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Timasheva Y, Putku M, Kivi R, Kožich V, Männik J, Laan M. Developmental programming of growth: genetic variant in GH2 gene encoding placental growth hormone contributes to adult height determination. Placenta 2013; 34:995-1001. [PMID: 24035309 PMCID: PMC3820034 DOI: 10.1016/j.placenta.2013.08.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 08/15/2013] [Accepted: 08/19/2013] [Indexed: 01/26/2023]
Abstract
INTRODUCTION Given the physiological role of placental growth hormone (PGH) during intrauterine development and growth, genetic variation in the coding Growth hormone 2 (GH2) gene may modulate developmental programming of adult stature. Two major GH2 variants were described worldwide, determined by single polymorphism (rs2006123; c.171 + 50C > A). We sought to study whether GH2 variants may contribute to adult anthropometric measurements. METHODS Genotyping of GH2 SNP rs2006123 by RFLP, testing its genetic association with adult height and Body Mass Index (BMI) by linear regression analysis, and combining the results of three individual study samples in meta-analysis. STUDY SAMPLES HYPEST (Estonia), n = 1464 (506 men/958 women), CADCZ (Czech), n = 871 (518/353); UFA (Bashkortostan), n = 954 (655/299); meta-analysis, n = 3289 (1679/1610). RESULTS Meta-analysis across HYPEST, CADCZ and UFA samples (n = 3289) resulted in significant association of GH2 rs2006123 with height (recessive model: AA-homozygote effect: beta (SE) = 1.26 (0.46), P = 5.90 × 10⁻³; additive model: A-allele effect: beta (SE) = 0.45 (0.18), P = 1.40 × 10⁻²). Among men (n = 1679), the association of the A-allele with taller stature remained significant after multiple-testing correction (additive effect: beta = 0.86 (0.28), P = 1.83 × 10⁻³). No association was detected with BMI. Notably, rs2006123 was in strong LD (r² ≥ 0.87) with SNPs significantly associated with height (rs2665838, rs7209435, rs11658329) and mapped near GH2 in three independent meta-analyses of GWA studies. CONCLUSIONS This is the first study demonstrating a link between a placental gene variant and programming of growth potential in adulthood. The detected association between PGH encoding GH2 and adult height promotes further research on the role of placental genes in prenatal programming of human metabolism.
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Affiliation(s)
- Y. Timasheva
- Human Molecular Genetics Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, Tartu 51010, Estonia
- Institute of Biochemistry and Genetics, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
| | - M. Putku
- Human Molecular Genetics Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, Tartu 51010, Estonia
| | - R. Kivi
- Human Molecular Genetics Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, Tartu 51010, Estonia
| | - V. Kožich
- Institute of Inherited Metabolic Diseases, Charles University – First Faculty of Medicine, Prague, Czech Republic
| | - J. Männik
- Human Molecular Genetics Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, Tartu 51010, Estonia
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - M. Laan
- Human Molecular Genetics Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, Tartu 51010, Estonia
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Köttgen A, Albrecht E, Teumer A, Vitart V, Krumsiek J, Hundertmark C, Pistis G, Ruggiero D, O'Seaghdha CM, Haller T, Yang Q, Tanaka T, Johnson AD, Kutalik Z, Smith AV, Shi J, Struchalin M, Middelberg RPS, Brown MJ, Gaffo AL, Pirastu N, Li G, Hayward C, Zemunik T, Huffman J, Yengo L, Zhao JH, Demirkan A, Feitosa MF, Liu X, Malerba G, Lopez LM, van der Harst P, Li X, Kleber ME, Hicks AA, Nolte IM, Johansson A, Murgia F, Wild SH, Bakker SJL, Peden JF, Dehghan A, Steri M, Tenesa A, Lagou V, Salo P, Mangino M, Rose LM, Lehtimäki T, Woodward OM, Okada Y, Tin A, Müller C, Oldmeadow C, Putku M, Czamara D, Kraft P, Frogheri L, Thun GA, Grotevendt A, Gislason GK, Harris TB, Launer LJ, McArdle P, Shuldiner AR, Boerwinkle E, Coresh J, Schmidt H, Schallert M, Martin NG, Montgomery GW, Kubo M, Nakamura Y, Tanaka T, Munroe PB, Samani NJ, Jacobs DR, Liu K, D'Adamo P, Ulivi S, Rotter JI, Psaty BM, Vollenweider P, Waeber G, Campbell S, Devuyst O, Navarro P, Kolcic I, Hastie N, Balkau B, Froguel P, Esko T, Salumets A, Khaw KT, Langenberg C, Wareham NJ, Isaacs A, Kraja A, Zhang Q, Wild PS, Scott RJ, Holliday EG, Org E, Viigimaa M, Bandinelli S, Metter JE, Lupo A, Trabetti E, Sorice R, Döring A, Lattka E, Strauch K, Theis F, Waldenberger M, Wichmann HE, Davies G, Gow AJ, Bruinenberg M, Stolk RP, Kooner JS, Zhang W, Winkelmann BR, Boehm BO, Lucae S, Penninx BW, Smit JH, Curhan G, Mudgal P, Plenge RM, Portas L, Persico I, Kirin M, Wilson JF, Mateo Leach I, van Gilst WH, Goel A, Ongen H, Hofman A, Rivadeneira F, Uitterlinden AG, Imboden M, von Eckardstein A, Cucca F, Nagaraja R, Piras MG, Nauck M, Schurmann C, Budde K, Ernst F, Farrington SM, Theodoratou E, Prokopenko I, Stumvoll M, Jula A, Perola M, Salomaa V, Shin SY, Spector TD, Sala C, Ridker PM, Kähönen M, Viikari J, Hengstenberg C, Nelson CP, Meschia JF, Nalls MA, Sharma P, Singleton AB, Kamatani N, Zeller T, Burnier M, Attia J, Laan M, Klopp N, Hillege HL, Kloiber S, Choi H, Pirastu M, Tore S, Probst-Hensch NM, Völzke H, Gudnason V, Parsa A, Schmidt R, Whitfield JB, Fornage M, Gasparini P, Siscovick DS, Polašek O, Campbell H, Rudan I, Bouatia-Naji N, Metspalu A, Loos RJF, van Duijn CM, Borecki IB, Ferrucci L, Gambaro G, Deary IJ, Wolffenbuttel BHR, Chambers JC, März W, Pramstaller PP, Snieder H, Gyllensten U, Wright AF, Navis G, Watkins H, Witteman JCM, Sanna S, Schipf S, Dunlop MG, Tönjes A, Ripatti S, Soranzo N, Toniolo D, Chasman DI, Raitakari O, Kao WHL, Ciullo M, Fox CS, Caulfield M, Bochud M, Gieger C. Genome-wide association analyses identify 18 new loci associated with serum urate concentrations. Nat Genet 2012; 45:145-54. [PMID: 23263486 DOI: 10.1038/ng.2500] [Citation(s) in RCA: 577] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 11/27/2012] [Indexed: 12/13/2022]
Abstract
Elevated serum urate concentrations can cause gout, a prevalent and painful inflammatory arthritis. By combining data from >140,000 individuals of European ancestry within the Global Urate Genetics Consortium (GUGC), we identified and replicated 28 genome-wide significant loci in association with serum urate concentrations (18 new regions in or near TRIM46, INHBB, SFMBT1, TMEM171, VEGFA, BAZ1B, PRKAG2, STC1, HNF4G, A1CF, ATXN2, UBE2Q2, IGF1R, NFAT5, MAF, HLF, ACVR1B-ACVRL1 and B3GNT4). Associations for many of the loci were of similar magnitude in individuals of non-European ancestry. We further characterized these loci for associations with gout, transcript expression and the fractional excretion of urate. Network analyses implicate the inhibins-activins signaling pathways and glucose metabolism in systemic urate control. New candidate genes for serum urate concentration highlight the importance of metabolic control of urate production and excretion, which may have implications for the treatment and prevention of gout.
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Affiliation(s)
- Anna Köttgen
- Renal Division, Freiburg University Hospital, Freiburg, Germany.
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Johnson T, Gaunt T, Newhouse S, Padmanabhan S, Tomaszewski M, Kumari M, Morris R, Tzoulaki I, O'Brien E, Poulter N, Sever P, Shields D, Thom S, Wannamethee S, Whincup P, Brown M, Connell J, Dobson R, Howard P, Mein C, Onipinla A, Shaw-Hawkins S, Zhang Y, Smith G, Day I, Lawlor D, Goodall A, Fowkes F, Abecasis G, Elliott P, Gateva V, Braund P, Burton P, Nelson C, Tobin M, van der Harst P, Glorioso N, Neuvrith H, Salvi E, Staessen J, Stucchi A, Devos N, Jeunemaitre X, Plouin PF, Tichet J, Juhanson P, Org E, Putku M, Sõber S, Veldre G, Viigimaa M, Levinsson A, Rosengren A, Thelle D, Hastie C, Hedner T, Lee W, Melander O, Wahlstrand B, Hardy R, Wong A, Cooper J, Palmen J, Chen L, Stewart A, Wells G, Westra HJ, Wolfs M, Clarke R, Franzosi M, Goel A, Hamsten A, Lathrop M, Peden J, Seedorf U, Watkins H, Ouwehand W, Sambrook J, Stephens J, Casas JP, Drenos F, Holmes M, Kivimaki M, Shah S, Shah T, Talmud P, Whittaker J, Wallace C, Delles C, Laan M, Kuh D, Humphries S, Nyberg F, Cusi D, Roberts R, Newton-Cheh C, Franke L, Stanton A, Dominiczak A, Farrall M, Hingorani A, Samani N, Caulfield M, Munroe P, Caulfield MJ, Munroe PB. Blood pressure loci identified with a gene-centric array. Am J Hum Genet 2011; 89:688-700. [PMID: 22100073 DOI: 10.1016/j.ajhg.2011.10.013] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 09/21/2011] [Accepted: 10/27/2011] [Indexed: 12/15/2022] Open
Abstract
Raised blood pressure (BP) is a major risk factor for cardiovascular disease. Previous studies have identified 47 distinct genetic variants robustly associated with BP, but collectively these explain only a few percent of the heritability for BP phenotypes. To find additional BP loci, we used a bespoke gene-centric array to genotype an independent discovery sample of 25,118 individuals that combined hypertensive case-control and general population samples. We followed up four SNPs associated with BP at our p < 8.56 × 10(-7) study-specific significance threshold and six suggestively associated SNPs in a further 59,349 individuals. We identified and replicated a SNP at LSP1/TNNT3, a SNP at MTHFR-NPPB independent (r(2) = 0.33) of previous reports, and replicated SNPs at AGT and ATP2B1 reported previously. An analysis of combined discovery and follow-up data identified SNPs significantly associated with BP at p < 8.56 × 10(-7) at four further loci (NPR3, HFE, NOS3, and SOX6). The high number of discoveries made with modest genotyping effort can be attributed to using a large-scale yet targeted genotyping array and to the development of a weighting scheme that maximized power when meta-analyzing results from samples ascertained with extreme phenotypes, in combination with results from nonascertained or population samples. Chromatin immunoprecipitation and transcript expression data highlight potential gene regulatory mechanisms at the MTHFR and NOS3 loci. These results provide candidates for further study to help dissect mechanisms affecting BP and highlight the utility of studying SNPs and samples that are independent of those studied previously even when the sample size is smaller than that in previous studies.
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Org E, Veldre G, Viigimaa M, Juhanson P, Putku M, Rosenberg M, Tomberg K, Uuetoa T, Laan M. HYPEST study: profile of hypertensive patients in Estonia. BMC Cardiovasc Disord 2011; 11:55. [PMID: 21880150 PMCID: PMC3179926 DOI: 10.1186/1471-2261-11-55] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 08/31/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND More than one third of adult population in Estonia has problems with elevated blood pressure (BP). The Hypertension in Estonia (HYPEST) study represents the country's first hypertension-targeted sample collection aiming to examine the epidemiological and genetic determinants for hypertension (HTN) and related cardiovascular diseases (CVD) in Estonian population. The HYPEST subjects (n = 1,966) were recruited across Estonia between 2004-2007 including clinically diagnosed HTN cases and population-based controls. The present report is focused on the clinical and epidemiological profile of HYPEST cases, and gender-specific effects on the pathophysiology of hypertension. METHODS Current analysis was performed on 1,007 clinically diagnosed HTN patients (617 women and 390 men) aged 18-85 years. The hypertensives were recruited to the study by BP specialists at the North Estonia Medical Center, Centre of Cardiology, Tallinn or at the Cardiology Clinic, Tartu University Hospital, Estonia. Longitudinal BP data was extracted retrospectively from clinical records. Current and retrospective data of patient's medical history, medication intake and lifestyle habits were derived from self-administrated questionnaire and each variable was examined separately for men and women. Eleven biochemical parameters were measured from fasting serum samples of 756 patients. RESULTS The distribution of recruited men and women was 39% and 61% respectively. Majority of Estonian HTN patients (85%) were overweight (BMI ≥ 25 kg/m2) and a total of 79% of patients had additional complications with cardiovascular system. In men, the hypertension started almost 5 years earlier than in women (40.5 ± 14.5 vs 46.1 ± 12.7 years), which led to earlier age of first myocardial infarction (MI) and overall higher incidence rate of MI among male patients (men 21.2%, women 8.9%, P < 0.0001). Heart arrhythmia, thyroid diseases, renal tubulo-intestinal diseases and hyperlipidemia were more prevalent in hypertensive women compared to men (P < 0.0001). An earlier age of HTN onset was significantly associated with smoking (P = 0.00007), obesity (BMI ≥ 30 kg/m2; P = 0.0003), increased stress (P = 0.0003) and alcohol consumption (P = 0.004). CONCLUSION Understanding the clinical profile of HTN patients contributes to CVD management. Estonian hypertension patients exhibited different disease and risk profiles of male and female patients. This well-characterized sample set provides a good resource for studying hypertension and other cardiovascular phenotypes.
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Affiliation(s)
- Elin Org
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
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Putku M, Kepp K, Org E, Sõber S, Comas D, Viigimaa M, Veldre G, Juhanson P, Hallast P, Tõnisson N, Shaw-Hawkins S, Caulfield MJ, Khusnutdinova E, Kožich V, Munroe PB, Laan M. Novel polymorphic AluYb8 insertion in the WNK1 gene is associated with blood pressure variation in Europeans. Hum Mutat 2011; 32:806-14. [PMID: 21520334 PMCID: PMC3298642 DOI: 10.1002/humu.21508] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 03/28/2011] [Indexed: 01/16/2023]
Abstract
Mutations in WNK1 and WNK4 cause familial hypertension, the Gordon syndrome. WNK1 and WNK4 conserved noncoding regions were targeted to polymorphism screening using DHPLC and DGGE. The scan identified an undescribed polymorphic AluYb8 insertion in WNK1 intron 10. Screening in primates revealed that this Alu-insertion has probably occurred in human lineage. Genotyping in 18 populations from Europe, Asia, and Africa (n = 854) indicated an expansion of the WNK1 AluYb8 bearing chromosomes out of Africa. The allele frequency in Sub-Saharan Africa was ∼3.3 times lower than in other populations (4.8 vs. 15.8%; P = 9.7 × 10−9). Meta-analysis across three European sample sets (n = 3,494; HYPEST, Estonians; BRIGHT, the British; CADCZ, Czech) detected significant association of the WNK1 AluYb8 insertion with blood pressure (BP; systolic BP, P = 4.03 × 10−3, effect 1.12; diastolic BP, P = 1.21 × 10−2, effect 0.67). Gender-stratified analysis revealed that this effect might be female-specific (n = 2,088; SBP, P = 1.99 × 10−3, effect 1.59; DBP P = 3.64 × 10−4, effect 1.23; resistant to Bonferroni correction), whereas no statistical support was identified for the association with male BP (n = 1,406). In leucocytes, the expressional proportions of the full-length WNK1 transcript and the splice-form skipping exon 11 were significantly shifted in AluYb8 carriers compared to noncarriers. The WNK1 AluYb8 insertion might affect human BP via altering the profile of alternatively spliced transcripts. Hum Mutat 32:1–9, 2011. © 2011 Wiley-Liss, Inc.
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Affiliation(s)
- Margus Putku
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of TartuTartu, Estonia
| | - Katrin Kepp
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of TartuTartu, Estonia
| | - Elin Org
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of TartuTartu, Estonia
| | - Siim Sõber
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of TartuTartu, Estonia
| | - David Comas
- Institute of Evolutionary Biology (UPF-CSIC), CEXS-UPF-PRBB, Universitat Pompeu FabraBarcelona, Spain
| | - Margus Viigimaa
- Centre of Cardiology, North Estonia Medical CentreTallinn, Estonia
- Tallinn University of Technology, Department of Biomedical Engineering, Chair of Medical PhysicsTallinn, Estonia
| | - Gudrun Veldre
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of TartuTartu, Estonia
- Department of Cardiology, University of TartuTartu, Estonia
| | - Peeter Juhanson
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of TartuTartu, Estonia
| | - Pille Hallast
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of TartuTartu, Estonia
| | - Neeme Tõnisson
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of TartuTartu, Estonia
| | - Sue Shaw-Hawkins
- Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of LondonLondon EC1M 6BQ, United Kingdom
| | - Mark J Caulfield
- Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of LondonLondon EC1M 6BQ, United Kingdom
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Science Center, Russian Academy of SciencesUfa, Bashkortostan, Russia
| | - Viktor Kožich
- Institute of Inherited Metabolic Diseases, Charles University—First Faculty of MedicinePrague, Czech Republic
| | - Patricia B Munroe
- Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of LondonLondon EC1M 6BQ, United Kingdom
| | - Maris Laan
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of TartuTartu, Estonia
- *Correspondence to: Maris Laan, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia. E-mail:
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Kepp K, Org E, Sõber S, Kelgo P, Viigimaa M, Veldre G, Tõnisson N, Juhanson P, Putku M, Kindmark A, Kozich V, Laan M. Hypervariable intronic region in NCX1 is enriched in short insertion-deletion polymorphisms and showed association with cardiovascular traits. BMC Med Genet 2010; 11:15. [PMID: 20109173 PMCID: PMC2832636 DOI: 10.1186/1471-2350-11-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 01/28/2010] [Indexed: 01/07/2023]
Abstract
Background Conserved non-coding regions (CNR) have been shown to harbor gene expression regulatory elements. Genetic variations in these regions may potentially contribute to complex disease susceptibility. Methods We targeted CNRs of cardiovascular disease (CVD) candidate gene, Na(+)-Ca(2+) exchanger (NCX1) with polymorphism screening among CVD patients (n = 46) using DHPLC technology. The flanking region (348 bp) of the 14 bp indel in intron 2 was further genotyped by DGGE assay in two Eastern-European CVD samples: essential hypertension (HYPEST; 470 cases, 652 controls) and coronary artery disease, CAD (CADCZ; 257 cases, controls 413). Genotype-phenotype associations were tested by regression analysis implemented in PLINK. Alignments of primate sequences were performed by ClustalW2. Results Nine of the identified NCX1 variants were either singletons or targeted by commercial platforms. The 14 bp intronic indel (rs11274804) was represented with substantial frequency in HYPEST (6.82%) and CADCZ (14.58%). Genotyping in Eastern-Europeans (n = 1792) revealed hypervariable nature of this locus, represented by seven alternative alleles. The alignments of human-chimpanzee-macaque sequences showed that the major human variant (allele frequency 90.45%) was actually a human-specific deletion compared to other primates. In humans, this deletion was surrounded by other short (5-43 bp) deletion variants and a duplication (40 bp) polymorphism possessing overlapping breakpoints. This indicates a potential indel hotspot, triggered by the initial deletion in human lineage. An association was detected between the carrier status of 14 bp indel ancestral allele and CAD (P = 0.0016, OR = 2.02; Bonferroni significance level alpha = 0.0045), but not with hypertension. The risk for the CAD development was even higher among the patients additionally diagnosed with metabolic syndrome (P = 0.0014, OR = 2.34). Consistent with the effect on metabolic processes, suggestive evidence for the association with heart rate, serum triglyceride and LDL levels was detected (P = 0.04). Conclusions Compared to SNPs targeted by large number of locus-specific and genome-wide assays, considerably less attention has been paid to short indel variants in the human genome. The data of genome dynamics, mutation rate and population genetics of short indels, as well as their impact on gene expressional profile and human disease susceptibility is limited. The characterization of NCX1 intronic hypervariable non-coding region enriched in human-specific indel variants contributes to this gap of knowledge.
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Affiliation(s)
- Katrin Kepp
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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Sõber S, Org E, Kepp K, Juhanson P, Eyheramendy S, Gieger C, Lichtner P, Klopp N, Veldre G, Viigimaa M, Döring A, Putku M, Kelgo P, Shaw-Hawkins S, Howard P, Onipinla A, Dobson RJ, Newhouse SJ, Brown M, Dominiczak A, Connell J, Samani N, Farrall M, Caulfield MJ, Munroe PB, Illig T, Wichmann HE, Meitinger T, Laan M. Targeting 160 candidate genes for blood pressure regulation with a genome-wide genotyping array. PLoS One 2009; 4:e6034. [PMID: 19562039 PMCID: PMC2699027 DOI: 10.1371/journal.pone.0006034] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Accepted: 05/25/2009] [Indexed: 01/08/2023] Open
Abstract
The outcome of Genome-Wide Association Studies (GWAS) has challenged the field of blood pressure (BP) genetics as previous candidate genes have not been among the top loci in these scans. We used Affymetrix 500K genotyping data of KORA S3 cohort (n = 1,644; Southern-Germany) to address (i) SNP coverage in 160 BP candidate genes; (ii) the evidence for associations with BP traits in genome-wide and replication data, and haplotype analysis. In total, 160 gene regions (genic region±10 kb) covered 2,411 SNPs across 11.4 Mb. Marker densities in genes varied from 0 (n = 11) to 0.6 SNPs/kb. On average 52.5% of the HAPMAP SNPs per gene were captured. No evidence for association with BP was obtained for 1,449 tested SNPs. Considerable associations (P<10−3) were detected for the genes, where >50% of HAPMAP SNPs were tagged. In general, genes with higher marker density (>0.2 SNPs/kb) revealed a better chance to reach close to significance associations. Although, none of the detected P-values remained significant after Bonferroni correction (P<0.05/2319, P<2.15×10−5), the strength of some detected associations was close to this level: rs10889553 (LEPR) and systolic BP (SBP) (P = 4.5×10−5) as well as rs10954174 (LEP) and diastolic BP (DBP) (P = 5.20×10−5). In total, 12 markers in 7 genes (ADRA2A, LEP, LEPR, PTGER3, SLC2A1, SLC4A2, SLC8A1) revealed considerable association (P<10−3) either with SBP, DBP, and/or hypertension (HYP). None of these were confirmed in replication samples (KORA S4, HYPEST, BRIGHT). However, supportive evidence for the association of rs10889553 (LEPR) and rs11195419 (ADRA2A) with BP was obtained in meta-analysis across samples stratified either by body mass index, smoking or alcohol consumption. Haplotype analysis highlighted LEPR and PTGER3. In conclusion, the lack of associations in BP candidate genes may be attributed to inadequate marker coverage on the genome-wide arrays, small phenotypic effects of the loci and/or complex interaction with life-style and metabolic parameters.
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Affiliation(s)
- Siim Sõber
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Elin Org
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Katrin Kepp
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Peeter Juhanson
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Susana Eyheramendy
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
- Department of Statistics, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
| | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
| | - Norman Klopp
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
| | - Gudrun Veldre
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Department of Cardiology, University of Tartu, Tartu, Estonia
| | - Margus Viigimaa
- Centre of Cardiology, North Estonia Medical Centre, Tallinn, Estonia
| | - Angela Döring
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
| | | | - Margus Putku
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Piret Kelgo
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | - Sue Shaw-Hawkins
- Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - Philip Howard
- Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - Abiodun Onipinla
- Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - Richard J. Dobson
- Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - Stephen J. Newhouse
- Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - Morris Brown
- Clinical Pharmacology Unit, University of Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom
| | - Anna Dominiczak
- Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - John Connell
- Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Nilesh Samani
- Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, United Kingdom
| | - Martin Farrall
- Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | | | - Mark J. Caulfield
- Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - Patricia B. Munroe
- Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - Thomas Illig
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
| | - H.-Erich Wichmann
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Maris Laan
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- * E-mail:
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