medicine, Seoul, South Korea
| | - Jihyun Lee
- Department of Forensic Medicine, Seoul National University, College of Medicine, Seoul, South Korea
| | - Hyung Jin Yu
- DNA Link, Seoul, South Korea, Seoul, South Korea
| | - Soong Deok Lee
- Department of Forensic Medicine, Seoul National University, College of Medicine, Seoul, South Korea; Institute of Forensic Science, Seoul National University, College of Medicine, Seoul, South Korea
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14
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Ben Halim N, Nagara M, Regnault B, Hsouna S, Lasram K, Kefi R, Azaiez H, Khemira L, Saidane R, Ammar SB, Besbes G, Weil D, Petit C, Abdelhak S, Romdhane L. Estimation of Recent and Ancient Inbreeding in a Small Endogamous Tunisian Community Through Genomic Runs of Homozygosity. Ann Hum Genet 2015; 79:402-17. [PMID: 26420437 DOI: 10.1111/ahg.12131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 07/08/2015] [Indexed: 01/21/2023]
Abstract
Runs of homozygosity (ROHs) are extended genomic regions of homozygous genotypes that record populations' mating patterns in the past. We performed microarray genotyping on 15 individuals from a small isolated Tunisian community. We estimated the individual and population genome-wide level of homozygosity from data on ROH above 0.5 Mb in length. We found a high average number of ROH per individual (48.2). The smallest ROH category (0.5-1.49 Mb) represents 0.93% of the whole genome, while medium-size (1.5-4.99 Mb) and long-size ROH (≥5 Mb) cover 1.18% and 0.95%, respectively. We found that genealogical individual inbreeding coefficients (Fped ) based on three- to four-generation pedigrees are not reliable indicators of the current proportion of genome-wide homozygosity inferred from ROH (FROH ) either for 0.5 or 1.5 Mb ROH length thresholds, while identity-by-descent sharing is a function of shared coancestry. This study emphasizes the effect of reproductive isolation and a prolonged practice of consanguinity that limits the genetic heterogeneity. It also provides evidence of both recent and ancient parental relatedness contribution to the current level of genome-wide homozygosity in the studied population. These findings may be useful for evaluation of long-term effects of inbreeding on human health and for future applications of ROHs in identifying recessive susceptibility genes.
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Affiliation(s)
- Nizar Ben Halim
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Majdi Nagara
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | | | - Sana Hsouna
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Khaled Lasram
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Hela Azaiez
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Laroussi Khemira
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Rachid Saidane
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Slim Ben Ammar
- Clinical Biochemistry Laboratory, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Ghazi Besbes
- ENT Department, la Rabta Hospital, Tunis, Tunisia
| | - Dominique Weil
- Inserm UMRS587, Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris Cedex 15, France
| | - Christine Petit
- Inserm UMRS587, Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris Cedex 15, France
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, Tunis, Le Belvédère, Tunisia
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15
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Burkhardt R, Kirsten H, Beutner F, Holdt LM, Gross A, Teren A, Tönjes A, Becker S, Krohn K, Kovacs P, Stumvoll M, Teupser D, Thiery J, Ceglarek U, Scholz M. Integration of Genome-Wide SNP Data and Gene-Expression Profiles Reveals Six Novel Loci and Regulatory Mechanisms for Amino Acids and Acylcarnitines in Whole Blood. PLoS Genet 2015; 11:e1005510. [PMID: 26401656 PMCID: PMC4581711 DOI: 10.1371/journal.pgen.1005510] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/17/2015] [Indexed: 01/23/2023] Open
Abstract
Profiling amino acids and acylcarnitines in whole blood spots is a powerful tool in the laboratory diagnosis of several inborn errors of metabolism. Emerging data suggests that altered blood levels of amino acids and acylcarnitines are also associated with common metabolic diseases in adults. Thus, the identification of common genetic determinants for blood metabolites might shed light on pathways contributing to human physiology and common diseases. We applied a targeted mass-spectrometry-based method to analyze whole blood concentrations of 96 amino acids, acylcarnitines and pathway associated metabolite ratios in a Central European cohort of 2,107 adults and performed genome-wide association (GWA) to identify genetic modifiers of metabolite concentrations. We discovered and replicated six novel loci associated with blood levels of total acylcarnitine, arginine (both on chromosome 6; rs12210538, rs17657775), propionylcarnitine (chromosome 10; rs12779637), 2-hydroxyisovalerylcarnitine (chromosome 21; rs1571700), stearoylcarnitine (chromosome 1; rs3811444), and aspartic acid traits (chromosome 8; rs750472). Based on an integrative analysis of expression quantitative trait loci in blood mononuclear cells and correlations between gene expressions and metabolite levels, we provide evidence for putative causative genes: SLC22A16 for total acylcarnitines, ARG1 for arginine, HLCS for 2-hydroxyisovalerylcarnitine, JAM3 for stearoylcarnitine via a trans-effect at chromosome 1, and PPP1R16A for aspartic acid traits. Further, we report replication and provide additional functional evidence for ten loci that have previously been published for metabolites measured in plasma, serum or urine. In conclusion, our integrative analysis of SNP, gene-expression and metabolite data points to novel genetic factors that may be involved in the regulation of human metabolism. At several loci, we provide evidence for metabolite regulation via gene-expression and observed overlaps with GWAS loci for common diseases. These results form a strong rationale for subsequent functional and disease-related studies.
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Affiliation(s)
- Ralph Burkhardt
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Holger Kirsten
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- Department for Cell Therapy, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Frank Beutner
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Heart Center Leipzig, Leipzig, Germany
| | - Lesca M. Holdt
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute for Laboratory Medicine, Ludwig-Maximilians University Munich, Munich, Germany
| | - Arnd Gross
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Andrej Teren
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Heart Center Leipzig, Leipzig, Germany
| | - Anke Tönjes
- Medical Department, Clinic for Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - Susen Becker
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Knut Krohn
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Interdisciplinary Centre for Clinical Research, University of Leipzig, Leipzig, Germany
| | - Peter Kovacs
- Integrated Research and Treatment Center Adiposity Diseases, University of Leipzig, Leipzig Germany
| | - Michael Stumvoll
- Medical Department, Clinic for Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
- Integrated Research and Treatment Center Adiposity Diseases, University of Leipzig, Leipzig Germany
| | - Daniel Teupser
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute for Laboratory Medicine, Ludwig-Maximilians University Munich, Munich, Germany
| | - Joachim Thiery
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Uta Ceglarek
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Markus Scholz
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- * E-mail:
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16
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Aghakhanian F, Yunus Y, Naidu R, Jinam T, Manica A, Hoh BP, Phipps ME. Unravelling the genetic history of Negritos and indigenous populations of Southeast Asia. Genome Biol Evol 2015; 7:1206-15. [PMID: 25877615 PMCID: PMC4453060 DOI: 10.1093/gbe/evv065] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Indigenous populations of Malaysia known as Orang Asli (OA) show huge morphological, anthropological, and linguistic diversity. However, the genetic history of these populations remained obscure. We performed a high-density array genotyping using over 2 million single nucleotide polymorphisms in three major groups of Negrito, Senoi, and Proto-Malay. Structural analyses indicated that although all OA groups are genetically closest to East Asian (EA) populations, they are substantially distinct. We identified a genetic affinity between Andamanese and Malaysian Negritos which may suggest an ancient link between these two groups. We also showed that Senoi and Proto-Malay may be admixtures between Negrito and EA populations. Formal admixture tests provided evidence of gene flow between Austro-Asiatic-speaking OAs and populations from Southeast Asia (SEA) and South China which suggest a widespread presence of these people in SEA before Austronesian expansion. Elevated linkage disequilibrium (LD) and enriched homozygosity found in OAs reflect isolation and bottlenecks experienced. Estimates based on Ne and LD indicated that these populations diverged from East Asians during the late Pleistocene (14.5 to 8 KYA). The continuum in divergence time from Negritos to Senoi and Proto-Malay in combination with ancestral markers provides evidences of multiple waves of migration into SEA starting with the first Out-of-Africa dispersals followed by Early Train and subsequent Austronesian expansions.
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Affiliation(s)
- Farhang Aghakhanian
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University (Malaysia), Selangor, Malaysia
| | - Yushima Yunus
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Selangor, Malaysia
| | - Rakesh Naidu
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University (Malaysia), Selangor, Malaysia
| | - Timothy Jinam
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Andrea Manica
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, United Kingdom
| | - Boon Peng Hoh
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Selangor, Malaysia
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University (Malaysia), Selangor, Malaysia
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Liu X, Hinney A, Scholz M, Scherag A, Tönjes A, Stumvoll M, Stadler PF, Hebebrand J, Böttcher Y. Indications for potential parent-of-origin effects within the FTO gene. PLoS One 2015; 10:e0119206. [PMID: 25793382 PMCID: PMC4368796 DOI: 10.1371/journal.pone.0119206] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 01/28/2015] [Indexed: 12/18/2022] Open
Abstract
Genome-Wide Association Studies (GWAS) were successfully applied to discover associations with obesity. However, the GWAS design is usually based on unrelated individuals and inheritance information on the parental origin of the alleles is missing. Taking into account parent-of-origin may provide further insights into the genetic mechanisms contributing to obesity. We hypothesized that there may be variants within the robustly replicated fat mass and obesity associated (FTO) gene that may confer different risk for obesity depending on transmission from mother or father. Genome-wide genotypes and pedigree information from the Sorbs population were used. Phased genotypes among 525 individuals were generated by AlphaImpute. Subsequently, 22 SNPs within FTO introns 1 to 3 were selected and parent-of-origin specific association analyses were performed using PLINK. Interestingly, we identified several SNPs conferring different genetic effects (P≤0.05) depending on parental origin—among them, rs1861868, rs1121980 and rs9939973 (all in intron 1). To confirm our findings, we investigated the selected variants in 705 German trios comprising an (extremely) obese child or adolescent and both parents. Again, we observed evidence for POE effects in intron 2 and 3 (P≤0.05) as indicated by the parental asymmetry test. Our results suggest that the obesity risk transmitted by several FTO variants may depend on the parental origin of the allele. Larger family-based studies are warranted to replicate our findings.
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Affiliation(s)
- Xuanshi Liu
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy Universitätsklinikum Essen, University of Duisburg-Essen, Essen, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - André Scherag
- Clinical Epidemiology, Integrated Research and Treatment Center (IFB) Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Michael Stumvoll
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Peter F. Stadler
- Fraunhofer Institute for Cell Therapy and Immunology, AG RNomics, Leipzig, Germany
- Interdisciplinary Center of Bioinformatics, University of Leipzig, Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
- Sante Fe Institute, Santa Fe, New Mexico, United States of America
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy Universitätsklinikum Essen, University of Duisburg-Essen, Essen, Germany
| | - Yvonne Böttcher
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- * E-mail: (YB)
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Karafet TM, Bulayeva KB, Bulayev OA, Gurgenova F, Omarova J, Yepiskoposyan L, Savina OV, Veeramah KR, Hammer MF. Extensive genome-wide autozygosity in the population isolates of Daghestan. Eur J Hum Genet 2015; 23:1405-12. [PMID: 25604856 DOI: 10.1038/ejhg.2014.299] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 12/09/2014] [Accepted: 12/19/2014] [Indexed: 01/01/2023] Open
Abstract
Isolated populations are valuable resources for mapping disease genes, as inbreeding increases genome-wide homozygosity and enhances the ability to map disease alleles on a genetically uniform background within a relatively homogenous environment. The populations of Daghestan are thought to have resided in the Caucasus Mountains for hundreds of generations and are characterized by a high prevalence of certain complex diseases. To explore the extent to which their unique population history led to increased levels of inbreeding, we genotyped >550 000 autosomal single-nucleotide polymorphisms (SNPs) in a set of 14 population isolates speaking Nakh-Daghestanian (ND) languages. The ND-speaking populations showed greatly elevated coefficients of inbreeding, very high numbers and long lengths of Runs of Homozygosity, and elevated linkage disequilibrium compared with surrounding groups from the Caucasus, the Near East, Europe, Central and South Asia. These results are consistent with the hypothesis that most ND-speaking groups descend from a common ancestral population that fragmented into a series of genetic isolates in the Daghestanian highlands. They have subsequently maintained a long-term small effective population size as a result of constant inbreeding and very low levels of gene flow. Given these findings, Daghestanian population isolates are likely to be useful for mapping genes associated with complex diseases.
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Affiliation(s)
- Tatiana M Karafet
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ, USA
| | - Kazima B Bulayeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Oleg A Bulayev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Farida Gurgenova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Jamilia Omarova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Levon Yepiskoposyan
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Olga V Savina
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ, USA
| | | | - Michael F Hammer
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ, USA
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Tönjes A, Scholz M, Breitfeld J, Marzi C, Grallert H, Gross A, Ladenvall C, Schleinitz D, Krause K, Kirsten H, Laurila E, Kriebel J, Thorand B, Rathmann W, Groop L, Prokopenko I, Isomaa B, Beutner F, Kratzsch J, Thiery J, Fasshauer M, Klöting N, Gieger C, Blüher M, Stumvoll M, Kovacs P. Genome wide meta-analysis highlights the role of genetic variation in RARRES2 in the regulation of circulating serum chemerin. PLoS Genet 2014; 10:e1004854. [PMID: 25521368 PMCID: PMC4270463 DOI: 10.1371/journal.pgen.1004854] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 10/27/2014] [Indexed: 11/18/2022] Open
Abstract
Chemerin is an adipokine proposed to link obesity and chronic inflammation of adipose tissue. Genetic factors determining chemerin release from adipose tissue are yet unknown. We conducted a meta-analysis of genome-wide association studies (GWAS) for serum chemerin in three independent cohorts from Europe: Sorbs and KORA from Germany and PPP-Botnia from Finland (total N = 2,791). In addition, we measured mRNA expression of genes within the associated loci in peripheral mononuclear cells by micro-arrays, and within adipose tissue by quantitative RT-PCR and performed mRNA expression quantitative trait and expression-chemerin association studies to functionally substantiate our loci. Heritability estimate of circulating chemerin levels was 16.2% in the Sorbs cohort. Thirty single nucleotide polymorphisms (SNPs) at chromosome 7 within the retinoic acid receptor responder 2 (RARRES2)/Leucine Rich Repeat Containing (LRRC61) locus reached genome-wide significance (p<5.0×10−8) in the meta-analysis (the strongest evidence for association at rs7806429 with p = 7.8×10−14, beta = −0.067, explained variance 2.0%). All other SNPs within the cluster were in linkage disequilibrium with rs7806429 (minimum r2 = 0.43 in the Sorbs cohort). The results of the subgroup analyses of males and females were consistent with the results found in the total cohort. No significant SNP-sex interaction was observed. rs7806429 was associated with mRNA expression of RARRES2 in visceral adipose tissue in women (p<0.05 after adjusting for age and body mass index). In conclusion, the present meta-GWAS combined with mRNA expression studies highlights the role of genetic variation in the RARRES2 locus in the regulation of circulating chemerin concentrations. Chemerin is an adipokine proposed to link obesity and chronic inflammation of adipose tissue. In the present study we show that circulating chemerin is a heritable trait. In a meta-analysis of genome-wide association studies (GWAS) of 2,791 individuals from Germany and Finland, we identified common genetic variants which associate with serum chemerin levels. The variants map within the retinoic acid receptor responder 2 (RARRES2)/Leucine Rich Repeat Containing (LRRC61) at chromosome 7. To better understand the potential functionality of the identified variants, we also provide insights into the mRNA expression of RARRES2 (encoding chemerin) in blood and adipose tissue. Our results highlight the role and function of genetic variation in the RARRES2 locus in the regulation of circulating chemerin concentrations.
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Affiliation(s)
- Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Markus Scholz
- Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center, University of Leipzig, Leipzig, Germany
| | - Jana Breitfeld
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Carola Marzi
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Arnd Gross
- Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center, University of Leipzig, Leipzig, Germany
| | - Claes Ladenvall
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University and Lund University Diabetes Centre, CRC at Skåne University Hospital, Malmö, Sweden
| | | | - Kerstin Krause
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Holger Kirsten
- Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center, University of Leipzig, Leipzig, Germany
- Department for Cell Therapy, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Esa Laurila
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University and Lund University Diabetes Centre, CRC at Skåne University Hospital, Malmö, Sweden
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Barbara Thorand
- Institute of Epidemiology II, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
| | - Wolfgang Rathmann
- Institute of Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University and Lund University Diabetes Centre, CRC at Skåne University Hospital, Malmö, Sweden
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom
- Department of Genomics of Common Diseases, Imperial College London, London, United Kingdom
| | - Bo Isomaa
- Department of Social Services and Health Care, Jakobstad, Finland
- Folkhälsan Research Centre, Helsinki, Finland
| | - Frank Beutner
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Jürgen Kratzsch
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Joachim Thiery
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Mathias Fasshauer
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Nora Klöting
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- * E-mail: (MSt); (PK)
| | - Peter Kovacs
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- * E-mail: (MSt); (PK)
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Genomic patterns of homozygosity in worldwide human populations. Am J Hum Genet 2012; 91:275-92. [PMID: 22883143 DOI: 10.1016/j.ajhg.2012.06.014] [Citation(s) in RCA: 303] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 05/09/2012] [Accepted: 06/25/2012] [Indexed: 12/20/2022] Open
Abstract
Genome-wide patterns of homozygosity runs and their variation across individuals provide a valuable and often untapped resource for studying human genetic diversity and evolutionary history. Using genotype data at 577,489 autosomal SNPs, we employed a likelihood-based approach to identify runs of homozygosity (ROH) in 1,839 individuals representing 64 worldwide populations, classifying them by length into three classes-short, intermediate, and long-with a model-based clustering algorithm. For each class, the number and total length of ROH per individual show considerable variation across individuals and populations. The total lengths of short and intermediate ROH per individual increase with the distance of a population from East Africa, in agreement with similar patterns previously observed for locus-wise homozygosity and linkage disequilibrium. By contrast, total lengths of long ROH show large interindividual variations that probably reflect recent inbreeding patterns, with higher values occurring more often in populations with known high frequencies of consanguineous unions. Across the genome, distributions of ROH are not uniform, and they have distinctive continental patterns. ROH frequencies across the genome are correlated with local genomic variables such as recombination rate, as well as with signals of recent positive selection. In addition, long ROH are more frequent in genomic regions harboring genes associated with autosomal-dominant diseases than in regions not implicated in Mendelian diseases. These results provide insight into the way in which homozygosity patterns are produced, and they generate baseline homozygosity patterns that can be used to aid homozygosity mapping of genes associated with recessive diseases.
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