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SAINI SIMMI, WALIA GAGANDEEPKAUR, SACHDEVA MOHINDERPAL, GUPTA VIPIN. Genomics of body fat distribution. J Genet 2021. [DOI: 10.1007/s12041-021-01281-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Chromosomal regions strongly associated with waist circumference and body mass index in metabolic syndrome in a family-based study. Sci Rep 2021; 11:6082. [PMID: 33727680 PMCID: PMC7966400 DOI: 10.1038/s41598-021-85741-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 03/05/2021] [Indexed: 11/24/2022] Open
Abstract
Obesity is the most crucial phenotype in metabolic syndrome (MetS), and waist circumference (WC) and body mass index (BMI) are two common indexes to define obesity. It is an accepted fact that genetic and environmental interaction influence obesity and MetS. Microsatellites are a subcategory of tandem repeats with a length of 1 to 10 nucleotides. Tandem repeats make up repetitive genomic regions. Differences in the number of tandem repeats or their variation (alleles) result in microsatellite polymorphisms. Thus, we attempted to find microsatellite variation associated with WC and BMI in a family-based study. Twelve microsatellite markers were selected to investigate possible genes or chromosomal regions in 91 families with at least one affected MetS. The cut-off values for BMI and WC were considered 25 kg/m2 and 90 cm, respectively. In all members of the families, the strongest association was observed between the marker D11S1304 (allele 1) with both WC and BMI, independently, by the biallelic model in the family-based association test analysis (P < 0.05). Besides, when we compared high- and low-level groups in members with MetS, the markers D8S1743 and D11S1304 (allele 1) showed a strong association with WC (P = 0.0080) and BMI (P = 0.0074), respectively. When the simultaneous detection of the high WC and MetS status was used as a trait, the strongest association was observed with the marker D8S1743 (P = 0.0034). Moreover, when BMI with the high MetS status was used as a trait, the strongest association was observed with the marker D8S1743 (allele 4) (P = 0.0034). The obtained results showed a relationship between obesity and MetS with markers on the selected regions on chromosomes 8 and 11, and to a lesser degree, on chromosome 12.
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Gao C, Langefeld CD, Ziegler JT, Taylor KD, Norris JM, Chen YDI, Hellwege JN, Guo X, Allison MA, Speliotes EK, Rotter JI, Bowden DW, Wagenknecht LE, Palmer ND. Genome-Wide Study of Subcutaneous and Visceral Adipose Tissue Reveals Novel Sex-Specific Adiposity Loci in Mexican Americans. Obesity (Silver Spring) 2018; 26:202-212. [PMID: 29178545 PMCID: PMC5740005 DOI: 10.1002/oby.22074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 01/02/2023]
Abstract
OBJECTIVE This study aimed to explore the genetic mechanisms of regional fat deposition, which is a strong risk factor for metabolic diseases beyond total adiposity. METHODS A genome-wide association study of 7,757,139 single-nucleotide polymorphisms (SNPs) in 983 Mexican Americans (nmale = 403; nfemale = 580) from the Insulin Resistance Atherosclerosis Family Study was performed. Association analyses were performed with and without sex stratification for subcutaneous adipose tissue, visceral adipose tissue (VAT), and visceral-subcutaneous ratio (VSR) obtained from computed tomography. RESULTS The strongest signal identified was SNP rs2185405 (minor allele frequencies [MAF] = 40%; PVAT = 1.98 × 10-8 ) with VAT. It is an intronic variant of the GLIS family zinc finger 3 gene (GLIS3). In addition, SNP rs12657394 (MAF = 19%) was associated with VAT in males (Pmale = 2.39×10-8 ; Pfemale = 2.5 × 10-3 ). It is located intronically in the serum response factor binding protein 1 gene (SRFBP1). On average, male carriers of the variant had 24.6 cm2 increased VAT compared with noncarriers. Subsequently, genome-wide SNP-sex interaction analysis was performed. SNP rs10913233 (MAF = 14%; Pint = 3.07 × 10-8 ) in PAPPA2 and rs10923724 (MAF = 38%; Pint = 2.89 × 10-8 ) upstream of TBX15 were strongly associated with the interaction effect for VSR. CONCLUSIONS Six loci were identified with genome-wide significant associations with fat deposition and interactive effects. These results provided genetic evidence for a differential basis of fat deposition between genders.
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Affiliation(s)
- Chuan Gao
- Molecular Genetics and Genomics Program; Wake Forest School of Medicine, Winston-Salem, NC
- Center for Genomics and Personalized Medicine Research; Wake Forest School of Medicine, Winston-Salem, NC
- Center for Public Health Genomics; Wake Forest School of Medicine, Winston-Salem, NC
| | - Carl D. Langefeld
- Center for Public Health Genomics; Wake Forest School of Medicine, Winston-Salem, NC
- Department of Biostatistical Sciences; Wake Forest School of Medicine, Winston-Salem, NC
| | - Julie T. Ziegler
- Center for Public Health Genomics; Wake Forest School of Medicine, Winston-Salem, NC
- Department of Biostatistical Sciences; Wake Forest School of Medicine, Winston-Salem, NC
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences; Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA
| | - Jill M. Norris
- Department of Epidemiology, Colorado School of Public Health; University of Colorado, Aurora, CO
| | - Yii-Der I. Chen
- Institute for Translational Genomics and Population Sciences; Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA
| | - Jacklyn N. Hellwege
- Center for Genomics and Personalized Medicine Research; Wake Forest School of Medicine, Winston-Salem, NC
- Center for Diabetes Research; Wake Forest School of Medicine, Winston-Salem, NC
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences; Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA
| | - Matthew A. Allison
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla CA
| | - Elizabeth K. Speliotes
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics; University of Michigan, Ann Arbor, MI
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences; Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA
- Department of Pediatrics; Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA
| | - Donald W. Bowden
- Center for Genomics and Personalized Medicine Research; Wake Forest School of Medicine, Winston-Salem, NC
- Center for Diabetes Research; Wake Forest School of Medicine, Winston-Salem, NC
- Department of Biochemistry; Wake Forest School of Medicine, Winston-Salem, NC
| | - Lynne E. Wagenknecht
- Division of Public Health Sciences; Wake Forest School of Medicine, Winston-Salem, NC
| | - Nicholette D. Palmer
- Center for Genomics and Personalized Medicine Research; Wake Forest School of Medicine, Winston-Salem, NC
- Center for Public Health Genomics; Wake Forest School of Medicine, Winston-Salem, NC
- Center for Diabetes Research; Wake Forest School of Medicine, Winston-Salem, NC
- Department of Biochemistry; Wake Forest School of Medicine, Winston-Salem, NC
- Correspondence to Nicholette D. Palmer, PhD, Department of Biochemistry, 1 Medical Center Blvd, Winston-Salem, NC 27040, Phone: 336-713-7534,
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Genome-Wide Linkage Analysis of Large Multiple Multigenerational Families Identifies Novel Genetic Loci for Coronary Artery Disease. Sci Rep 2017; 7:5472. [PMID: 28710368 PMCID: PMC5511258 DOI: 10.1038/s41598-017-05381-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 05/30/2017] [Indexed: 01/10/2023] Open
Abstract
Coronary artery disease (CAD) is the leading cause of death, and genetic factors contribute significantly to risk of CAD. This study aims to identify new CAD genetic loci through a large-scale linkage analysis of 24 large and multigenerational families with 433 family members (GeneQuest II). All family members were genotyped with markers spaced by every 10 cM and a model-free nonparametric linkage (NPL-all) analysis was carried out. Two highly significant CAD loci were identified on chromosome 17q21.2 (NPL score of 6.20) and 7p22.2 (NPL score of 5.19). We also identified four loci with significant NPL scores between 4.09 and 4.99 on 2q33.3, 3q29, 5q13.2 and 9q22.33. Similar analyses in individual families confirmed the six significant CAD loci and identified seven new highly significant linkages on 9p24.2, 9q34.2, 12q13.13, 15q26.1, 17q22, 20p12.3, and 22q12.1, and two significant loci on 2q11.2 and 11q14.1. Two loci on 3q29 and 9q22.33 were also successfully replicated in our previous linkage analysis of 428 nuclear families. Moreover, two published risk variants, SNP rs46522 in UBE2Z and SNP rs6725887 in WDR12 by GWAS, were found within the 17q21.2 and 2q33.3 loci. These studies lay a foundation for future identification of causative variants and genes for CAD.
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Abstract
Adhesion G protein-coupled receptors (aGPCRs) have a long evolutionary history dating back to very basal unicellular eukaryotes. Almost every vertebrate is equipped with a set of different aGPCRs. Genomic sequence data of several hundred extinct and extant species allows for reconstruction of aGPCR phylogeny in vertebrates and non-vertebrates in general but also provides a detailed view into the recent evolutionary history of human aGPCRs. Mining these sequence sources with bioinformatic tools can unveil many facets of formerly unappreciated aGPCR functions. In this review, we extracted such information from the literature and open public sources and provide insights into the history of aGPCR in humans. This includes comprehensive analyses of signatures of selection, variability of human aGPCR genes, and quantitative traits at human aGPCR loci. As indicated by a large number of genome-wide genotype-phenotype association studies, variations in aGPCR contribute to specific human phenotypes. Our survey demonstrates that aGPCRs are significantly involved in adaptation processes, phenotype variations, and diseases in humans.
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Affiliation(s)
- Peter Kovacs
- Integrated Research and Treatment Center (IFB) AdiposityDiseases, Medical Faculty, University of Leipzig, Liebigstr. 21, Leipzig, 04103, Germany.
| | - Torsten Schöneberg
- Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, Leipzig, 04103, Germany.
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Gao C, Wang N, Guo X, Ziegler JT, Taylor KD, Xiang AH, Hai Y, Kridel SJ, Nadler JL, Kandeel F, Raffel LJ, Chen YDI, Norris JM, Rotter JI, Watanabe RM, Wagenknecht LE, Bowden DW, Speliotes EK, Goodarzi MO, Langefeld CD, Palmer ND. A Comprehensive Analysis of Common and Rare Variants to Identify Adiposity Loci in Hispanic Americans: The IRAS Family Study (IRASFS). PLoS One 2015; 10:e0134649. [PMID: 26599207 PMCID: PMC4658008 DOI: 10.1371/journal.pone.0134649] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/10/2015] [Indexed: 11/18/2022] Open
Abstract
Obesity is growing epidemic affecting 35% of adults in the United States. Previous genome-wide association studies (GWAS) have identified numerous loci associated with obesity. However, the majority of studies have been completed in Caucasians focusing on total body measures of adiposity. Here we report the results from genome-wide and exome chip association studies focusing on total body measures of adiposity including body mass index (BMI), percent body fat (PBF) and measures of fat deposition including waist circumference (WAIST), waist-hip ratio (WHR), subcutaneous adipose tissue (SAT), and visceral adipose tissue (VAT) in Hispanic Americans (nmax = 1263) from the Insulin Resistance Atherosclerosis Family Study (IRASFS). Five SNPs from two novel loci attained genome-wide significance (P<5.00x10-8) in IRASFS. A missense SNP in the isocitrate dehydrogenase 1 gene (IDH1) was associated with WAIST (rs34218846, MAF = 6.8%, PDOM = 1.62x10-8). This protein is postulated to play an important role in fat and cholesterol biosynthesis as demonstrated in cell and knock-out animal models. Four correlated intronic SNPs in the Zinc finger, GRF-type containing 1 gene (ZGRF1; SNP rs1471880, MAF = 48.1%, PDOM = 1.00x10-8) were strongly associated with WHR. The exact biological function of ZGRF1 and the connection with adiposity remains unclear. SNPs with p-values less than 5.00x10-6 from IRASFS were selected for replication. Meta-analysis was computed across seven independent Hispanic-American cohorts (nmax = 4156) and the strongest signal was rs1471880 (PDOM = 8.38x10-6) in ZGRF1 with WAIST. In conclusion, a genome-wide and exome chip association study was conducted that identified two novel loci (IDH1 and ZGRF1) associated with adiposity. While replication efforts were inconclusive, when taken together with the known biology, IDH1 and ZGRF1 warrant further evaluation.
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Affiliation(s)
- Chuan Gao
- Molecular Genetics and Genomics Program, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Nan Wang
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Physiology and Biophysics, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Julie T. Ziegler
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Anny H. Xiang
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California, United States of America
| | - Yang Hai
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Steven J. Kridel
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Jerry L. Nadler
- Department of Internal Medicine, Strelitz Diabetes Center, Eastern Virginia Medical School, Norfolk, Virginia, United States of America
| | - Fouad Kandeel
- Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute of City of Hope, Duarte, California, United States of America
| | - Leslie J. Raffel
- Medical Genetics Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Yii-Der I. Chen
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Jill M. Norris
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Richard M. Watanabe
- Physiology and Biophysics, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Lynne E. Wagenknecht
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Donald W. Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Elizabeth K. Speliotes
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Mark O. Goodarzi
- Medical Genetics Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Division of Endocrinology, Diabetes, and Metabolism, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Carl D. Langefeld
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Nicholette D. Palmer
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- * E-mail:
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Di Renzo L, Marsella LT, Sarlo F, Soldati L, Gratteri S, Abenavoli L, De Lorenzo A. C677T gene polymorphism of MTHFR and metabolic syndrome: response to dietary intervention. J Transl Med 2014; 12:329. [PMID: 25432492 PMCID: PMC4260200 DOI: 10.1186/s12967-014-0329-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 11/12/2014] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms were found associated with body mass index (BMI)-defined obesity and lean mass. The aim of our study was to examine the role of the C677T MTHFR gene polymorphism in the response to diet in the management of metabolic syndrome. We investigated the body composition and metabolic factor changes after an hysocaloric balanced diet (HBD), in Italian obese women affected by metabolic syndrome (MS). METHODS Forty four obese women affected by MS were eligible for the study. A HBD for 12 weeks was assigned. Study participation included a complete screening for dietary habits, anthropometry, body composition, blood biochemical markers and C677T MTHFR polymorphism genotyping. The study has been registrated by ClinicalTrials.gov Id: NCT01890070. RESULTS The highest number of responders to HBD nutritional intervention were T(-) carriers (p ≤ 0.05). In the 81% of the total population a loss of Total Body Lean was observed. A significative loss (p ≤ 0.05) of Total Body Lean was observed in the 47% of T(-) carriers and in the 53% of T(+) carriers. Diastolic and systolic blood pressure, and waist circumference were reduced (p ≤ 0.05). The prevalence of MS parameters decreased by 84% for systolic and diastolic blood pressure; 79,5% for HDL cholesterol, 82% for fasting glucose and 77% for triglycerides. CONCLUSIONS MTHFR genetic variations analysis would be an innovative tool for the nutritional assessment. Our data provide the basis for personalized dietary recommendations based on the individual's genetic makeup and nutritional status. TRIAL REGISTRATION The study has been registrated by ClinicalTrials.gov Id: NCT01890070.
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Affiliation(s)
- Laura Di Renzo
- Division of Clinical Nutrition and Nutrigenomics, Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, 00133, Italy.
| | - Luigi Tonino Marsella
- Division of Legal Medicine and Social Security, Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, 00133, Italy.
| | - Francesca Sarlo
- Department of Agriculture, University of Naples "Federico II", Portici, 80055 (Na), Italy.
| | - Laura Soldati
- Department of Health Sciences, University of Milan, Milan, Italy.
| | - Santo Gratteri
- Department of Surgery and Medical Science, University "Magna Græcia", Germaneto, (CZ), 88100, Italy.
| | - Ludovico Abenavoli
- Department of Health Science, University "Magna Græcia", Germaneto, (CZ), 88100, Italy.
| | - Antonino De Lorenzo
- Division of Clinical Nutrition and Nutrigenomics, Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, 00133, Italy.
- Clinic "Nuova Annunziatella", Rome, 00147, Italy.
- I.N.Di.M, National Institute for Mediterranean Diet and Nutrigenomic, Amantea, (CS), 87032, Italy.
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Go MJ, Hwang JY, Park TJ, Kim YJ, Oh JH, Kim YJ, Han BG, Kim BJ. Genome-wide association study identifies two novel Loci with sex-specific effects for type 2 diabetes mellitus and glycemic traits in a korean population. Diabetes Metab J 2014; 38:375-87. [PMID: 25349825 PMCID: PMC4209352 DOI: 10.4093/dmj.2014.38.5.375] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 12/31/2013] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Until recently, genome-wide association study (GWAS)-based findings have provided a substantial genetic contribution to type 2 diabetes mellitus (T2DM) or related glycemic traits. However, identification of allelic heterogeneity and population-specific genetic variants under consideration of potential confounding factors will be very valuable for clinical applicability. To identify novel susceptibility loci for T2DM and glycemic traits, we performed a two-stage genetic association study in a Korean population. METHODS We performed a logistic analysis for T2DM, and the first discovery GWAS was analyzed for 1,042 cases and 2,943 controls recruited from a population-based cohort (KARE, n=8,842). The second stage, de novo replication analysis, was performed in 1,216 cases and 1,352 controls selected from an independent population-based cohort (Health 2, n=8,500). A multiple linear regression analysis for glycemic traits was further performed in a total of 14,232 nondiabetic individuals consisting of 7,696 GWAS and 6,536 replication study participants. A meta-analysis was performed on the combined results using effect size and standard errors estimated for stage 1 and 2, respectively. RESULTS A combined meta-analysis for T2DM identified two new (rs11065756 and rs2074356) loci reaching genome-wide significance in CCDC63 and C12orf51 on the 12q24 region. In addition, these variants were significantly associated with fasting plasma glucose and homeostasis model assessment of β-cell function. Interestingly, two independent single nucleotide polymorphisms were associated with sex-specific stratification in this study. CONCLUSION Our study showed a strong association between T2DM and glycemic traits. We further observed that two novel loci with multiple diverse effects were highly specific to males. Taken together, these findings may provide additional insights into the clinical assessment or subclassification of disease risk in a Korean population.
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Affiliation(s)
- Min Jin Go
- Division of Structural and Functional Genomics, Center for Genome Science, Korea National Institute of Health, Cheongwon, Korea
| | - Joo-Yeon Hwang
- Division of Structural and Functional Genomics, Center for Genome Science, Korea National Institute of Health, Cheongwon, Korea
| | - Tae-Joon Park
- Division of Structural and Functional Genomics, Center for Genome Science, Korea National Institute of Health, Cheongwon, Korea
| | - Young Jin Kim
- Division of Structural and Functional Genomics, Center for Genome Science, Korea National Institute of Health, Cheongwon, Korea
| | - Ji Hee Oh
- Division of Structural and Functional Genomics, Center for Genome Science, Korea National Institute of Health, Cheongwon, Korea
| | - Yeon-Jung Kim
- Division of Structural and Functional Genomics, Center for Genome Science, Korea National Institute of Health, Cheongwon, Korea
| | - Bok-Ghee Han
- Division of Structural and Functional Genomics, Center for Genome Science, Korea National Institute of Health, Cheongwon, Korea
| | - Bong-Jo Kim
- Division of Structural and Functional Genomics, Center for Genome Science, Korea National Institute of Health, Cheongwon, Korea
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Abstract
Obesity is a disorder characterized by an excess accumulation of body fat resulting from a mismatch between energy intake and expenditure. Incidence of obesity has increased dramatically in the past few years, almost certainly fuelled by a shift in dietary habits owing to the widespread availability of low-cost, hypercaloric foods. However, clear differences exist in obesity susceptibility among individuals exposed to the same obesogenic environment, implicating genetic risk factors. Numerous genes have been shown to be involved in the development of monofactorial forms of obesity. In genome-wide association studies, a large number of common variants have been associated with adiposity levels, each accounting for only a small proportion of the predicted heritability. Although the small effect sizes of obesity variants identified in genome-wide association studies currently preclude their utility in clinical settings, screening for a number of monogenic obesity variants is now possible. Such regular screening will provide more informed prognoses and help in the identification of at-risk individuals who could benefit from early intervention, in evaluation of the outcomes of current obesity treatments, and in personalization of the clinical management of obesity. This Review summarizes current advances in obesity genetics and discusses the future of research in this field and the potential relevance to personalized obesity therapy.
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Kraja AT, Lawson HA, Arnett DK, Borecki IB, Broeckel U, de las Fuentes L, Hunt SC, Province MA, Cheverud J, Rao D. Obesity-insulin targeted genes in the 3p26-25 region in human studies and LG/J and SM/J mice. Metabolism 2012; 61:1129-41. [PMID: 22386932 PMCID: PMC3586585 DOI: 10.1016/j.metabol.2012.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 01/05/2012] [Accepted: 01/06/2012] [Indexed: 01/05/2023]
Abstract
Identifying metabolic syndrome (MetS) genes is important for novel drug development and health care. This study extends the findings on human chromosome 3p26-25 for an identified obesity-insulin factor QTL, with an LOD score above 3. A focused association analysis comprising up to 9578 African American and Caucasian subjects from the HyperGEN Network (908 African Americans and 1025 whites), the Family Heart Study (3035 whites in time 1 and 1943 in time 2), and the Framingham Heart Study (1317 in Offspring and 1320 in Generation 3) was performed. The homologous mouse region was explored in an F(16) generation of an advanced intercross between the LG/J and SM/J inbred strains, in an experiment where 1002 animals were fed low-fat (247 males; 254 females) or high-fat (253 males; 248 females) diets. Association results in humans indicate pleiotropic effects for SNPs within or surrounding CNTN4 on obesity, lipids and blood pressure traits and for SNPs near IL5RA, TRNT1, CRBN, and LRRN1 on central obesity and blood pressure. Linkage analyses of this region in LG/J×SM/J mice identify a highly significant pleiotropic QTL peak for insulin and glucose levels, as well as response to glucose challenge. The mouse results show that insulin and glucose levels interact with high and low fat diets and differential gene expression was identified for Crbn and Arl8b. In humans, ARL8B resides ~137kbps away from BHLHE40, expression of which shows up-regulation in response to insulin treatment. This focused human genetic analysis, incorporating mouse research evidenced that 3p26-25 has important genetic contributions to MetS components. Several of the candidate genes have functions in the brain. Their interaction with MetS and the brain warrants further investigation.
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Affiliation(s)
- Aldi T. Kraja
- Division of Statistical Genomics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Corresponding authors. Aldi Kraja, is to be contacted at Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO 63110 USA. Heather Lawson, Department of Anatomy and Neurobiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Heather A. Lawson
- Department of Anatomy and Neurobiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Corresponding authors. Aldi Kraja, is to be contacted at Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO 63110 USA. Heather Lawson, Department of Anatomy and Neurobiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Donna K. Arnett
- Department of Epidemiology, University of Alabama, Birmingham, AL 35294, USA
| | - Ingrid B. Borecki
- Division of Statistical Genomics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ulrich Broeckel
- Individualized Medicine Institute, Medical College of Wisconsin, WI 53226, USA
| | - Lisa de las Fuentes
- Cardiovascular Division Department of Medicine, Cardiovascular Imaging and Clinical Research Core Laboratory, Washington University School of Medicine 63110, St. Louis, MO, USA
| | - Steven C. Hunt
- Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Michael A. Province
- Division of Statistical Genomics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - James Cheverud
- Department of Anatomy and Neurobiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - D.C. Rao
- Division of Biostatistics, Washington University School of Medicine 63110, St. Louis, MO, USA
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11
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Engelman CD, Meyers KJ, Ziegler JT, Taylor KD, Palmer ND, Haffner SM, Fingerlin TE, Wagenknecht LE, Rotter JI, Bowden DW, Langefeld CD, Norris JM. Genome-wide association study of vitamin D concentrations in Hispanic Americans: the IRAS family study. J Steroid Biochem Mol Biol 2010; 122:186-92. [PMID: 20600896 PMCID: PMC2949505 DOI: 10.1016/j.jsbmb.2010.06.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 06/18/2010] [Accepted: 06/21/2010] [Indexed: 12/24/2022]
Abstract
Vitamin D deficiency is associated with many adverse health outcomes. There are several well established environmental predictors of vitamin D concentrations, yet studies of the genetic determinants of vitamin D concentrations are in their infancy. Our objective was to conduct a pilot genome-wide association (GWA) study of 25-hydroxyvitamin D (25[OH]D) and 1,25-dihydroxyvitamin D (1,25[OH](2)D) concentrations in a subset of 229 Hispanic subjects, followed by replication genotyping of 50 single nucleotide polymorphisms (SNPs) in the entire sample of 1190 Hispanics from San Antonio, Texas and San Luis Valley, Colorado. Of the 309,200 SNPs that met all quality control criteria, three SNPs in high linkage disequilibrium (LD) with each other were significantly associated with 1,25[OH](2)D (rs6680429, rs9970802, and rs10889028) at a Bonferroni corrected P-value threshold of 1.62 × 10(-7), however none met the threshold for 25[OH]D. Of the 50 SNPs selected for replication genotyping, five for 25[OH]D (rs2806508, rs10141935, rs4778359, rs1507023, and rs9937918) and eight for 1,25[OH](2)D (rs6680429, rs1348864, rs4559029, rs12667374, rs7781309, rs10505337, rs2486443, and rs2154175) were replicated in the entire sample of Hispanics (P<0.01). In conclusion, we identified several SNPs that were associated with vitamin D metabolite concentrations in Hispanics. These candidate polymorphisms merit further investigation in independent populations and other ethnicities.
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Affiliation(s)
- Corinne D Engelman
- Department of Population Health Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA.
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12
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Chiu YF, Chuang LM, Kao HY, Shih KC, Lin MW, Lee WJ, Quertermous T, Curb JD, Chen I, Rodriguez BL, Hsiung CA. Sex-specific genetic architecture of human fatness in Chinese: the SAPPHIRe Study. Hum Genet 2010; 128:501-13. [PMID: 20725740 DOI: 10.1007/s00439-010-0877-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 08/11/2010] [Indexed: 01/02/2023]
Abstract
To dissect the genetic architecture of sexual dimorphism in obesity-related traits, we evaluated the sex-genotype interaction, sex-specific heritability and genome-wide linkages for seven measurements related to obesity. A total of 1,365 non-diabetic Chinese subjects from the family study of the Stanford Asia-Pacific Program of Hypertension and Insulin Resistance were used to search for quantitative trait loci (QTLs) responsible for the obesity-related traits. Pleiotropy and co-incidence effects from the QTLs were also examined using the bivariate linkage approach. We found that sex-specific differences in heritability and the genotype-sex interaction effects were substantially significant for most of these traits. Several QTLs with strong linkage evidence were identified after incorporating genotype by sex (G × S) interactions into the linkage mapping, including one QTL for hip circumference [maximum LOD score (MLS) = 4.22, empirical p = 0.000033] and two QTLs: for BMI on chromosome 12q with MLS 3.37 (empirical p = 0.0043) and 3.10 (empirical p = 0.0054). Sex-specific analyses demonstrated that these linkage signals all resulted from females rather than males. Most of these QTLs for obesity-related traits replicated the findings in other ethnic groups. Bivariate linkage analyses showed several obesity traits were influenced by a common set of QTLs. All regions with linkage signals were observed in one gender, but not in the whole sample, suggesting the genetic architecture of obesity-related traits does differ by gender. These findings are useful for further identification of the liability genes for these phenotypes through candidate genes or genome-wide association analysis.
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Affiliation(s)
- Y-F Chiu
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, 35 Keyan Rd, Zhunan, Miaoli 350, Taiwan, ROC
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13
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Johansson A, Marroni F, Hayward C, Franklin CS, Kirichenko AV, Jonasson I, Hicks AA, Vitart V, Isaacs A, Axenovich T, Campbell S, Floyd J, Hastie N, Knott S, Lauc G, Pichler I, Rotim K, Wild SH, Zorkoltseva IV, Wilson JF, Rudan I, Campbell H, Pattaro C, Pramstaller P, Oostra BA, Wright AF, van Duijn CM, Aulchenko YS, Gyllensten U. Linkage and genome-wide association analysis of obesity-related phenotypes: association of weight with the MGAT1 gene. Obesity (Silver Spring) 2010; 18:803-8. [PMID: 19851299 DOI: 10.1038/oby.2009.359] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
As major risk-factors for diabetes and cardiovascular diseases, the genetic contribution to obesity-related traits has been of interest for decades. Recently, a limited number of common genetic variants, which have replicated in different populations, have been identified. One approach to increase the statistical power in genetic mapping studies is to focus on populations with increased levels of linkage disequilibrium (LD) and reduced genetic diversity. We have performed joint linkage and genome-wide association analyses for weight and BMI in 3,448 (linkage) and 3,925 (association) partly overlapping healthy individuals from five European populations. A total of four chromosomal regions (two for weight and two for BMI) showed suggestive linkage (lod >2.69) either in one of the populations or in the joint data. At the genome-wide level (nominal P < 1.6 x 10(-7), Bonferroni-adjusted P < 0.05) one single-nucleotide polymorphism (SNP) (rs12517906) (nominal P = 7.3 x 10(-8)) was associated with weight, whereas none with BMI. The SNP associated with weight is located close to MGAT1. The monoacylglycerol acyltransferase (MGAT) enzyme family is known to be involved in dietary fat absorption. There was no overlap between the linkage regions and the associated SNPs. Our results show that genetic effects influencing weight and BMI are shared across diverse European populations, even though some of these populations have experienced recent population bottlenecks and/or been affected by genetic drift. The analysis enabled us to identify a new candidate gene, MGAT1, associated with weight in women.
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Affiliation(s)
- Asa Johansson
- Department of Genetics and Pathology, Rudbeck laboratory, Uppsala University, Uppsala, Sweden
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14
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Norris JM, Langefeld CD, Talbert ME, Wing MR, Haritunians T, Fingerlin TE, Hanley AJG, Ziegler JT, Taylor KD, Haffner SM, Chen YDI, Bowden DW, Wagenknecht LE. Genome-wide association study and follow-up analysis of adiposity traits in Hispanic Americans: the IRAS Family Study. Obesity (Silver Spring) 2009; 17:1932-41. [PMID: 19461586 PMCID: PMC2832211 DOI: 10.1038/oby.2009.143] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We investigated candidate genomic regions associated with computed tomography (CT)-derived measures of adiposity in Hispanics from the Insulin Resistance Atherosclerosis Study Family Study (IRASFS). In 1,190 Hispanic individuals from 92 families 3 from the San Luis Valley, Colorado and San Antonio, Texas, we measured CT-derived visceral adipose tissue (VAT), subcutaneous adipose tissue (SAT), and visceral:subcutaneous ratio (VSR). A genome-wide association study (GWAS) was completed using the Illumina HumanHap 300 BeadChip (approximately 317K single-nucleotide polymorphisms (SNPs)) in 229 individuals from the San Antonio site (stage 1). In total, 297 SNPs with evidence for association with VAT, SAT, or VSR, adjusting for age and sex (P<0.001), were genotyped in the remaining 961 Hispanic samples. The entire Hispanic cohort (n=1,190) was then tested for association, adjusting for age, sex, site of recruitment, and admixture estimates (stage 2). In stage 3, additional SNPs were genotyped in four genic regions showing evidence of association in stage 2. Several SNPs were associated in the GWAS (P<1x10(-5)) and were confirmed to be significantly associated in the entire Hispanic cohort (P<0.01), including: rs7543757 for VAT, rs4754373 and rs11212913 for SAT, and rs4541696 and rs4134351 for VSR. Numerous SNPs were associated with multiple adiposity phenotypes. Targeted analysis of four genes whose SNPs were significant in stage 2 suggests candidate genes for influencing the distribution (RGS6) and amount of adiposity (NGEF). Several candidate loci, including RGS6 and NGEF, are associated with CT-derived adipose fat measures in Hispanic Americans in a three-stage genetic association study.
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Affiliation(s)
- Jill M Norris
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, USA.
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15
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Talbert ME, Langefeld CD, Ziegler JT, Haffner SM, Norris JM, Bowden DW. INSIG2 SNPs associated with obesity and glucose homeostasis traits in Hispanics: the IRAS Family Study. Obesity (Silver Spring) 2009; 17:1554-62. [PMID: 19360016 PMCID: PMC2916685 DOI: 10.1038/oby.2009.94] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The genome-wide association study by Herbert et al. identified the INSIG2 single-nucleotide polymorphism (SNP) rs7566605 as contributing to increased BMI in ethnically distinct cohorts. The present study sought to further clarify the matter, by testing whether SNPs of INSIG2 influenced quantitative adiposity or glucose homeostasis traits in Hispanics of the Insulin Resistance Atherosclerosis Family Study (IRASFS). Using a tagging SNP approach, rs7566605 and 31 additional SNPs were genotyped in 1,425 IRASFS Hispanics. SNPs were tested for association with six adiposity measures: BMI, waist circumference (WAIST), waist-to-hip ratio (WHR), subcutaneous adipose tissue (SAT), visceral adipose tissue (VAT), and VAT to SAT ratio (VSR). SNPs were also tested for association with fasting glucose (GFAST), fasting insulin (FINS), and three measures obtained from the frequently sampled intravenous glucose tolerance test: insulin sensitivity (S(I)), acute insulin response (AIR), and disposition index (DI). Most prominent association was observed with direct computed tomography (CT)-measured adiposity phenotypes, including VAT, SAT, and VSR (P values range from 0.007 to 0.044 for rs17586756, rs17047718, rs17047731, rs9308762, rs12623648, and rs11673900). Multiple SNP associations were observed with all glucose homeostasis traits (P values range from 0.001 to 0.031 for rs17047718, rs17047731, rs2161829, rs10490625, rs889904, and rs12623648). Using BMI as a covariate in evaluation of glucose homeostasis traits slightly reduced their association. However, association with adiposity and glucose homeostasis phenotypes is not significant following multiple comparisons adjustment. Trending association after multiple comparisons adjustment remains suggestive of a role for genetic variation of INSIG2 in obesity, but these results require validation.
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Affiliation(s)
- Matthew E Talbert
- Program in Molecular Medicine and Translational Sciences, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
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16
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Murphy A, Tantisira KG, Soto-Quirós ME, Avila L, Klanderman BJ, Lake S, Weiss ST, Celedón JC. PRKCA: a positional candidate gene for body mass index and asthma. Am J Hum Genet 2009; 85:87-96. [PMID: 19576566 DOI: 10.1016/j.ajhg.2009.06.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Revised: 05/05/2009] [Accepted: 06/16/2009] [Indexed: 12/13/2022] Open
Abstract
Asthma incidence and prevalence are higher in obese individuals. A potential mechanistic basis for this relationship is pleiotropy. We hypothesized that significant linkage and candidate-gene association would be found for body mass index (BMI) in a population ascertained on asthma affection status. Linkage analysis for BMI was performed on 657 subjects in eight Costa Rican families enrolled in a study of asthma. Family-based association studies were conducted for BMI with SNPs within a positional candidate gene, PRKCA. SNPs within PRKCA were also tested for association with asthma. Association studies were conducted in 415 Costa Rican parent-child trios and 493 trios participating in the Childhood Asthma Management Program (CAMP). Although only modest evidence of linkage for BMI was obtained for the whole cohort, significant linkage was noted for BMI in females on chromosome 17q (peak LOD = 3.39). Four SNPs in a candidate gene in this region (PRKCA) had unadjusted association p values < 0.05 for BMI in both cohorts, with the joint p value for two SNPs remaining significant after adjustment for multiple comparisons (rs228883 and rs1005651, joint p values = 9.5 x 10(-)(5) and 5.6 x 10(-)(5)). Similarly, eight SNPs had unadjusted association p values < 0.05 for asthma in both populations, with one SNP remaining significant after adjustment for multiple comparisons (rs11079657, joint p value = 2.6 x 10(-)(5)). PRKCA is a pleiotropic locus that is associated with both BMI and asthma and that has been identified via linkage analysis of BMI in a population ascertained on asthma.
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Affiliation(s)
- Amy Murphy
- Channing Laboratory, Brigham and Women's Hospital, Boston, MA 02115, USA
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17
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Sutton BS, Palmer ND, Langefeld CD, Xue B, Proctor A, Ziegler JT, Haffner SM, Norris JM, Bowden DW. Association of SSTR2 polymorphisms and glucose homeostasis phenotypes: the Insulin Resistance Atherosclerosis Family Study. Diabetes 2009; 58:1457-62. [PMID: 19324939 PMCID: PMC2682669 DOI: 10.2337/db08-0189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE This study evaluated the influence of somatostatin receptor type 2 (SSTR2) polymorphisms on measures of glucose homeostasis in the Insulin Resistance Atherosclerosis Family Study (IRASFS). SSTR2 is a G-protein-coupled receptor that, in response to somatostatin, mediates inhibition of insulin, glucagon, and growth hormone release and thus may affect glucose homeostasis. RESEARCH DESIGN AND METHODS Ten single nucleotide polymorphisms (SNPs) spanning the gene were chosen using a SNP density selection algorithm and genotyped on 1,425 Hispanic-American individuals from 90 families in the IRASFS. These families comprised two samples (set 1 and set 2), which were analyzed individually and as a combined set. Single SNP tests of association were performed for four glucose homeostasis measures--insulin sensitivity (S(I)), acute insulin response (AIR), disposition index (DI), and fasting blood glucose (FBG)--using generalized estimating equations. RESULTS The SSTR2 locus was encompassed by a single linkage disequilibrium (LD) block (D' = 0.91-1.00; r(2) = 0.09-0.97) that contained four of the ten SNPs evaluated. Within the SSTR2-containing LD block, evidence of association was observed in each of the two sets and in a combined analysis with decreased S(I)(beta(homozygous) = -0.16; P(meta-analysis) = 0.0024-0.0030), decreased DI (beta(homozygous) = -0.35 to -5.16; P(meta-analysis) = 0.0075-0.027), and increased FBG (beta(homozygous) = 2.30; P(meta-analysis) = 0.045). SNPs outside the SSTR2-containing LD block were not associated with measures of glucose homeostasis. CONCLUSIONS We observed evidence for association of SSTR2 polymorphisms with measures of glucose homeostasis. Thus, variants in SSTR2 may influence pathways of S(I)to modulate glucose homeostasis.
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Affiliation(s)
- Beth S. Sutton
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Carl D. Langefeld
- Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Bingzhong Xue
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Alexandria Proctor
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Julie T. Ziegler
- Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Steven M. Haffner
- Department of Medicine, University of Texas Health Sciences Center at San Antonio, San Antonio, Texas
| | - Jill M. Norris
- Department of Preventive Medicine and Biometrics, University of Colorado Denver, Denver, Colorado
| | - Donald W. Bowden
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Department of Internal Medicine, University of Texas Health Sciences Center at San Antonio, San Antonio, Texas
- Corresponding author: Donald W. Bowden,
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18
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McCarthy JJ, Somji A, Weiss LA, Steffy B, Vega R, Barrett-Connor E, Talavera G, Glynne R. Polymorphisms of the scavenger receptor class B member 1 are associated with insulin resistance with evidence of gene by sex interaction. J Clin Endocrinol Metab 2009; 94:1789-96. [PMID: 19276229 PMCID: PMC2684479 DOI: 10.1210/jc.2008-2800] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Genetic variation in diabetes-associated genes cumulatively explain little of the overall heritability of this trait. We sought to determine whether polymorphisms of the scavenger receptor class B, member I (SCARB1), an estrogen-regulated chromosome 12q24 positional candidate diabetes gene, were associated with type 2 diabetes or insulin resistance in a sex-specific fashion. METHODS We evaluated 34 haplotype-tagged single-nucleotide polymorphisms (SNPs) of SCARB1 for their association with type 2 diabetes and measures of insulin resistance in two populations: a clinic-based sample of 444 Mexican-American women from Proyecto SALSA and a community-based sample of 830 white women from the Rancho Bernardo Study. RESULTS We identified significant associations between a tagged SNP in intron 9, rs9919713, and fasting glucose in the SALSA population (P = 2.3 x 10(-4)). In the Rancho Bernardo Study, the same SNP also showed significant association with the related traits homeostasis model assessment for insulin resistance (P = 3.0 x 10(-4)), fasting glucose (P = 1.1 x 10(-3)), and type 2 diabetes (P = 9.0 x 10(-3)). In men from the Rancho Bernardo population, the opposite effect was found (genotype by sex interaction in the Rancho Bernardo population P < 10(-3) for insulin resistance). CONCLUSIONS Our data support an association between SCARB1 variants and insulin resistance, especially in women, with evidence of significant gene by sex interaction. These findings warrant further investigation in additional populations and prompt exploration of a role for SR-BI in the development of insulin resistance.
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Affiliation(s)
- Jeanette J McCarthy
- Graduate School of Public Health, San Diego State University, San Diego, California 92182, USA.
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19
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Voruganti VS, Nath SD, Cole SA, Thameem F, Jowett JB, Bauer R, MacCluer JW, Blangero J, Comuzzie AG, Abboud HE, Arar NH. Genetics of variation in serum uric acid and cardiovascular risk factors in Mexican Americans. J Clin Endocrinol Metab 2009; 94:632-8. [PMID: 19001525 PMCID: PMC2646516 DOI: 10.1210/jc.2008-0682] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Accepted: 10/31/2008] [Indexed: 12/22/2022]
Abstract
BACKGROUND Elevated serum uric acid is associated with several cardiovascular disease (CVD) risk factors such as hypertension, inflammation, endothelial dysfunction, insulin resistance, dyslipidemia, and obesity. However, the role of uric acid as an independent risk factor for CVD is not yet clear. OBJECTIVE The aim of the study was to localize quantitative trait loci regulating variation in serum uric acid and also establish the relationship between serum uric acid and other CVD risk factors in Mexican Americans (n = 848; men = 310, women = 538) participating in the San Antonio Family Heart Study. METHODS Quantitative genetic analysis was conducted using variance components decomposition method, implemented in the software program SOLAR. RESULTS Mean +/- SD of serum uric acid was 5.35 +/- 1.38 mg/dl. Univariate genetic analysis showed serum uric acid and other CVD risk markers to be significantly heritable (P < 0.005). Bivariate analysis showed significant correlation of serum uric acid with body mass index, waist circumference, waist/hip ratio, total body fat, plasma insulin, serum triglycerides, high-density lipoprotein cholesterol, C-reactive protein, and granulocyte macrophage-colony stimulating factor (P < 0.05). A genome-wide scan for detecting quantitative trait loci regulating serum uric acid variation showed a significant logarithm of odds (LOD) score of 4.72 (empirical LOD score = 4.62; P < 0.00001) on chromosome 3p26. One LOD support interval contains 25 genes, of which an interesting candidate gene is chemokine receptor 2. SUMMARY There is a significant genetic component in the variation in serum uric acid and evidence of pleiotropy between serum uric acid and other cardiovascular risk factors.
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Affiliation(s)
- V Saroja Voruganti
- Department of Genetics, Southwest Foundation for Biomedical Research, P.O. Box 760549, San Antonio, Texas 78227, USA.
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20
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Talbert ME, Langefeld CD, Ziegler J, Mychaleckyj JC, Haffner SM, Norris JM, Bowden DW. Polymorphisms near SOCS3 are associated with obesity and glucose homeostasis traits in Hispanic Americans from the Insulin Resistance Atherosclerosis Family Study. Hum Genet 2008; 125:153-62. [PMID: 19083014 DOI: 10.1007/s00439-008-0608-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2008] [Accepted: 12/06/2008] [Indexed: 11/30/2022]
Abstract
The SOCS3 gene product participates in the feedback inhibition of a range of cytokine signals. Most notably, SOCS3 inhibits the functioning of leptin and downstream steps in insulin signaling after being expressed by terminal transcription factors, such as STAT3 and c-fos. The SOCS3 gene is located in the chromosome region 17q24-17q25, previously linked to body mass index (BMI), visceral adipose tissue (VAT), and waist circumference (WAIST) in Hispanic families in the Insulin Resistance Atherosclerosis Family Study (IRASFS). A high density map of 1,536 single nucleotide polymorphisms (SNPs) was constructed to cover a portion of the 17q linkage interval in 1,425 Hispanic subjects from 90 extended families in IRASFS. Analysis of this dense SNP map data revealed evidence of association of rs9914220 (located 10 kb 5' of the SOCS3 gene) with BMI, VAT, and WAIST (P-value ranging from 0.003 to 0.017). Using a tagging SNP approach, rs9914220 and 22 additional SOCS3 SNPs were genotyped for genetic association analysis with measures of adiposity and glucose homeostasis. The adiposity phenotypes utilized in association analyses included BMI, WAIST, waist to hip ratio (WHR), subcutaneous adipose tissue, VAT, and visceral to subcutaneous ratio (VSR). Linkage disequilibrium calculations revealed three haplotype blocks near SOCS3. Haplotype Block 3 (5' of SOCS3) contained SNPs consistently associated with BMI, WAIST, WHR, and VAT (P-values ranging from 2.00 x 10(-4) to 0.036). Haplotype Block 1 contained single-SNPs that were associated with most adiposity traits except for VSR (P-values ranging from 0.002 to 0.047). When trait associated SNPs were included in linkage analyses as covariates, a reduction of VAT LOD score from 1.26 to 0.76 above the SOCS3 locus (110 cM) was observed. Multi-SNP haplotype testing using the quantitative pedigree disequilibrium test was broadly consistent with the single-SNP associations. In conclusion, these results support a role for SOCS3 genetic variants in human obesity.
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Affiliation(s)
- Matthew E Talbert
- Program in Molecular Medicine, Wake Forest University School of Medicine, Medical Center Blvd., Winston-Salem, NC 27157, USA.
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21
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Larkin EK, Patel SR, Elston RC, Gray-McGuire C, Zhu X, Redline S. Using linkage analysis to identify quantitative trait loci for sleep apnea in relationship to body mass index. Ann Hum Genet 2008; 72:762-73. [PMID: 18754839 DOI: 10.1111/j.1469-1809.2008.00472.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
To understand the genetics of sleep apnea, we evaluated the relationship between the apnea hypopnea index (AHI) and body mass index (BMI) through linkage analysis to identify genetic loci that may influence AHI and BMI jointly and AHI independent of BMI. Haseman-Elston sibling regression was conducted on AHI, AHI adjusted for BMI and BMI in African-American and European-American pedigrees. A comparison of the magnitude of linkage peaks was used to assess the relationship between AHI and BMI. In EAs, the strongest evidence for linkage to AHI was on 6q23-25 and 10q24-q25, both decreasing after BMI adjustment, suggesting loci with pleiotropic effects. Also, a promising area of linkage to AHI but not BMI was observed on 6p11-q11 near the orexin-2 receptor, suggesting BMI independent pathways. In AAs the strongest evidence of linkage for AHI after adjusting for BMI was on chromosome 8p21.3 with linkage increasing after BMI adjustment and on 8q24.1 with linkage decreasing after BMI adjustment. Novel linkage peaks were also observed in AAs to both BMI and AHI on chromosome 13 near the serotonin-2a receptor. These analyses suggest genetic loci for sleep apnea that operate both independently of BMI and through BMI-related pathways.
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Affiliation(s)
- E K Larkin
- Center for Clinical Investigation, Case Western Reserve University, School of Medicine, Cleveland, OH 44106-6083, USA.
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22
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The MTHFR gene polymorphism is associated with lean body mass but not fat body mass. Hum Genet 2008; 123:189-96. [DOI: 10.1007/s00439-007-0463-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Accepted: 12/23/2007] [Indexed: 01/25/2023]
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23
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Dai F, Keighley ED, Sun G, Indugula SR, Roberts ST, Aberg K, Smelser D, Tuitele J, Jin L, Deka R, Weeks DE, McGarvey ST. Genome-wide scan for adiposity-related phenotypes in adults from American Samoa. Int J Obes (Lond) 2007; 31:1832-42. [PMID: 17621312 DOI: 10.1038/sj.ijo.0803675] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To detect quantitative trait loci influencing adiposity-related phenotypes assessed by body mass index (BMI), abdominal circumference (ABDCIR), percent body fat (%BFAT) and fasting serum leptin and adiponectin using a whole genome linkage scan of families from American Samoa. DESIGN Family-based linkage analysis, the probands and family members were unselected for obesity. SUBJECTS A total of 583 phenotyped American Samoan adults, of which 578 were genotyped in 34 pedigrees. MEASUREMENTS A total of 377 autosomal and 18 X chromosome microsatellite markers were typed at an approximate average spacing of 10 cM spanning the genome. Multipoint LOD (logarithm of the odds) scores were calculated using variance-components approaches and SOLAR/LOKI software. The covariates simultaneously evaluated were age, sex, education, farm work and cigarette smoking, with a significance level of 0.1. Due to the stochastic nature of LOKI, we report the average of maximum LOD scores from 10 runs. RESULTS Significant linkage to leptin was found at 6q32.2 with LOD of 3.83. Suggestive linkage to leptin was found at 16q21:LOD=2.98, 1q42.2:LOD=1.97, 5q11.2:LOD=2.08, 12q24.23:LOD=2.00, 19p13.3:LOD=2.05; adiponectin was linked to 13q33.1-q22.1:LOD=2.41; %BFAT was linked to 16q12.2-q21, LOD=2.24; ABDCIR was linked to 16q23.1:LOD=1.95; %BFAT-adjusted leptin to 14q12, LOD=2.01; %BFAT-adjusted ABDCIR to 1q31.1, LOD=2.36, to 3q27.3-q28, LOD=2.10 and to 12p12.3, LOD=2.04. CONCLUSION We found strong evidence for a major locus on 6q23.2 influencing serum leptin levels in American Samoans. The 16q21 region appears to harbor a susceptibility locus that has significant pleiotrophic effects on phenotypes BMI, %BFAT, leptin and ABDCIR as shown by bivariate linkage analyses. Several other loci of varying significance were detected across the genome.
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Affiliation(s)
- F Dai
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 02912, USA
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Gu CC, Hunt SC, Kardia S, Turner ST, Chakravarti A, Schork N, Olshen R, Curb D, Jaquish C, Boerwinkle E, Rao DC. An investigation of genome-wide associations of hypertension with microsatellite markers in the family blood pressure program (FBPP). Hum Genet 2007; 121:577-90. [PMID: 17372766 DOI: 10.1007/s00439-007-0349-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Accepted: 02/26/2007] [Indexed: 12/24/2022]
Abstract
The Family Blood Pressure Program (FBPP) has data on 387 microsatellite markers in 13,524 subjects from four major ethnic groups. We investigated genetic association with hypertension of the linkage markers. Family-based methods were used to test association of the 387 loci with resting blood pressures (BPs) [systolic blood pressure (SBP) and diastolic blood pressure (DBP)] and the hypertension status (HT). We applied a vote-counting approach to pool results across the three correlated traits, network samples, and ethnic groups to refine the selection of susceptibility loci. The association analyses captured signals missed by previous linkage scans. We found 71 loci associated with at least one of the three traits in at least one of the four ethnic groups at the significance level of 0.01. After validation across multiple samples and related traits, we identified by vote-counting 21 candidate loci for hypertension. Two loci, D3S2459 and D10S1412 confirmed findings in Network-specific linkage scans (GENOA and SAPPHIRe). Many of the candidate loci were reported by others in linkage to BPs, body weight, heart disease, and diabetes. We also observed frequent presence of quantitative trait loci (QTLs) involved in autoimmune and neurological disorders (e.g., NOD2). The vote-counting method of pooling results recognizes the potential that a gene may be involved in varying ways among different samples, which we believe is responsible for identifying genes in the less explored inflammatory pathways to hypertension.
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Affiliation(s)
- C Charles Gu
- Division of Biostatistics, Washington University School of Medicine, 660 S. Euclid Avenue, Campus Box 8067, St Louis, MO 63110, USA.
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Elbers CC, Onland-Moret NC, Franke L, Niehoff AG, van der Schouw YT, Wijmenga C. A strategy to search for common obesity and type 2 diabetes genes. Trends Endocrinol Metab 2007; 18:19-26. [PMID: 17126559 DOI: 10.1016/j.tem.2006.11.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2006] [Revised: 11/01/2006] [Accepted: 11/14/2006] [Indexed: 12/24/2022]
Abstract
Worldwide, the incidence of type 2 diabetes is rising rapidly, mainly because of the increase in the incidence of obesity, which is an important risk factor for this condition. Both obesity and type 2 diabetes are complex genetic traits but they also share some nongenetic risk factors. Hence, it is tempting to speculate that the susceptibility to type 2 diabetes and obesity might also partly be due to shared genes. By comparing all of the published genome scans for type 2 diabetes and obesity, five overlapping chromosomal regions for both diseases (encompassing 612 candidate genes) have been identified. By analysing these five susceptibility loci for type 2 diabetes and obesity, using six freely available bioinformatics tools for disease gene identification, 27 functional candidate genes have been pinpointed that are involved in eating behaviour, metabolism and inflammation. These genes might reveal a molecular link between the two disorders.
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Affiliation(s)
- Clara C Elbers
- Complex Genetics Section, Department of Biomedical Genetics, University Medical Centre Utrecht, PO Box 85060, 3508 AB Utrecht, the Netherlands
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Barendse W, Bunch RJ, Kijas JW, Thomas MB. The effect of genetic variation of the retinoic acid receptor-related orphan receptor C gene on fatness in cattle. Genetics 2006; 175:843-53. [PMID: 17151246 PMCID: PMC1800623 DOI: 10.1534/genetics.106.064535] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genotypes at the retinoic acid receptor-related orphan receptor C (RORC) gene were associated with fatness in 1750 cattle. Ten SNPs were genotyped in RORC and the adjacent gene leucine-rich repeat neuronal 6D (LRRN6D) to map the QTL, 7 of which are in a 4.2-kb sequence around the ligand-binding domain of the RORC gene. Of the 29 inferred haplotypes for these SNPs, 2 have a combined frequency of 54.6% while the top 5 haplotypes have a combined frequency of 85.3%. The average D' value of linkage disequilibrium was 0.92 although the average r2 was a low 0.18. The RORC:g.3290T>G SNP had the strongest association with marbling. The inferred haplotypes were significantly associated with marbling and the difference between the most divergent haplotypes was 0.35 sigma(p) of marbling and 0.28 sigma(p) of rump fat, explaining the previously reported QTL effect. cDNA for RORC were sequenced and 2 new alternative transcripts were found. Fetal tissue shows 40 times greater transcription of RORC than adult tissue. The highest expression in fetal tissue was found in liver and kidney, but in adults the longissimus muscle had the greatest expression of the tissues tested.
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Affiliation(s)
- W Barendse
- CSIRO Livestock Industries, Queensland Bioscience Precinct, Saint Lucia, Queensland 4067, Australia.
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Rankinen T, Zuberi A, Chagnon YC, Weisnagel SJ, Argyropoulos G, Walts B, Pérusse L, Bouchard C. The human obesity gene map: the 2005 update. Obesity (Silver Spring) 2006; 14:529-644. [PMID: 16741264 DOI: 10.1038/oby.2006.71] [Citation(s) in RCA: 685] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This paper presents the 12th update of the human obesity gene map, which incorporates published results up to the end of October 2005. Evidence from single-gene mutation obesity cases, Mendelian disorders exhibiting obesity as a clinical feature, transgenic and knockout murine models relevant to obesity, quantitative trait loci (QTL) from animal cross-breeding experiments, association studies with candidate genes, and linkages from genome scans is reviewed. As of October 2005, 176 human obesity cases due to single-gene mutations in 11 different genes have been reported, 50 loci related to Mendelian syndromes relevant to human obesity have been mapped to a genomic region, and causal genes or strong candidates have been identified for most of these syndromes. There are 244 genes that, when mutated or expressed as transgenes in the mouse, result in phenotypes that affect body weight and adiposity. The number of QTLs reported from animal models currently reaches 408. The number of human obesity QTLs derived from genome scans continues to grow, and we now have 253 QTLs for obesity-related phenotypes from 61 genome-wide scans. A total of 52 genomic regions harbor QTLs supported by two or more studies. The number of studies reporting associations between DNA sequence variation in specific genes and obesity phenotypes has also increased considerably, with 426 findings of positive associations with 127 candidate genes. A promising observation is that 22 genes are each supported by at least five positive studies. The obesity gene map shows putative loci on all chromosomes except Y. The electronic version of the map with links to useful publications and relevant sites can be found at http://obesitygene.pbrc.edu.
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Affiliation(s)
- Tuomo Rankinen
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA 70808-4124, USA
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Sutton BS, Langefeld CD, Campbell JK, Haffner SM, Norris JM, Scherzinger AL, Wagenknecht LE, Bowden DW. Genetic mapping of a 17q chromosomal region linked to obesity phenotypes in the IRAS family study. Int J Obes (Lond) 2006; 30:1433-41. [PMID: 16520807 DOI: 10.1038/sj.ijo.0803298] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Obesity is widely accepted to be influenced by both environmental and genetic factors. Several recent studies have used the positional cloning approach in an attempt to discover genes contributing to obesity. In the IRAS Family Study a genomewide scan was performed on 1425 individuals of Hispanic descent (90 extended pedigree families) to identify regions of the genome linked to obesity phenotypes. METHODS Nonparametric QTL linkage analysis was performed using a variance components approach. The genome scan was performed in two phases: an initial genome scan in 45 families and a replication scan in 45 families. Fine mapping and candidate gene analyses were also performed. General estimating equations (GEE1) and quantitative pedigree disequilibrium tests (QPDT) were used for association analysis of single SNP and haplotype data. RESULTS Evidence for linkage to obesity traits was observed in each scan on the long arm of chromosome 17. When data from both scans was combined, a region on chromosome 17q was identified with evidence of linkage to visceral adipose tissue (VAT; LOD 3.11), waist circumference (WAIST) (LOD 2.5) and body mass index (BMI) (LOD 2.81). Nine additional microsatellite markers were identified and genotyped on all Hispanic individuals, with a mean marker density of approximately 1 marker/3 cM. Evidence of linkage remained significant with LOD 3.05 for VAT, LOD 2.44 for BMI and LOD 1.92 for WAIST. Fine mapping analyses suggest the possibility of two different obesity loci. In addition, the LOD - 1 interval of the major VAT peak decreased from 83-108 to 95-111 cM. Three positional candidate genes under the peak: somatostatin receptor 2 (SSTR2), galanin receptor 2 (GALR2), and growth hormone bound protein receptor 2 (GRB2) were chosen for detailed evaluation. Multiple polymorphisms within each candidate were genotyped and tested for association with the obesity phenotypes. Little evidence of association was detected between polymorphisms and obesity traits. CONCLUSION In conclusion, replication of linkage and fine mapping suggest that a region on chromosome 17q contains a gene (or genes) that contributes to the genetic etiology of obesity with the strongest evidence for linkage to VAT. Candidate genes in the region do not appear to account for the evidence of linkage. Additional studies are necessary to identify the obesity-related polymorphisms.
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Affiliation(s)
- B S Sutton
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
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