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Sex-Related Differences in Allelic Frequency of the Human Beta T Cell Receptor SNP rs1800907: A Retrospective Analysis from Milan Metropolitan Area. Vaccines (Basel) 2021; 9:vaccines9040333. [PMID: 33915945 PMCID: PMC8066715 DOI: 10.3390/vaccines9040333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 03/01/2021] [Accepted: 03/18/2021] [Indexed: 11/30/2022] Open
Abstract
This paper aims at retrospectively re-analyzing the different distribution, between males and females, in the allelic frequency of the human β T cell receptor (TCR β) single nucleotide polymorphism (SNPs) rs1800907 in Caucasian patients in the Milan metropolitan area. The allelic frequency significantly differed between sexes. Females showed higher frequency of C/C genotype than males, but lower T/C genotype (p < 0.0001). Heterozygous (T/C) versus homozygous (T/T + C/C) genotypes resulted in a different distribution of frequencies in males than in females, the latter possessing higher homozygosis (p < 0.0001). Within the limitations of this work (small number of included studies that concerned just a specific geographical area), allelic distribution according to sex might account the role of TCRβ-related SNPs in autoimmune diseases and further investigations are required to explain better this genetic background, in the perspective of a sex-related T cell immune responsiveness and auto-immunity.
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Kingsmore SF, Lindquist IE, Mudge J, Beavis WD. Genome-Wide Association Studies: Progress in Identifying Genetic Biomarkers in Common, Complex Diseases. Biomark Insights 2017. [DOI: 10.1177/117727190700200019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Novel, comprehensive approaches for biomarker discovery and validation are urgently needed. One particular area of methodologic need is for discovery of novel genetic biomarkers in complex diseases and traits. Here, we review recent successes in the use of genome wide association (GWA) approaches to identify genetic biomarkers in common human diseases and traits. Such studies are yielding initial insights into the allelic architecture of complex traits. In general, it appears that complex diseases are associated with many common polymorphisms, implying profound genetic heterogeneity between affected individuals.
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Affiliation(s)
| | | | - Joann Mudge
- National Center for Genome Resources, Santa Fe, NM 87505, U.S.A
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Himes BE, Ortega VE. Making progress toward understanding the genetic architecture of asthma in the most affected US ethnic group. Eur Respir J 2017; 49:49/5/1700329. [PMID: 28461304 DOI: 10.1183/13993003.00329-2017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Blanca E Himes
- Dept of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Victor E Ortega
- Center for Genomics and Personalized Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
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Lemas DJ, Klimentidis YC, Aslibekyan S, Wiener HW, O'Brien DM, Hopkins SE, Stanhope KL, Havel PJ, Allison DB, Fernandez JR, Tiwari HK, Boyer BB. Polymorphisms in stearoyl coa desaturase and sterol regulatory element binding protein interact with N-3 polyunsaturated fatty acid intake to modify associations with anthropometric variables and metabolic phenotypes in Yup'ik people. Mol Nutr Food Res 2016; 60:2642-2653. [PMID: 27467133 DOI: 10.1002/mnfr.201600170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 07/09/2016] [Accepted: 07/21/2016] [Indexed: 11/08/2022]
Abstract
SCOPE n-3 polyunsaturated fatty acid (n-3 PUFA) intake is associated with protection from obesity; however, the mechanisms of protection remain poorly characterized. The stearoyl CoA desaturase (SCD), insulin-sensitive glucose transporter (SLC2A4), and sterol regulatory element binding protein (SREBF1) genes are transcriptionally regulated by n-3 PUFA intake and harbor polymorphisms associated with obesity. The present study investigated how consumption of n-3 PUFA modifies associations between SCD, SLC2A4, and SREBF1 polymorphisms and anthropometric variables and metabolic phenotypes. MATERIALS AND METHODS Anthropometric variables and metabolic phenotypes were measured in a cross-sectional sample of Yup'ik individuals (n = 1135) and 33 polymorphisms were tested for main effects and interactions using linear models that account for familial correlations. n-3 PUFA intake was estimated using red blood cell nitrogen stable isotope ratios. SCD polymorphisms were associated with ApoA1 concentration and n-3 PUFA interactions with SCD polymorphisms were associated with reduced fasting cholesterol levels and waist-to-hip ratio. SLC2A4 polymorphisms were associated with hip circumference, high-density lipoprotein and ApoA1 concentrations. SREBF1 polymorphisms were associated with low-density lipoprotein and HOMA-IR and n-3 PUFA interactions were associated with reduced fasting insulin and HOMA-IR levels. CONCLUSION The results suggest that an individual's genotype may interact with dietary n-3 PUFAs in ways that are associated with protection from obesity-related diseases in Yup'ik people.
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Affiliation(s)
- Dominick J Lemas
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA.,Department of Pediatrics, Section of Neonatology, University of Colorado Denver, Aurora, CO, USA
| | - Yann C Klimentidis
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Howard W Wiener
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Diane M O'Brien
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Scarlett E Hopkins
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Kimber L Stanhope
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA.,Department of Nutrition, University of California, Davis, CA, USA
| | - Peter J Havel
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA.,Department of Nutrition, University of California, Davis, CA, USA
| | - David B Allison
- Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.,Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, USA.,Office of Energetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jose R Fernandez
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, USA.,Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hemant K Tiwari
- Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Bert B Boyer
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
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An R, Yan H. Body weight status and telomere length in U.S. middle-aged and older adults. Obes Res Clin Pract 2016; 11:51-62. [PMID: 26895795 DOI: 10.1016/j.orcp.2016.01.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/08/2015] [Accepted: 01/30/2016] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Telomere length has been proposed as a biomarker of biological aging. This study examined the relationship between body weight status and telomere length in U.S. middle-aged and older adults. METHODS Nationally representative data (N=2749) came from the Health and Retirement Study. Linear regressions were performed to examine the relationship between baseline body weight status reported in 1992 and telomere length measured in 2008 in the overall sample and by sex and racial/ethnic groups, adjusted for individual characteristics. RESULTS Baseline overweight (25kg/m2≤body mass index [BMI]<30kg/m2) and obesity (BMI≥30kg/m2) status positively predicted telomere length 17 years later. Compared with their normal weight counterparts, telomere length ratio was on average 0.062 (95% confidence interval=0.016, 0.109) and 0.125 (0.048, 0.202) larger among overweight and obese adults, respectively. In comparison to women and racial/ethnic minorities, the estimated positive associations between overweight and obesity status and telomere length were more salient among men and non-Hispanic whites, respectively. CONCLUSIONS The positive association between body weight status and telomere length found in this study was opposite to what existing biological model predicts, and could partially relate to the nonlinear relationship between body weight status and telomere length across age cohorts, and/or the lack of reliability of BMI as an indicator for adiposity in the older population. Large-scale longitudinal studies with baseline telomere length measures are warranted to replicate this study finding and explore the potential heterogeneous relationship between body weight status and telomere length.
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Affiliation(s)
- Ruopeng An
- Department of Kinesiology and Community Health, College of Applied Health Sciences, University of Illinois at Urbana-Champaign, USA.
| | - Hai Yan
- Department of Kinesiology and Community Health, College of Applied Health Sciences, University of Illinois at Urbana-Champaign, USA
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Xie B, Li D, London SJ, Palmer PH, Johnshon CA, Li Y, Shih J, Bergen AW, Nishita D, Swan GE, Ahn R, Conti DV. Gender difference in interactions between MAOA promoter uVNTR polymorphism and negative familial stressors on body mass index among Chinese adolescents. Pediatr Obes 2014; 9:e80-90. [PMID: 23761378 PMCID: PMC4159439 DOI: 10.1111/j.2047-6310.2013.00181.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 03/07/2013] [Accepted: 04/29/2013] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Monoamine oxidase A (MAOA) modulates metabolism of serotonin and dopamine metabolism, neurotransmitters involved in regulation of appetite and food intake. The gene coding for MAOA contains a 30-bp tandem repeat (uVNTR) polymorphism in its promoter region that has been previously identified to be associated with obesity with mixed findings in the literature. Our goals were to replicate the population effects of this functional polymorphism on obesity risk, and to further explore gender differences and interaction effects with negative stressors. METHODS Analyses were conducted with data on genotypes, measured weight and height, and self-reported behavioural characteristics among 1101 Chinese adolescents 11-15 years old living in Wuhan, China. RESULTS Girls with the high-activity allele had significantly lower body mass index (BMI; β = -0.25 ± 0.98, P = 0.011) compared to those with the low activity allele. Experience of negative familial stressors (e.g., death or illness of family members, hit or scolded by parents and increased quarrelling with parents, parents argued frequently) significantly weakened this protective genetic effect on BMI (P for interaction = 0.043). Stratified analyses showed a significant protective genetic effect on BMI only within the stratum of low stress level (β = -0.44 ± 0.14, P = 0.002). No similar effect was observed among boys. CONCLUSIONS Our findings confirm the genetic effects of MAOA uVNTR polymorphism on BMI in a Chinese adolescent population and suggest potential genetic interactions with negative familial stressors.
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Affiliation(s)
- Bin Xie
- School of Community and Global Health, Claremont Graduate University, Claremont, CA 91711
| | - Dalin Li
- Medical Genetics Institute, Cedars-Sinai Medical Center/University of California at Los Angeles, Los Angeles, CA 90048
| | - Stephanie J. London
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709
| | - Paula H. Palmer
- School of Community and Global Health, Claremont Graduate University, Claremont, CA 91711
| | - C. Anderson Johnshon
- School of Community and Global Health, Claremont Graduate University, Claremont, CA 91711
| | - Yan Li
- Wuhan City Food and Drug Administration, Wuhan, P. R. China
| | - Jean Shih
- School of Pharmacy, University of Southern California, Los Angeles, CA 90089
| | - Andrew W. Bergen
- Center for Health Sciences, SRI International, Menlo Park, CA 94025
| | - Denise Nishita
- Center for Health Sciences, SRI International, Menlo Park, CA 94025
| | - Gary E. Swan
- Center for Health Sciences, SRI International, Menlo Park, CA 94025
| | - Rosa Ahn
- Joint Science Program, Scripps College, Claremont, CA 91711
| | - David V. Conti
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
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Coletta RRD, Jorge AAL, D'Alva CB, Pinto EM, Billerbeck AEC, Pachi PR, Longui CA, Garcia RM, Boguszewski M, Arnhold IJP, Mendonca BB, Costa EMF. Insulin-like growth factor 1 gene (CA)n repeats and a variable number of tandem repeats of the insulin gene in Brazilian children born small for gestational age. Clinics (Sao Paulo) 2013; 68:785-91. [PMID: 23778474 PMCID: PMC3674288 DOI: 10.6061/clinics/2013(06)10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 02/13/2013] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVE To investigate the influence of (CA)n repeats in the insulin-like growth factor 1 gene and a variable number of tandem repeats of the insulin gene on birth size in children who are small or adequate-sized for gestational age and to correlate these polymorphisms with serum insulin-like growth factor 1 levels and insulin sensitivity in children who are small for gestational age, with and without catch-up growth. PATIENTS AND METHODS We evaluated 439 infants: 297 that were adequate-sized for gestational age and 142 that were small for gestational age (66 with and 76 without catch-up). The number of (CA)n repeat in the insulin-like growth factor 1 gene and a variable number of tandem repeats in the insulin gene were analyzed using GENESCAN software and polymerase chain reaction followed by enzymatic digestion, respectively. Clinical and laboratory data were obtained from all patients. RESULTS The height, body mass index, paternal height, target height and insulin-like growth factor 1 serum levels were higher in children who were small for gestational age with catch-up. There was no difference in the allelic and genotypic distributions of both polymorphisms between the adequate-sized and small infants or among small infants with and without catch-up. Similarly, the polymorphisms were not associated with clinical or laboratory variables. CONCLUSION Polymorphisms of the (CA)n repeats of the insulin-like growth factor 1 gene and a variable number of tandem repeats of the insulin gene, separately or in combination, did not influence pre- or postnatal growth, insulin-like growth factor 1 serum levels or insulin resistance.
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Affiliation(s)
- Rocio R D Coletta
- Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormonios e Genetica Molecular LIM/42, São Paulo/SP, Brazil
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Yang BZ, Zhang H, Ge W, Weder N, Douglas-Palumberi H, Perepletchikova F, Gelernter J, Kaufman J. Child abuse and epigenetic mechanisms of disease risk. Am J Prev Med 2013; 44:101-7. [PMID: 23332324 PMCID: PMC3758252 DOI: 10.1016/j.amepre.2012.10.012] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 07/24/2012] [Accepted: 10/05/2012] [Indexed: 01/01/2023]
Abstract
BACKGROUND Child abuse is highly prevalent and associated with increased risk for a range of health problems, including cancer, cardiovascular disease, diabetes, psychiatric disorders, and other health problems. Little is currently known about the mechanism by which early adversity confers risk for health problems later in life. PURPOSE To determine if there are epigenetic differences associated with child maltreatment that may help explain association between adverse childhood experiences and later health problems. METHODS As part of a study examining genetic and environmental factors associated with depression, saliva DNA specimens were collected on 96 maltreated children removed from their parents due to abuse or neglect and 96 demographically matched control children between 2003 and 2010. In 2011, the Illumina 450K BeadChip was used on stored DNA specimens and analyzed to examine whole-genome methylation differences between maltreated and control children. RESULTS After controlling for multiple comparisons, maltreated and control children had significantly different methylation values at 2868 CpG sites (p<5.0 × 10(-7), all sites; average methylation difference per site=17%; range=1%-62%). The gene set contained numerous markers of diseases and biological processes related to the health problems associated with early childhood adversity. CONCLUSIONS Although replication is required, this study suggests that epigenetic mechanisms may be associated with risk for health problems later in life in maltreated children. This study lays the groundwork for future studies examining health and methylation measures to further characterize the role of epigenetic mechanisms in conferring risk for medical problems in individuals with histories of early adversity.
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Affiliation(s)
- Bao-Zhu Yang
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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Vazquez-Chantada M, Gonzalez-Lahera A, Martinez-Arranz I, Garcia-Monzon C, Regueiro MM, Garcia-Rodriguez JL, Schlangen KA, Mendibil I, Rodriguez-Ezpeleta N, Lozano JJ, Banasik K, Justesen JM, Joergensen T, Witte DR, Lauritzen T, Hansen T, Pedersen O, Veyrie N, Clement K, Tordjman J, Tran A, Le Marchand-Brustel Y, Buque X, Aspichueta P, Echevarria-Uraga JJ, Martin-Duce A, Caballeria J, Gual P, Castro A, Mato JM, Martinez-Chantar ML, Aransay AM. Solute carrier family 2 member 1 is involved in the development of nonalcoholic fatty liver disease. Hepatology 2013; 57:505-14. [PMID: 22961556 DOI: 10.1002/hep.26052] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 08/06/2012] [Indexed: 01/01/2023]
Abstract
UNLABELLED Susceptibility to develop nonalcoholic fatty liver disease (NAFLD) has genetic bases, but the associated variants are uncertain. The aim of the present study was to identify genetic variants that could help to prognose and further understand the genetics and development of NAFLD. Allele frequencies of 3,072 single-nucleotide polymorphisms (SNPs) in 92 genes were characterized in 69 NAFLD patients and 217 healthy individuals. The markers that showed significant allele-frequency differences in the pilot groups were subsequently studied in 451 NAFLD patients and 304 healthy controls. Besides this, 4,414 type 2 diabetes mellitus (T2DM) cases and 4,567 controls were genotyped. Liver expression of the associated gene was measured and the effect of its potential role was studied by silencing the gene in vitro. Whole genome expression, oxidative stress (OS), and the consequences of oleic acid (OA)-enriched medium on lipid accumulation in siSLC2A1-THLE2 cells were studied by gene-expression analysis, dihydroethidium staining, BODIPY, and quantification of intracellular triglyceride content, respectively. Several SNPs of SLC2A1 (solute carrier family 2 [facilitated glucose transporter] member 1) showed association with NAFLD, but not with T2DM, being the haplotype containing the minor allele of SLC2A1 sequence related to the susceptibility to develop NAFLD. Gene-expression analysis demonstrated a significant down-regulation of SLC2A1 in NAFLD livers. Enrichment functional analyses of transcriptome profiles drove us to demonstrate that in vitro silencing of SLC2A1 induces an increased OS activity and a higher lipid accumulation under OA treatment. CONCLUSIONS Genetic variants of SLC2A1 are associated with NAFLD, and in vitro down-regulation of this gene promotes lipid accumulation. Moreover, the oxidative response detected in siSLC2A1-THLE2 cells corroborated the antioxidant properties previously related to this gene and linked the most representative clinical characteristics of NAFLD patients: oxidative injury and increased lipid storage.
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Affiliation(s)
- Mercedes Vazquez-Chantada
- CIC bioGUNE, Centro de Investigación Biomédica en red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Spain
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Abstract
AbstractThe science of genetics is undergoing a paradigm shift. Recent discoveries, including the activity of retrotransposons, the extent of copy number variations, somatic and chromosomal mosaicism, and the nature of the epigenome as a regulator of DNA expressivity, are challenging a series of dogmas concerning the nature of the genome and the relationship between genotype and phenotype. According to three widely held dogmas, DNA is the unchanging template of heredity, is identical in all the cells and tissues of the body, and is the sole agent of inheritance. Rather than being an unchanging template, DNA appears subject to a good deal of environmentally induced change. Instead of identical DNA in all the cells of the body, somatic mosaicism appears to be the normal human condition. And DNA can no longer be considered the sole agent of inheritance. We now know that the epigenome, which regulates gene expressivity, can be inherited via the germline. These developments are particularly significant for behavior genetics for at least three reasons: First, epigenetic regulation, DNA variability, and somatic mosaicism appear to be particularly prevalent in the human brain and probably are involved in much of human behavior; second, they have important implications for the validity of heritability and gene association studies, the methodologies that largely define the discipline of behavior genetics; and third, they appear to play a critical role in development during the perinatal period and, in particular, in enabling phenotypic plasticity in offspring. I examine one of the central claims to emerge from the use of heritability studies in the behavioral sciences, the principle of minimal shared maternal effects, in light of the growing awareness that the maternal perinatal environment is a critical venue for the exercise of adaptive phenotypic plasticity. This consideration has important implications for both developmental and evolutionary biology.
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An R, Sturm R. School and residential neighborhood food environment and diet among California youth. Am J Prev Med 2012; 42:129-35. [PMID: 22261208 PMCID: PMC3298889 DOI: 10.1016/j.amepre.2011.10.012] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 08/25/2011] [Accepted: 10/20/2011] [Indexed: 11/24/2022]
Abstract
BACKGROUND Various hypotheses link neighborhood food environments and diet. Greater exposure to fast-food restaurants and convenience stores is thought to encourage overconsumption; supermarkets and large grocery stores are claimed to encourage healthier diets. For youth, empirical evidence for any particular hypothesis remains limited. PURPOSE This study examines the relationship between school and residential neighborhood food environment and diet among youth in California. METHODS Data from 8226 children (aged 5-11 years) and 5236 adolescents (aged 12-17 years) from the 2005 and 2007 California Health Interview Survey were analyzed in 2011. The dependent variables are daily servings of fruits, vegetables, juice, milk, soda, high-sugar foods, and fast food, which were regressed on measures of food environments. Food environments were measured by counts and density of businesses, distinguishing fast-food restaurants, convenience stores, small food stores, grocery stores, and large supermarkets within a specific distance (varying from 0.1 to 1.5 miles) from a respondent's home or school. RESULTS No robust relationship between food environment and consumption is found. A few significant results are sensitive to small modeling changes and more likely to reflect chance than true relationships. CONCLUSIONS This correlational study has measurement and design limitations. Longitudinal studies that can assess links between environmental, dependent, and intervening food purchase and consumption variables are needed. Reporting a full range of studies, methods, and results is important as a premature focus on correlations may lead policy astray.
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Affiliation(s)
- Ruopeng An
- RAND Corporation, Santa Monica, California, USA.
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12
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Lemas DJ, Wiener HW, O'Brien DM, Hopkins S, Stanhope KL, Havel PJ, Allison DB, Fernandez JR, Tiwari HK, Boyer BB. Genetic polymorphisms in carnitine palmitoyltransferase 1A gene are associated with variation in body composition and fasting lipid traits in Yup'ik Eskimos. J Lipid Res 2011; 53:175-84. [PMID: 22045927 DOI: 10.1194/jlr.p018952] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Variants of carnitine palmitoyltransferase 1A (CPT1A), a key hepatic lipid oxidation enzyme, may influence how fatty acid oxidation contributes to obesity and metabolic outcomes. CPT1A is regulated by diet, suggesting interactions between gene variants and diet may influence outcomes. The objective of this study was to test the association of CPT1A variants with body composition and lipids, mediated by consumption of polyunsaturated fatty acids (PUFA). Obesity phenotypes and fasting lipids were measured in a cross-sectional sample of Yup'ik Eskimo individuals (n = 1141) from the Center of Alaska Native Health Research (CANHR) study. Twenty-eight tagging CPT1A SNPs were evaluated with outcomes of interest in regression models accounting for family structure. Several CPT1A polymorphisms were associated with HDL-cholesterol and obesity phenotypes. The P479L (rs80356779) variant was associated with all obesity-related traits and fasting HDL-cholesterol. Interestingly, the association of P479L with HDL-cholesterol was still significant after correcting for body mass index (BMI), percentage body fat (PBF), or waist circumference (WC). Our findings are consistent with the hypothesis that the L479 allele of the CPT1A P479L variant confers a selective advantage that is both cardioprotective (through increased HDL-cholesterol) and associated with reduced adiposity.
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Affiliation(s)
- Dominick J Lemas
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
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Curran S, Bolton P, Rozsnyai K, Chiocchetti A, Klauck SM, Duketis E, Poustka F, Schlitt S, Freitag CM, Lee I, Muglia P, Poot M, Staal W, de Jonge MV, Ophoff RA, Lewis C, Skuse D, Mandy W, Vassos E, Fossdal R, Magnusson P, Hreidarsson S, Saemundsen E, Stefansson H, Stefansson K, Collier D. No association between a common single nucleotide polymorphism, rs4141463, in the MACROD2 gene and autism spectrum disorder. Am J Med Genet B Neuropsychiatr Genet 2011; 156B:633-9. [PMID: 21656903 DOI: 10.1002/ajmg.b.31201] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 04/25/2011] [Indexed: 01/23/2023]
Abstract
The Autism Genome Project (AGP) Consortium recently reported genome-wide significant association between autism and an intronic single nucleotide polymorphism marker, rs4141463, within the MACROD2 gene. In the present study we attempted to replicate this finding using an independent case-control design of 1,170 cases with autism spectrum disorder (ASD) (874 of which fulfilled narrow criteria for Autism (A)) from five centers within Europe (UK, Germany, the Netherlands, Italy, and Iceland), and 35,307 controls. The combined sample size gave us a non-centrality parameter (NCP) of 11.9, with 93% power to detect allelic association of rs4141463 at an alpha of 0.05 with odds ratio of 0.84 (the best odds ratio estimate of the AGP Consortium data), and for the narrow diagnosis of autism, an NCP of 8.9 and power of 85%. Our case-control data were analyzed for association, stratified by each center, and the summary statistics were combined using the meta-analysis program, GWAMA. This resulted in an odds ratio (OR) of 1.03 (95% CI 0.944-1.133), with a P-value of 0.5 for ASD and OR of 0.99 (95% CI 0.88-1.11) with P-value = 0.85 for the Autism (A) sub-group. Therefore, this study does not provide support for the reported association between rs4141463 and autism.
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Affiliation(s)
- Sarah Curran
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Kings College London, UK.
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14
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Association of 5-HTT gene polymorphisms with migraine: a systematic review and meta-analysis. J Neurol Sci 2011; 305:57-66. [PMID: 21450309 DOI: 10.1016/j.jns.2011.03.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 02/27/2011] [Accepted: 03/07/2011] [Indexed: 12/13/2022]
Abstract
BACKGROUND/AIMS Serotonin is known to play an important role in the pathogenesis of migraine, but individual genetic association studies that examine the relationship between polymorphisms of serotonin transporter (5-HTT) gene and migraine have yielded inconsistent results. This study aimed to evaluate the association between 5-HTT gene variants (including 5-HTTLPR, VNTR and SNP) and migraine using systematic review with meta-analysis. METHODS Relevant studies were identified by searching English and Chinese databases extensively. Allele and genotype frequencies for each included study were extracted. The odds ratio (OR) was calculated using a random-effects or fixed-effects model. Q statistic was used to evaluate homogeneity, and Egger's test and Funnel plot were used to assess publication bias. For family-based association studies, a descriptive analysis was carried out. RESULTS A total of 15 studies were identified for meta-analysis. It was found that the 5-HTT VNTR Stin2.12 allele or 12/12 genotype had an increased risk for migraine in the general population (Stin2.12 allele: OR, 95% CI: 1.34, 1.09-1.64, p=0.006; 12/12 genotype: OR, 95% CI: 1.55, 1.17-2.05, p=0.002), but there was no significant association between migraine and 5-HTTLPR or SNP rs2020942. CONCLUSIONS Existing evidence indicates that the 5-HTT VNTR polymorphism (mainly the STin2.12 genotype) is associated with an increased risk of migraine in the general population. Future studies with larger sample sizes will be necessary to confirm the present results.
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Milet J, Le Gac G, Scotet V, Gourlaouen I, Thèze C, Mosser J, Bourgain C, Deugnier Y, Férec C. A common SNP near BMP2 is associated with severity of the iron burden in HFE p.C282Y homozygous patients: A follow-up study. Blood Cells Mol Dis 2010; 44:34-7. [DOI: 10.1016/j.bcmd.2009.10.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Accepted: 09/23/2009] [Indexed: 12/29/2022]
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van Vliet-Ostaptchouk JV, Hofker MH, van der Schouw YT, Wijmenga C, Onland-Moret NC. Genetic variation in the hypothalamic pathways and its role on obesity. Obes Rev 2009; 10:593-609. [PMID: 19712437 DOI: 10.1111/j.1467-789x.2009.00597.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Over recent decades, the prevalence of obesity has increased dramatically worldwide. Although this epidemic is mainly attributable to modern (western) lifestyle, multiple twin and adoption studies indicate the significant role of genes in the individual's predisposition to becoming obese. As the hypothalamus plays a central role in controlling body weight, its regulatory circuits may represent a crucial system in the pathogenesis of the disorder. Genetic variations in genes in the hypothalamic pathways may therefore contribute to the susceptibility for obesity in humans and animals. We summarize current knowledge on the physiological role of the hypothalamus in body-weight regulation and review genetic studies on the hypothalamic candidate genes in relation to obesity. Together, data from functional and genetic studies as well as the new, common, obesity loci identified in genome-wide association scans support an important role for the hypothalamic genes in predisposing to obesity. However, findings are still inconclusive for many candidate genes. To improve our understanding of the genetic architecture of common obesity, we suggest that specific obesity phenotypes should be considered and different analytical approaches used. Such studies should consider multiple genes from the same physiological pathways, together with environmental risk factors.
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Affiliation(s)
- J V van Vliet-Ostaptchouk
- Molecular Genetics, Medical Biology Section, Department of Pathology and Medical Biology, University Medical Center and University of Groningen, Groningen, the Netherlands.
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Rosenberg NA, Vanliere JM. Replication of genetic associations as pseudoreplication due to shared genealogy. Genet Epidemiol 2009; 33:479-87. [PMID: 19191270 DOI: 10.1002/gepi.20400] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The genotypes of individuals in replicate genetic association studies have some level of correlation due to shared descent in the complete pedigree of all living humans. As a result of this genealogical sharing, replicate studies that search for genotype-phenotype associations using linkage disequilibrium between marker loci and disease-susceptibility loci can be considered as "pseudoreplicates" rather than true replicates. We examine the size of the pseudoreplication effect in association studies simulated from evolutionary models of the history of a population, evaluating the excess probability that both of a pair of studies detect a disease association compared to the probability expected under the assumption that the two studies are independent. Each of nine combinations of a demographic model and a penetrance model leads to a detectable pseudoreplication effect, suggesting that the degree of support that can be attributed to a replicated genetic association result is less than that which can be attributed to a replicated result in a context of true independence.
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Affiliation(s)
- Noah A Rosenberg
- Department of Human Genetics, Center for Computational Medicine and Biology, and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109-2218, USA.
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Peeters A, Beckers S, Verrijken A, Mertens I, Van Gaal L, Van Hul W. Possible role for ENPP1 polymorphism in obesity but not for INSIG2 and PLIN variants. Endocrine 2009; 36:103-9. [PMID: 19399648 DOI: 10.1007/s12020-009-9194-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 03/13/2009] [Accepted: 04/01/2009] [Indexed: 10/20/2022]
Abstract
Previous studies have suggested that ENPP1, INSIG2, and PLIN may be linked with a higher risk for obesity or with increased phenotypic measures of obesity. We selected polymorphisms in these candidate genes based on their prior associations with obesity risk or obesity parameters. K121Q (rs1044498) in ENPP1, rs7566605 in INSIG2, and rs894160 in PLIN were genotyped by Taqman assays in a Belgian sample of 1,078 obese subjects (body mass index (BMI) > 30 kg/m(2)) and 323 lean controls (18.5 < BMI < 25 kg/m(2)). BMI, waist circumference, and waist-to-hip ratio (WHR) were assessed by standard methods while a computerized tomography-scan was used to measure visceral (VFA), subcutaneous (SFA), and total (TFA) abdominal fat areas. Presence of the rare allele was not significantly different between cases and controls for the three variants that were tested, while only WHR was associated with ENPP1 in obese subjects. Our data thus indicate that K121Q, rs7566605, and rs894160 are not major contributing factors for obesity.
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Affiliation(s)
- Armand Peeters
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, 2610, Antwerp, Belgium.
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Neale BM, Faraone SV. Perspective on the genetics of attention deficit/hyperactivity disorder. Am J Med Genet B Neuropsychiatr Genet 2008; 147B:1334-6. [PMID: 18951432 DOI: 10.1002/ajmg.b.30875] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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20
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Different allelic distribution of a single SNP between sexes in humans. Biochem Genet 2008; 46:733-6. [PMID: 18777093 DOI: 10.1007/s10528-008-9188-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 05/23/2008] [Indexed: 10/21/2022]
Abstract
We searched for a difference in allele distribution between males and females of a single nucleotide polymorphism located in the human beta T-cell receptor, in 500 subjects (200 males and 300 females). Genotype analysis gave the following results: among the males, 114 (57%) were heterozygous for the T/C polymorphism, 52 (26%) were homozygous (T/T), and 34 (17%) were homozygous (C/C). Among the females, 142 (47.3%) were heterozygous, 73 (24.3%) were homozygous (T/T), and 85 (28.3%) were homozygous (C/C). The allele frequency was significantly different between sexes (chi2 = 8.799, P = 0.012).
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Golembesky AK, Gammon MD, North KE, Bensen JT, Schroeder JC, Teitelbaum SL, Neugut AI, Santella RM. Peroxisome proliferator-activated receptor-alpha (PPARA) genetic polymorphisms and breast cancer risk: a Long Island ancillary study. Carcinogenesis 2008; 29:1944-9. [PMID: 18586686 DOI: 10.1093/carcin/bgn154] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Peroxisome proliferator-activated receptor-alpha (PPARA) has been shown to increase fatty acid oxidation and decrease cytokine levels and has been implicated in insulin production. Genetic variants of PPARA have been associated with cardiovascular disease, obesity and type II diabetes mellitus. Although no research to date has investigated the possible link between PPARA and breast cancer, the function of this gene suggests that it could play a role in breast cancer development. Six PPARA polymorphisms were evaluated in association with incident breast cancer in a population-based case-control study (n = 1073 cases and n = 1112 controls) using unconditional logistic and multilevel regression and haplotype-based analyses. The odds of breast cancer were doubled among women with PPARA polymorphism rs4253760 (odds ratio = 1.97 for rare versus common homozygote alleles; 95% confidence interval: 1.14, 3.43). This association remained constant with the inclusion of all interrogated polymorphisms studied in hierarchical models. No additive interactions with body mass index or weight gain were present, but there was some evidence of interaction between PPARA variants and aspirin use, defined as use at least once per week for 6 months or longer. Fourteen haplotypes were imputed with frequencies >1% among postmenopausal women, but no statistically significant differences in haplotype frequencies between cases and controls were evident. Our results are the first to evaluate the relationship between PPARA and breast cancer incidence and suggest that replication in an independent cohort is warranted.
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Affiliation(s)
- Amanda K Golembesky
- Department of Epidemiology, School of Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.
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Kalra M, Chakraborty R. Leptin and Leptin Receptor Gene Polymorphisms in Obstructive Sleep Apnea Syndrome. Chest 2008. [DOI: 10.1378/chest.08-0294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Genome-wide association studies: progress and potential for drug discovery and development. Nat Rev Drug Discov 2008; 7:221-30. [PMID: 18274536 DOI: 10.1038/nrd2519] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Although genetic studies have been critically important for the identification of therapeutic targets in Mendelian disorders, genetic approaches aiming to identify targets for common, complex diseases have traditionally had much more limited success. However, during the past year, a novel genetic approach - genome-wide association (GWA) - has demonstrated its potential to identify common genetic variants associated with complex diseases such as diabetes, inflammatory bowel disease and cancer. Here, we highlight some of these recent successes, and discuss the potential for GWA studies to identify novel therapeutic targets and genetic biomarkers that will be useful for drug discovery, patient selection and stratification in common diseases.
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Windemuth A, Calhoun VD, Pearlson GD, Kocherla M, Jagannathan K, Ruaño G. Physiogenomic analysis of localized FMRI brain activity in schizophrenia. Ann Biomed Eng 2008; 36:877-88. [PMID: 18330705 DOI: 10.1007/s10439-008-9475-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Accepted: 02/15/2008] [Indexed: 11/29/2022]
Abstract
The search for genetic factors associated with disease is complicated by the complexity of the biological pathways linking genotype and phenotype. This analytical complexity is particularly concerning in diseases historically lacking reliable diagnostic biological markers, such as schizophrenia and other mental disorders. We investigate the use of functional magnetic resonance imaging (fMRI) as an intermediate phenotype (endophenotype) to identify physiogenomic associations to schizophrenia. We screened 99 subjects, 30 subjects diagnosed with schizophrenia, 13 unaffected relatives of schizophrenia patients, and 56 unrelated controls, for gene polymorphisms associated with fMRI activation patterns at two locations in temporal and frontal lobes previously implied in schizophrenia. A total of 22 single nucleotide polymorphisms (SNPs) in 15 genes from the dopamine and serotonin neurotransmission pathways were genotyped in all subjects. We identified three SNPs in genes that are significantly associated with fMRI activity. SNPs of the dopamine beta-hydroxylase (DBH) gene and of the dopamine receptor D4 (DRD4) were associated with activity in the temporal and frontal lobes, respectively. One SNP of serotonin-3A receptor (HTR3A) was associated with temporal lobe activity. The results of this study support the physiogenomic analysis of neuroimaging data to discover associations between genotype and disease-related phenotypes.
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Sinsheimer JS, Plaisier CL, Huertas-Vazquez A, Aguilar-Salinas C, Tusie-Luna T, Pajukanta P, Lange K. Estimating ethnic admixture from pedigree data. Am J Hum Genet 2008; 82:748-55. [PMID: 18319077 DOI: 10.1016/j.ajhg.2007.12.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Revised: 10/01/2007] [Accepted: 12/11/2007] [Indexed: 12/26/2022] Open
Abstract
This paper introduces a likelihood method of estimating ethnic admixture that uses individuals, pedigrees, or a combination of individuals and pedigrees. For each founder of a pedigree, admixture proportions are calculated by conditioning on the pedigree-wide genotypes at all ancestry-informative markers. These estimates are then propagated down the pedigree to the nonfounders by a simple averaging process. The large-sample standard errors of the founders' proportions can be similarly transformed into standard errors for the admixture proportions of the descendants. These standard errors are smaller than the corresponding standard errors when each individual is treated independently. Both hard and soft information on a founder's ancestry can be accommodated in this scheme, which has been implemented in the genetic software package Mendel. The utility of the method is demonstrated on simulated data and a real data example involving Mexican families of mixed Amerindian and Spanish ancestry.
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26
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Tripputi P, Bianchi S, Fedele L. A possible mechanism for non-replication of allelic association between a single nucleotide polymorphism of the human beta T-cell receptor and autoimmune diseases. Int J Immunogenet 2008; 35:141-4. [PMID: 18279372 DOI: 10.1111/j.1744-313x.2008.00751.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gene polymorphisms, in particular single nucleotide polymorphisms (SNPs), have been associated to multifactorial diseases such as cancer, inflammation and autoimmunity. Indeed for some autoimmune diseases, it has been possible to identify critical residues that play a major role in susceptibility to diseases. The association of a common T/C polymorphism in the promoter region of the beta 2 constant chain of the T-cell receptor with autoimmune diseases, such as insulin-dependent diabetes, autoimmune hepatitis, IgA nephropathy, membranous nephropathy, Graves' disease and Hashimoto's thyroiditis, was described in the 1990 s. These reports have not been confirmed in the last few years. We also failed in a previous study to detect any difference between 70 normal subjects and 70 patients with primary biliary cirrhosis; however, we found a difference in allelic frequency between males and females. This finding led us to make an allele frequency study of this single nucleotide polymorphism between sexes in a new series of patients. We studied 165 subjects, 80 males and 85 females, and we found a significant difference between sexes especially for the CC homozygous genotype: 34% of females vs. 14% of males (P = 0.008). If the higher frequency of CC homozygous genotype (that is associated with an increased risk of autoimmune diseases) in females would be confirmed in normal population, this could be an explanation of the controversial results obtained by association studies made between this SNP and autoimmune diseases.
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Affiliation(s)
- P Tripputi
- Department of Medicine, Surgery and Dentistry, University of Milan, Milan, Italy.
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Fuemmeler BF, Agurs-Collins TD, McClernon FJ, Kollins SH, Kail ME, Bergen AW, Ashley-Koch AE. Genes implicated in serotonergic and dopaminergic functioning predict BMI categories. Obesity (Silver Spring) 2008; 16:348-55. [PMID: 18239643 PMCID: PMC2919156 DOI: 10.1038/oby.2007.65] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE This study addressed the hypothesis that variation in genes associated with dopamine function (SLC6A3, DRD2, DRD4), serotonin function (SLC6A4, and regulation of monoamine levels (MAOA) may be predictive of BMI categories (obese and overweight + obese) in young adulthood and of changes in BMI as adolescents transition into young adulthood. Interactions with gender and race/ethnicity were also examined. METHODS AND PROCEDURES Participants were a subsample of individuals from the National Longitudinal Study of Adolescent Health (Add Health), a nationally representative sample of adolescents followed from 1995 to 2002. The sample analyzed included a subset of 1,584 unrelated individuals with genotype data. Multiple logistic regressions were conducted to evaluate the associations between genotypes and obesity (BMI > 29.9) or overweight + obese combined (BMI > or = 25) with normal weight (BMI = 18.5-24.9) as a referent. Linear regression models were used to examine change in BMI from adolescence to young adulthood. RESULTS Significant associations were found between SLC6A4 5HTTLPR and categories of BMI, and between MAOA promoter variable number tandem repeat (VNTR) among men and categories of BMI. Stratified analyses revealed that the association between these two genes and excess BMI was significant for men overall and for white and Hispanic men specifically. Linear regression models indicated a significant effect of SLC6A4 5HTTLPR on change in BMI from adolescence to young adulthood. DISCUSSION Our findings lend further support to the involvement of genes implicated in dopamine and serotonin regulation on energy balance.
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Affiliation(s)
- Bernard F Fuemmeler
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC, USA.
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Required sample size and nonreplicability thresholds for heterogeneous genetic associations. Proc Natl Acad Sci U S A 2008; 105:617-22. [PMID: 18174335 DOI: 10.1073/pnas.0705554105] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Many gene-disease associations proposed to date have not been consistently replicated across different populations. Nonreplication often reflects false positives in the original claims. However, occasionally, nonreplication may be due to heterogeneity due to biases or even genuine diversity of the genetic effects in different populations. Here, we propose methods for estimating the required sample size to replicate an association across many studies with different amounts of between-study heterogeneity, when data are summarized through metaanalysis. We demonstrate thresholds of between-study heterogeneity (tau(0)(2)) above which one cannot reach adequate power to replicate a proposed association at a specified level of statistical significance when k studies are performed (regardless of how large these studies are). Based on empirical evidence from 91 proposed gene-disease associations (50 on candidate genes and 41 from genome-wide association efforts), the observed between-study heterogeneity is often close to or even surpasses nonreplicability thresholds. With more modest between-study heterogeneity, the required sample size increases considerably compared with when no between-study heterogeneity exists. Increases are steep as tau(0)(2) is approached. Therefore, some true associations may not be practically possible to replicate with consistency, no matter how large studies are conducted. Efforts should be made to minimize between-study heterogeneity in targeted genetic effects.
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Lack of association of VDR gene polymorphisms with thyroid autoimmune disorders: familial and case/control studies. J Clin Immunol 2007; 28:21-5. [PMID: 17943423 DOI: 10.1007/s10875-007-9124-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 07/31/2007] [Indexed: 12/31/2022]
Abstract
We study the association between three Vitamin D receptor gene polymorphisms (rs10735810, rs1544410, rs731236) and susceptibility to thyroid autoimmune diseases. Seventy-six affected subjects, belonging to a large family, as well as one hundred unrelated Tunisian patients and one hundred healthy Tunisian controls were genotyped. A family-based association test and a standard chi-square test were used to assess association in family and case-control data, respectively. Our results showed no significant association of the Vitamin D receptor gene polymorphisms with the susceptibility to thyroid autoimmune diseases in the family. Moreover, allele frequencies for the three polymorphisms in the Tunisian population were similar to those reported in the Tunisian control population and none was associated with the disease. These results suggest a lack of association between the Vitamin D receptor gene polymorphisms and susceptibility to thyroid autoimmune diseases in Tunisian population, in agreement with data from the UK, but in conflict with studies from the Far East.
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De Cosmo S, Prudente S, Andreozzi F, Morini E, Rauseo A, Scarpelli D, Zhang YY, Xu R, Perticone F, Dallapiccola B, Sesti G, Doria A, Trischitta V. Glutamine to Arginine Substitution at Amino Acid 84 of Mammalian Tribbles Homolog TRIB3 and CKD in Whites With Type 2 Diabetes. Am J Kidney Dis 2007; 50:688-9. [PMID: 17900474 DOI: 10.1053/j.ajkd.2007.06.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Accepted: 06/18/2007] [Indexed: 11/11/2022]
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Abstract
While the authors agree with John Ioannidis that "most research findings are false," here they show that replication of research findings enhances the positive predictive value of research findings being true.
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Affiliation(s)
- Ramal Moonesinghe
- National Office of Public Health Genomics, Coordinating Center for Health Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.
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González-Martínez SC, Wheeler NC, Ersoz E, Nelson CD, Neale DB. Association genetics in Pinus taeda L. I. Wood property traits. Genetics 2007; 175:399-409. [PMID: 17110498 PMCID: PMC1775017 DOI: 10.1534/genetics.106.061127] [Citation(s) in RCA: 164] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2006] [Accepted: 10/26/2006] [Indexed: 11/18/2022] Open
Abstract
Genetic association is a powerful method for dissecting complex adaptive traits due to (i) fine-scale mapping resulting from historical recombination, (ii) wide coverage of phenotypic and genotypic variation within a single experiment, and (iii) the simultaneous discovery of loci and alleles. In this article, genetic association among single nucleotide polymorphisms (58 SNPs) from 20 wood- and drought-related candidate genes and an array of wood property traits with evolutionary and commercial importance, namely, earlywood and latewood specific gravity, percentage of latewood, earlywood microfibril angle, and wood chemistry (lignin and cellulose content), was tested using mixed linear models (MLMs) that account for relatedness among individuals by using a pairwise kinship matrix. Population structure, a common systematic bias in association studies, was assessed using 22 nuclear microsatellites. Different phenotype:genotype associations were found, some of them confirming previous evidence from collocation of QTL and genes in linkage maps (for example, 4cl and percentage of latewood) and two that involve nonsynonymous polymorphisms (cad SNP M28 with earlywood specific gravity and 4cl SNP M7 with percentage of latewood). The strongest genetic association found in this study was between allelic variation in alpha-tubulin, a gene involved in the formation of cortical microtubules, and earlywood microfibril angle. Intragenic LD decays rapidly in conifers; thus SNPs showing genetic association are likely to be located in close proximity to the causative polymorphisms. This first multigene association genetic study in forest trees has shown the feasibility of candidate gene strategies for dissecting complex adaptive traits, provided that genes belonging to key pathways and appropriate statistical tools are used. This approach is of particular utility in species such as conifers, where genomewide strategies are limited by their large genomes.
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Santos JL, Boutin P, Verdich C, Holst C, Larsen LH, Toubro S, Dina C, Saris WHM, Blaak EE, Hoffstedt J, Taylor MA, Polak J, Clement K, Langin D, Astrup A, Froguel P, Pedersen O, Sorensen TIA, Martinez JA. Genotype-by-nutrient interactions assessed in European obese women. A case-only study. Eur J Nutr 2006; 45:454-62. [PMID: 17080261 DOI: 10.1007/s00394-006-0619-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Accepted: 08/29/2006] [Indexed: 01/12/2023]
Abstract
BACKGROUND The development of obesity is influenced by both genetic and environmental risk factors. Whereas changes in the environment appear to be responsible for the increasing prevalence of obesity, genetic factors interacting with environmental factors would contribute to explain obesity onset and severity. AIM To explore epidemiologic genotype-by-nutrient interactions in obesity. METHODS A total of 42 polymorphisms of 26 candidate genes for obesity were genotyped in 549 adult obese women recruited from eight European centres in a case-only study. The nutritional variables assessed in this study were the dietary fibre intake (grams per day), the ratio of dietary polyunsaturated fat to saturated fat (P:S ratio) and the percentage of energy derived from fat in the diet as calculated from a weighed three-day food record (%E). Under the assumption of genotype-nutrient independence in the population, the odds ratio calculated in a sample of obese women would indicate the existence of genotype-by-nutrient interactions, measured as deviations from the multiplicative effects of the genetic and the nutrient factors separately. RESULTS No new but confirmaty evidences for genotype-by-nutrient interactions in obesity were detected in this case-only study. The test of interaction between fibre intake and the -514 C > T polymorphism of the hepatic lipase gene (LIPC) yielded P-values of 0.01 across different statistical models. Likewise, the -11377G > C polymorphism of the adiponectin gene (ADIPOQ) and the -681 C > G polymorphism of the PPARG3 gene might interact with the percentage of energy derived from fat in the diet for the development of obesity (P-values in the range of 0.01-0.05 across different statistical models). The P-values were not adjusted for multiple testing, so these results should be considered with caution. CONCLUSIONS Although the use of obese-only samples is theoretically a useful approach to detect interactions, few genotype-by-nutrient interactions have been suggested in obese European women after the analysis of candidate polymorphisms and the selected nutrient variables. The most remarkable multiplicative interaction found in this study refers to the combination of the hepatic lipase gene polymorphism -514 C > T and fibre intake.
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Affiliation(s)
- Jose L Santos
- Dept. of Physiology and Nutrition, University of Navarra, 31008, Pamplona, Spain
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Rodríguez S, Gaunt TR, Dennison E, Chen XH, Syddall HE, Phillips DIW, Cooper C, Day INM. Replication of IGF2-INS-TH*5 haplotype effect on obesity in older men and study of related phenotypes. Eur J Hum Genet 2006; 14:109-16. [PMID: 16251897 DOI: 10.1038/sj.ejhg.5201505] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Interindividual variation of the IGF2-INS-TH region influences risk of a variety of diseases and complex traits. Previous studies identified a haplotype (designated IGF2-INS-TH(*)5 and tagged by allele A of IGF2 ApaI, allele 9 of TH01 and class I alleles of INS VNTR) associated with low body mass index (BMI) in a cohort of UK men. We aimed here both to study whether previous findings relating (*)5 with weight are replicated in a different cohort of men (East Hertfordshire) characterised in more phenotypic detail and to test the effect of this haplotype on related subphenotypes. The PHASE program was used to identify (*)5 and not(*)5 haplotypes. A total of 490 haplotypes were derived from 131 men and 114 women, the frequency of (*)5 being around 9%. Specific tests of (*)5 haplotype (vs not(*)5 haplotypes) conducted included Student's t-test and multiple regression analyses. We observed replication of weight effect for the (*)5 haplotype in men: significant associations with lower BMI (-1.81 kg/m(2), P=0.009), lower waist circumference (-6.3 cm, P=0.001) and lower waist-hip ratio (-5%, P<0.001). This haplotype also marks nearly two-fold lower 120 min insulin (P=0.004) as well as low baseline insulin (-11.02 pmol/l, P=0.043) and low 30 min insulin (-64.44 pmol/l, P=0.072) in a glucose tolerance test. No association between (*)5 and these traits was found in women. Our results, taken together with other data on IGFII levels and TH activity, point to the importance of (*)5 as an integrated polygenic haplotype relevant to obesity and insulin response to glucose in men.
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Affiliation(s)
- Santiago Rodríguez
- Human Genetics Division, University of Southampton, School of Medicine, Southampton General Hospital, Southampton, UK
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Nobuhara Y, Usuku K, Saito M, Izumo S, Arimura K, Bangham CRM, Osame M. Genetic variability in the extracellular matrix protein as a determinant of risk for developing HTLV-I-associated neurological disease. Immunogenetics 2006; 57:944-52. [PMID: 16402214 DOI: 10.1007/s00251-005-0075-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Accepted: 12/04/2005] [Indexed: 10/25/2022]
Abstract
Aggrecan, which is a well-known proteoglycan in joint cartilage, also exists in the spinal cord and plays an important role in maintaining water content in the extracellular matrix structure. In this study, we first examined the variable number of tandem repeat (VNTR) polymorphism of the aggrecan gene in 227 HTLV-I associated myelopathy/tropical spastic paraparesis (HAM/TSP) patients, in 217 HTLV-I-infected healthy carriers (HCs), and in 85 normal controls. The VNTR allele 28 (1,630 bp) was more frequently observed in HAM/TSP patients than in HCs (chi2=12.02, p=0.0005, odds ratio 1.79, 95% C.I. 1.29-2.50) and in controls (chi2=13.43, p=0.0002, odds ratio 2.54, 95% C.I. 1.52-4.25), although this allele was not related to disease progression or to HTLV-I provirus load. We also found that the aggrecan concentration in cerebrospinal fluid (CSF) from rapidly progressive HAM/TSP patients was significantly higher than in slowly progressive patients (corrected p=0.0145) but not in infected non-inflammatory neurological other disease controls (OND) (corrected p=0.078). We then analyzed this aggrecan VNTR polymorphism in the different set of patients with HAM/TSP (n=58) and healthy carriers (n=70). This analysis, again, revealed that allele 28 was detected more frequently in HAM/TSP group than in HCs (chi2=11.03, p=0.0009, odd ratio 3.04, 95% C.I. 1.55-5.97). The reproducibility of our study was regarded as a second- or third-class association by comparing combined p values and the Better Associations for Disease and GEnes (BADGE) system. Our results suggest that aggrecan polymorphism can be a novel genetic risk factor for developing HAM/TSP.
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Affiliation(s)
- Yasuyuki Nobuhara
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
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Heiman GA, Hodge SE, Gorroochurn P, Zhang J, Greenberg DA. Effect of population stratification on case-control association studies. I. Elevation in false positive rates and comparison to confounding risk ratios (a simulation study). Hum Hered 2005; 58:30-9. [PMID: 15604562 DOI: 10.1159/000081454] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2004] [Accepted: 08/06/2004] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES This is the first of two articles discussing the effect of population stratification on the type I error rate (i.e., false positive rate). This paper focuses on the confounding risk ratio (CRR). It is accepted that population stratification (PS) can produce false positive results in case-control genetic association. However, which values of population parameters lead to an increase in type I error rate is unknown. Some believe PS does not represent a serious concern, whereas others believe that PS may contribute to contradictory findings in genetic association. We used computer simulations to estimate the effect of PS on type I error rate over a wide range of disease frequencies and marker allele frequencies, and we compared the observed type I error rate to the magnitude of the confounding risk ratio. METHODS We simulated two populations and mixed them to produce a combined population, specifying 160 different combinations of input parameters (disease prevalences and marker allele frequencies in the two populations). From the combined populations, we selected 5000 case-control datasets, each with either 50, 100, or 300 cases and controls, and determined the type I error rate. In all simulations, the marker allele and disease were independent (i.e., no association). RESULTS The type I error rate is not substantially affected by changes in the disease prevalence per se. We found that the CRR provides a relatively poor indicator of the magnitude of the increase in type I error rate. We also derived a simple mathematical quantity, Delta, that is highly correlated with the type I error rate. In the companion article (part II, in this issue), we extend this work to multiple subpopulations and unequal sampling proportions. CONCLUSION Based on these results, realistic combinations of disease prevalences and marker allele frequencies can substantially increase the probability of finding false evidence of marker disease associations. Furthermore, the CRR does not indicate when this will occur.
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Affiliation(s)
- Gary A Heiman
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.
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Abstract
Genetic association studies are central to efforts to identify and characterise genomic variants underlying susceptibility to multifactorial disease. However, obtaining robust replication of initial association findings has proved difficult. Much of this inconsistency can be attributed to inadequacies in study design, implementation, and interpretation--inadequately powered sample groups are a major concern. Several additional factors affect the quality of any given association study, with appropriate sample-recruitment strategy, logical variant selection, minimum genotyping error, relevant data analysis, and valid interpretation all essential to generation of robust findings. Replication has a vital role in showing that associations that are identified reflect interesting biological processes rather than methodological quirks. For an unbiased view of the evidence for and against any particular association, study quality, rather than significance value, needs to play the dominant part.
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Affiliation(s)
- Andrew T Hattersley
- Institute of Biomedical and Clinical Science, Peninsula Medical School, Exeter, UK
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Redden DT, Shields PG, Epstein L, Wileyto EP, Zakharkin SO, Allison DB, Lerman C. Catechol-O-methyl-transferase functional polymorphism and nicotine dependence: an evaluation of nonreplicated results. Cancer Epidemiol Biomarkers Prev 2005; 14:1384-9. [PMID: 15941945 DOI: 10.1158/1055-9965.epi-04-0649] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Review articles have focused attention on and cited possible reasons for the nonreplication of genetic association studies. Herein, we illustrate how one might work through these possible reasons to make a judgment about the most plausible reason(s) when faced with two or more studies which yield seemingly inconsistent results. In the first study, 342 treatment-seeking smokers were genotyped for the Val108Met polymorphism in the functional catechol-O-methyl-transferase (COMT) locus. Alleles coding Val at codon 108 are denoted as H and those coding Met are denoted as L. An association between presence of the "H" (high activity) allele and pretreatment level of nicotine dependence level using the Fagerstrom Test for Nicotine Dependence was detected (P = 0.0072), after controlling for baseline body mass index (BMI, kg/m2), depression symptoms, and age. To validate this initial finding, 443 treatment-seeking smokers from an independent smoking cessation clinical trial were genotyped for the COMT polymorphism. Within the second study, no association between presence of the "H" allele and nicotine dependence was detected (P = 0.6418) after controlling for baseline BMI, depression symptoms, and age. We critically reviewed both studies with regard to often cited reasons for nonreplication, including type I error, population stratification, low statistical power, and imprecise measures of phenotype. Although in our opinion the failure to replicate the initial association in the second study is likely either the result of low statistical power to detect a small effect or effect heterogeneity, thorough analyses failed to definitively identify the reason for nonreplication.
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Affiliation(s)
- David T Redden
- Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Alabama 35294-0022, USA.
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Swarbrick MM, Waldenmaier B, Pennacchio LA, Lind DL, Cavazos MM, Geller F, Merriman R, Ustaszewska A, Malloy M, Scherag A, Hsueh WC, Rief W, Mauvais-Jarvis F, Pullinger CR, Kane JP, Dent R, McPherson R, Kwok PY, Hinney A, Hebebrand J, Vaisse C. Lack of support for the association between GAD2 polymorphisms and severe human obesity. PLoS Biol 2005; 3:e315. [PMID: 16122350 PMCID: PMC1193520 DOI: 10.1371/journal.pbio.0030315] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Accepted: 07/11/2005] [Indexed: 12/28/2022] Open
Abstract
The demonstration of association between common genetic variants and chronic human diseases such as obesity could have profound implications for the prediction, prevention, and treatment of these conditions. Unequivocal proof of such an association, however, requires independent replication of initial positive findings. Recently, three (−243 A>G, +61450 C>A, and +83897 T>A) single nucleotide polymorphisms (SNPs) within glutamate decarboxylase 2 (GAD2) were found to be associated with class III obesity (body mass index > 40 kg/m2). The association was observed among 188 families (612 individuals) segregating the condition, and a case-control study of 575 cases and 646 lean controls. Functional data supporting a pathophysiological role for one of the SNPs (−243 A>G) were also presented. The gene GAD2 encodes the 65-kDa subunit of glutamic acid decarboxylase—GAD65. In the present study, we attempted to replicate this association in larger groups of individuals, and to extend the functional studies of the −243 A>G SNP. Among 2,359 individuals comprising 693 German nuclear families with severe, early-onset obesity, we found no evidence for a relationship between the three GAD2 SNPs and obesity, whether SNPs were studied individually or as haplotypes. In two independent case-control studies (a total of 680 class III obesity cases and 1,186 lean controls), there was no significant relationship between the −243 A>G SNP and obesity (OR = 0.99, 95% CI 0.83–1.18, p = 0.89) in the pooled sample. These negative findings were recapitulated in a meta-analysis, incorporating all published data for the association between the −243G allele and class III obesity, which yielded an OR of 1.11 (95% CI 0.90–1.36, p = 0.28) in a total sample of 1,252 class III obese cases and 1,800 lean controls. Moreover, analysis of common haplotypes encompassing the GAD2 locus revealed no association with severe obesity in families with the condition. We also obtained functional data for the −243 A>G SNP that does not support a pathophysiological role for this variant in obesity. Potential confounding variables in association studies involving common variants and complex diseases (low power to detect modest genetic effects, overinterpretation of marginal data, population stratification, and biological plausibility) are also discussed in the context of GAD2 and severe obesity. A large genetic study involving multiple populations is not able to replicate previous findings linking variation in the GAD2 gene to susceptibility to obesity.
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Affiliation(s)
- Michael M Swarbrick
- 1Diabetes Center, University of California, San Francisco, California, United States of America
| | - Björn Waldenmaier
- 2Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, Essen, Germany
| | - Len A Pennacchio
- 3Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Denise L Lind
- 4Cardiovascular Research Institute, University of California, San Francisco, California, United States of America
| | - Martha M Cavazos
- 1Diabetes Center, University of California, San Francisco, California, United States of America
| | - Frank Geller
- 5Institute of Medical Biometry and Epidemiology, Phillips-University of Marburg, Marburg, Germany
| | - Raphael Merriman
- 6Department of Medicine, University of California, San Francisco, California, United States of America
| | - Anna Ustaszewska
- 3Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Mary Malloy
- 4Cardiovascular Research Institute, University of California, San Francisco, California, United States of America
| | - André Scherag
- 5Institute of Medical Biometry and Epidemiology, Phillips-University of Marburg, Marburg, Germany
| | - Wen-Chi Hsueh
- 1Diabetes Center, University of California, San Francisco, California, United States of America
| | - Winfried Rief
- 7Department of Psychology, University of Marburg, Marburg, Germany
| | - Franck Mauvais-Jarvis
- 8Division of Diabetes, Endocrinology and Metabolism, Baylor College of Medicine, Houston, Texas, United States of America
| | - Clive R Pullinger
- 4Cardiovascular Research Institute, University of California, San Francisco, California, United States of America
| | - John P Kane
- 4Cardiovascular Research Institute, University of California, San Francisco, California, United States of America
| | - Robert Dent
- 9Ottawa Health Research Institute, Ottawa, Ontario, Canada
| | - Ruth McPherson
- 10University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Pui-Yan Kwok
- 4Cardiovascular Research Institute, University of California, San Francisco, California, United States of America
| | - Anke Hinney
- 2Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, Essen, Germany
| | - Johannes Hebebrand
- 2Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, Essen, Germany
| | - Christian Vaisse
- 1Diabetes Center, University of California, San Francisco, California, United States of America
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Fisler JS, Warden CH. Dietary fat and genotype: toward individualized prescriptions for lifestyle changes. Am J Clin Nutr 2005; 81:1255-6. [PMID: 15941873 DOI: 10.1093/ajcn/81.6.1255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Manly KF. Conventional P-values fail to assure reproducibility for genetic association tests. Trends Genet 2005; 21:268-9; author reply 269-71. [PMID: 15851061 DOI: 10.1016/j.tig.2005.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Abstract
Genetic susceptibility modulates the impact of obesity on risk for type 2 diabetes. The present study evaluates the role of ENPP1 K121Q polymorphism in prediction of type 2 diabetes in three populations that differ in susceptibility to diabetes and environmental exposure. The three cohorts included 679 nonmigrant South Asians living in Chennai, India (223 with type 2 diabetes); 1,083 migrant South Asians living in Dallas, Texas (121 with type 2 diabetes); and 858 nonmigrant Caucasians living in Dallas, Texas (141 with type 2 diabetes). Patients with type 2 diabetes were included in these cohorts if they had diabetes onset before the age of 60 years. The prevalence of subjects carrying the polymorphic ENPP1 121Q allele was 25% in the nondiabetic group and 34% in the diabetic group of South Asians living in Chennai (P = 0.01). The prevalence in the nondiabetic and diabetic groups were 33 and 45% (P = 0.01) for the South Asians living in Dallas and 26 and 39% (P = 0.003) for the Caucasians. Although further replication studies are necessary to test the validity of the described genotype-phenotype relationship, our study supports the hypothesis that ENPP1 121Q predicts genetic susceptibility to type 2 diabetes in both South Asians and Caucasians.
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Mitchell LE. Epidemiology of neural tube defects. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2005; 135C:88-94. [PMID: 15800877 DOI: 10.1002/ajmg.c.30057] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The epidemiological investigation of the common open neural tube defects (NTDs), anencephaly, and spina bifida, has a long history. The most significant finding from these past studies of NTDs was the identification of the protective effect of maternal, periconceptional supplementation with folic acid. Fortuitously, the association between folic acid and NTDs became widely accepted in the early 1990s, at a time when genetic association studies of complex traits were becoming increasingly feasible. The confluence of these events has had a major impact on the direction of epidemiological, NTD research. Association studies to evaluate genes that may influence the risk of NTDs through their role in folate-related processes, or through other metabolic or developmental pathways are now commonplace. Moreover, the study of genetic as well as non-genetic, factors that may influence NTD risk through effects on the nutrient status of the mother or embryo has emerged as a major research focus. Research efforts over the past decade indicate that gene-gene, gene-environment, and higher-order interactions, as well as maternal genetic effects influence NTD risk, highlighting the complexity of the factors that underlie these conditions. The challenge for the future is to design studies that address these complexities, and are adequately powered to detect the factors or combination of factors that influence the development of NTDs.
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Affiliation(s)
- Laura E Mitchell
- Center for Environmental and Genetic Medicine, Institute of Biosciences and Technology, Texas A&M University System Health Science Center, Houston, Texas 77030, USA.
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Franks PW, Knowler WC, Nair S, Koska J, Lee YH, Lindsay RS, Walker BR, Looker HC, Permana PA, Tataranni PA, Hanson RL. Interaction Between an 11βHSD1 Gene Variant and Birth Era Modifies the Risk of Hypertension in Pima Indians. Hypertension 2004; 44:681-8. [PMID: 15452033 DOI: 10.1161/01.hyp.0000144294.28985.d5] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
11beta-hydroxysteroid dehydrogenase type 1 (11betaHSD1) is a candidate gene for hypertension, diabetes, and obesity through altered glucocorticoid production. This study explored the association of 11betaHSD1 gene variants with diabetes, hypertension, and obesity in a longitudinal population study of American Indians (N=918; exams=5508). In multivariate mixed models assuming an additive effect of genotype, a 5' upstream variant (rs846910) was associated with blood pressure (diastolic blood pressure beta=1.58 mm Hg per copy of the A allele, P=0.0008; systolic blood pressure beta=2.28 mm Hg per copy of the A allele, P=0.004; mean arterial blood pressure beta=1.83 mm Hg per copy of the A allele, P=0.0006) and hypertension (odds ratio=1.27 per copy of the A allele, P=0.02). However, birth date modified these associations (test for interaction: diastolic blood pressure P=0.16; systolic blood pressure P=0.007; mean arterial blood pressure P=0.01), such that the magnitude and direction of association between genotype and blood pressure changed with time. Finally, in models controlling for potential confounding by population stratification, we observed evidence of within-family effects for blood pressure (diastolic blood pressure beta=1.77 mm Hg per copy of the A allele, P=0.004; systolic blood pressure beta=2.04 mm Hg per copy of the A allele, P=0.07; mean arterial blood pressure beta=1.85 mm Hg per copy of the A allele, P=0.01) and for hypertension (odds ratio=1.26 per copy of the A allele; P=0.08). No association was observed for obesity. Associations with diabetes were similar in magnitude as reported previously but were not statistically significant. These data demonstrate association between genetic variability at 11betaHSD1 with hypertension, but these effects are modified by environmental factors.
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Affiliation(s)
- Paul W Franks
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 1550 E Indian School Rd, Phoenix, AZ 85014, USA.
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Coffey CS, Hebert PR, Ritchie MD, Krumholz HM, Gaziano JM, Ridker PM, Brown NJ, Vaughan DE, Moore JH. An application of conditional logistic regression and multifactor dimensionality reduction for detecting gene-gene interactions on risk of myocardial infarction: the importance of model validation. BMC Bioinformatics 2004; 5:49. [PMID: 15119966 PMCID: PMC419697 DOI: 10.1186/1471-2105-5-49] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2003] [Accepted: 04/30/2004] [Indexed: 11/15/2022] Open
Abstract
Background To examine interactions among the angiotensin converting enzyme (ACE) insertion/deletion, plasminogen activator inhibitor-1 (PAI-1) 4G/5G, and tissue plasminogen activator (t-PA) insertion/deletion gene polymorphisms on risk of myocardial infarction using data from 343 matched case-control pairs from the Physicians Health Study. We examined the data using both conditional logistic regression and the multifactor dimensionality reduction (MDR) method. One advantage of the MDR method is that it provides an internal prediction error for validation. We summarize our use of this internal prediction error for model validation. Results The overall results for the two methods were consistent, with both suggesting an interaction between the ACE I/D and PAI-1 4G/5G polymorphisms. However, using ten-fold cross validation, the 46% prediction error for the final MDR model was not significantly lower than that expected by chance. Conclusions The significant interaction initially observed does not validate and may represent a type I error. As data-driven analytic methods continue to be developed and used to examine complex genetic interactions, it will become increasingly important to stress model validation in order to ensure that significant effects represent true relationships rather than chance findings.
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Affiliation(s)
- Christopher S Coffey
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294-0022, USA
| | - Patricia R Hebert
- Section of Cardiovascular Medicine, Department of Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Marylyn D Ritchie
- Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN 37232-0700, USA
| | - Harlan M Krumholz
- Section of Cardiovascular Medicine, Department of Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
- Section of Health Policy and Administration, Department of Epidemiology and Public Health and Robert Wood Johnson Clinical Scholars Program, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale-New Haven Hospital Center for Outcomes Research and Evaluation, New Haven, CT 06510, USA
| | - J Michael Gaziano
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Paul M Ridker
- Center for Cardiovascular Disease Prevention, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Nancy J Brown
- Departments of Medicine and Pharmacology, Vanderbilt University Medical School, Nashville, TN 37232-0700, USA
| | - Douglas E Vaughan
- Departments of Medicine and Pharmacology, Vanderbilt University Medical School, Nashville, TN 37232-0700, USA
| | - Jason H Moore
- Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN 37232-0700, USA
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Tiwari HK, Allison DB. Do allelic variants of SLC6A14 predispose to obesity? J Clin Invest 2004; 112:1633-6. [PMID: 14660737 PMCID: PMC281657 DOI: 10.1172/jci20448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Obesity is arguably the world's most prevalent nutritional disorder and is a substantial contributor to morbidity and early mortality. Obesity is known to have a strong genetic component, but the specific influential genes in humans are largely unknown. A new paper describes a genetic variant that appears as though it may cause some people to be fatter or thinner than others (see the related article beginning on page 1762). This commentary considers the strength of the evidence in support of this finding and discusses additional research questions that should be addressed in further evaluations of this genetic variant as a putative contributor to human obesity.
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Affiliation(s)
- Hemant K Tiwari
- Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, 35294, USA
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Coffey CS, Hebert PR, Krumholz HM, Morgan TM, Williams SM, Moore JH. Reporting of model validation procedures in human studies of genetic interactions. Nutrition 2004; 20:69-73. [PMID: 14698017 DOI: 10.1016/j.nut.2003.09.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Christopher S Coffey
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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