A comprehensive analysis of common and rare variants to identify adiposity loci in hispanic Americans: The IRAS family study (IRASFS)

PLoS ONE

Volumn 10, Issue 11, 2015, Pages

  Gao, Chuan ^a   Wang, Nan ^a,b   Guo, Xiuqing ^c   Ziegler, Julie T ^a   Taylor, Kent D ^c   Xiang, Anny H ^d   Hai, Yang ^c   Kridel, Steven J ^a   Nadler, Jerry L ^e   Kandeel, Fouad ^f   Raffel, Leslie J ^g   Chen, Yii Der I ^c   Norris, Jill M ^h   Rotter, Jerome I ^c   Watanabe, Richard M ^b   Wagenknecht, Lynne E ^a   Bowden, Donald W ^a   Speliotes, Elizabeth K ⁱ   Goodarzi, Mark O ^g   Langefeld, Carl D ^a   Palmer, Nicholette D ^a   more..

^a WAKE FOREST SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^c HARBOR UCLA MEDICAL CENTER   (United States)

^d KAISER PERMANENTE   (United States)

^e EASTERN VIRGINIA MEDICAL SCHOOL   (United States)

^f CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

^g CEDARS SINAI MEDICAL CENTER   (United States)

^h Food Science and Human Nutrition   (United States)

ⁱ UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ISOCITRATE DEHYDROGENASE 1; ZINC FINGER PROTEIN; IDH1 PROTEIN, HUMAN; ISOCITRATE DEHYDROGENASE; MEMBRANE PROTEIN; ZGRF1 PROTEIN, HUMAN;

ADULT; ANTHROPOMETRIC PARAMETERS; ARTICLE; BODY MASS; CONTROLLED STUDY; EXOME; FEMALE; GENE; GENE LOCUS; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HEREDITY; HISPANIC; HUMAN; IDH1 GENE; INTRAABDOMINAL FAT; LIPID STORAGE; MALE; OBESITY; PERCENT BODY FAT; PHENOTYPE; POPULATION DISTRIBUTION; PROTEIN FUNCTION; SINGLE NUCLEOTIDE POLYMORPHISM; SUBCUTANEOUS FAT; WAIST CIRCUMFERENCE; WAIST HIP RATIO; ZGRF1 GENE; GENETIC ASSOCIATION STUDY; GENETIC PREDISPOSITION; GENETICS; META ANALYSIS;

ADIPOSITY; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; HISPANIC AMERICANS; HUMANS; ISOCITRATE DEHYDROGENASE; MEMBRANE PROTEINS; OBESITY; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84957554752     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0134649     Document Type: Article

References (53)

1. Frayling TM, Timpson NJ, Weedon MN, Zeggini E, Freathy RM, Lindgren CM, et al. A Common Variant in the FTO Gene Is Associated with Body Mass Index and Predisposes to Childhood and Adult Obesity. Science. 2007; 316(5826):889-94. doi: 10.1126/science.1141634 PMID: 17434869
2. Narkiewicz K. Obesity and hypertension - the issue is more complex than we thought. Nephrology Dialysis Transplantation. 2005; 21(2):264-7. doi: 10.1093/ndt/gfi290
3. Haslam DW, James WPT. Obesity. The Lancet. 2005; 366(9492):1197-209. doi: 10.1016/s0140-6736 (05)67483-1
4. Taylor RW, Jones IE, Williams SM, Goulding A. Evaluation of waist circumference, waist-to-hip ratio, and the conicity index as screening tools for high trunk fat mass, as measured by dual-energy X-ray absorptiometry, in children aged 3-19 y. Am J Clin Nutr. 2000; 72(2):490-5. Epub 2000/08/02. PMID: 10919946.
5. Blaak E. Gender differences in fat metabolism. Curr Opin Clin Nutr Metab Care. 2001; 4(6):499-502. Epub 2001/11/14. PMID: 11706283.
6. Lafontan M, Berlan M. Do regional differences in adipocyte biology provide new pathophysiological insights? Trends Pharmacol Sci. 2003; 24(6):276-83. Epub 2003/06/26. doi: S0165-6147(03)00132-9 [pii] doi: 10.1016/S0165-6147(03)00132-9 PMID: 12823953.
7. Montague CT, O'Rahilly S. The perils of portliness: causes and consequences of visceral adiposity. Diabetes. 2000; 49(6):883-8. Epub 2000/06/24. PMID: 10866038.
8. Wagenknecht LE, Langefeld CD, Scherzinger AL, Norris JM, Haffner SM, Saad MF, et al. Insulin sensitivity, insulin secretion, and abdominal fat: the Insulin Resistance Atherosclerosis Study (IRAS) Family Study. Diabetes. 2003; 52(10):2490-6. Epub 2003/09/30. PMID: 14514631.
9. Going SB, Lohman TG, Cussler EC, Williams DP, Morrison JA, Horn PS. Percent body fat and chronic disease risk factors in U.S. children and youth. Am J Prev Med. 2011; 41(4 Suppl 2):S77-86. Epub 2011/10/14. doi: 10.1016/j.amepre.2011.07.006 S0749-3797(11)00492-2 [pii]. PMID: 21961616.
10. Hindorff LAMJEBI, Morales J (European Bioinformatics Institute), Junkins HA, Hall PN, Klemm AK, and Manolio TA. A Catalog of Published Genome-Wide Association Studies. Available at: www. genome.gov/gwastudies. Accessed 11/25/2014.
11. Heid IM, Jackson AU, Randall JC, Winkler TW, Qi L, Steinthorsdottir V, et al. Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Nat Genet. 2010; 42(11):949-60. Epub 2010/10/12. doi: 10.1038/ng.685 ng.685 [pii]. PMID: 20935629; PubMed Central PMCID: PMC3000924.
12. Speliotes EK, Willer CJ, Berndt SI, Monda KL, Thorleifsson G, Jackson AU, et al. Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat Genet. 2010; 42 (11):937-48. Epub 2010/10/12. doi: 10.1038/ng.686 ng.686 [pii]. PMID: 20935630; PubMed Central PMCID: PMC3014648.
13. Kilpelainen TO, Zillikens MC, Stancakova A, Finucane FM, Ried JS, Langenberg C, et al. Genetic variation near IRS1 associates with reduced adiposity and an impaired metabolic profile. Nat Genet. 2011; 43(8):753-60. Epub 2011/06/28. doi: 10.1038/ng.866 ng.866 [pii]. PMID: 21706003; PubMed Central PMCID: PMC3262230.
14. Fox CS, White CC, Lohman K, Heard-Costa N, Cohen P, Zhang Y, et al. Genome-wide association of pericardial fat identifies a unique locus for ectopic fat. PLoS Genet. 2012; 8(5):e1002705. Epub 2012/05/17. doi: 10.1371/journal.pgen.1002705 PGENETICS-D-11-02554 [pii]. PMID: 22589742; PubMed Central PMCID: PMC3349742.
15. Berndt SI, Gustafsson S, Magi R, Ganna A, Wheeler E, Feitosa MF, et al. Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. Nat Genet. 2013; 45(5):501-12. Epub 2013/04/09. doi: 10.1038/ng.2606 ng.2606 [pii]. PMID: 23563607; PubMed Central PMCID: PMC3973018.
16. Liu CT, Monda KL, Taylor KC, Lange L, Demerath EW, Palmas W, et al. Genome-wide association of body fat distribution in African ancestry populations suggests new loci. PLoS Genet. 2013; 9(8): e1003681. Epub 2013/08/24. doi: 10.1371/journal.pgen.1003681 PGENETICS-D-12-02200 [pii]. PMID: 23966867; PubMed Central PMCID: PMC3744443.
17. Monda KL, Chen GK, Taylor KC, Palmer C, Edwards TL, Lange LA, et al. A meta-analysis identifies new loci associated with body mass index in individuals of African ancestry. Nat Genet. 2013; 45 (6):690-6. Epub 2013/04/16. doi: 10.1038/ng.2608 ng.2608 [pii]. PMID: 23583978; PubMed Central PMCID: PMC3694490.
18. Randall JC, Winkler TW, Kutalik Z, Berndt SI, Jackson AU, Monda KL, et al. Sex-stratified Genomewide Association Studies Including 270,000 Individuals Show Sexual Dimorphism in Genetic Loci for Anthropometric Traits. PLoS Genet. 2013; 9(6):e1003500. Epub 2013/06/12. doi: 10.1371/journal. pgen.1003500 PGENETICS-D-12-01098 [pii]. PMID: 23754948; PubMed Central PMCID: PMC3674993.
19. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, et al. Finding the missing heritability of complex diseases. Nature. 2009; 461(7265):747-53. Epub 2009/10/09. doi: 10.1038/nature08494 nature08494 [pii]. PMID: 19812666; PubMed Central PMCID: PMC2831613.
20. Choquet H, Meyre D. Genetics of Obesity: What have we Learned? Curr Genomics. 2011; 12(3):169-79. Epub 2011/11/02. doi: 10.2174/138920211795677895 CG-12-169 [pii]. PMID: 22043165; PubMed Central PMCID: PMC3137002.
21. Gibson G. Rare and common variants: twenty arguments. Nat Rev Genet. 2011; 13(2):135-45. Epub 2012/01/19. doi: 10.1038/nrg3118 nrg3118 [pii]. PMID: 22251874.
22. Flegal KM, Carroll MD, Kit BK, Ogden CL. Prevalence of obesity and trends in the distribution of body mass index among US adults, 1999-2010. JAMA. 2012; 307(5):491-7. Epub 2012/01/19. doi: 10.1001/jama.2012.39 jama.2012.39 [pii]. PMID: 22253363.
23. Comuzzie AG, Cole SA, Laston SL, Voruganti VS, Haack K, Gibbs RA, et al. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. PLoS One. 2012; 7(12): e51954. Epub 2012/12/20. doi: 10.1371/journal.pone.0051954 PONE-D-12-24984 [pii]. PMID: 23251661; PubMed Central PMCID: PMC3522587.
24. Henkin L, Bergman RN, Bowden DW, Ellsworth DL, Haffner SM, Langefeld CD, et al. Genetic epidemiology of insulin resistance and visceral adiposity. The IRAS Family Study design and methods. Ann Epidemiol. 2003; 13(4):211-7. Epub 2003/04/10. doi: S104727970200412X [pii]. PMID: 12684185.
25. Norris JM, Langefeld CD, Scherzinger AL, Rich SS, Bookman E, Beck SR, et al. Quantitative trait loci for abdominal fat and BMI in Hispanic-Americans and African-Americans: the IRAS Family study. Int J Obes (Lond). 2005; 29(1):67-77. Epub 2004/11/10. doi: 0802793 [pii] doi: 10.1038/sj.ijo.0802793 PMID: 15534617.
26. Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009; 19(9):1655-64. Epub 2009/08/04. doi: 10.1101/gr.094052.109 gr.094052.109 [pii]. PMID: 19648217; PubMed Central PMCID: PMC2752134.
27. Almasy L, Blangero J. Multipoint quantitative-trait linkage analysis in general pedigrees. Am J Hum Genet. 1998; 62(5):1198-211. Epub 1998/05/23. doi: S0002-9297(07)61542-0 [pii] doi: 10.1086/301844 PMID: 9545414; PubMed Central PMCID: PMC1377101.
28. O'Connell JR, Weeks DE. PedCheck: a program for identification of genotype incompatibilities in linkage analysis. Am J Hum Genet. 1998; 63(1):259-66. PMID: 9634505.
29. Goodarzi MO, Langefeld CD, Xiang AH, Chen YD, Guo X, Hanley AJ, et al. Insulin sensitivity and insulin clearance are heritable and have strong genetic correlation in Mexican Americans. Obesity (Silver Spring). 2014; 22(4):1157-64. Epub 2013/10/15. doi: 10.1002/oby.20639 PMID: 24124113; PubMed Central PMCID: PMC3968231.
30. Wagenknecht LE, Mayer EJ, Rewers M, Haffner S, Selby J, Borok GM, et al. The insulin resistance atherosclerosis study (IRAS) objectives, design, and recruitment results. Ann Epidemiol. 1995; 5(6):464-72. Epub 1995/11/01. doi: 1047279795000623 [pii]. PMID: 8680609.
31. Watanabe RM, Allayee H, Xiang AH, Trigo E, Hartiala J, Lawrence JM, et al. Transcription factor 7-like 2 (TCF7L2) is associated with gestational diabetes mellitus and interacts with adiposity to alter insulin secretion in Mexican Americans. Diabetes. 2007; 56(5):1481-5. Epub 2007/02/24. doi: db06-1682 [pii] doi: 10.2337/db06-1682 PMID: 17317761; PubMed Central PMCID: PMC2925638.
32. Black MH, Fingerlin TE, Allayee H, Zhang W, Xiang AH, Trigo E, et al. Evidence of interaction between PPARG2 and HNF4A contributing to variation in insulin sensitivity in Mexican Americans. Diabetes. 2008; 57(4):1048-56. Epub 2007/12/29. doi: db07-0848 [pii] doi: 10.2337/db07-0848 PMID: 18162503.
33. Li X, Allayee H, Xiang AH, Trigo E, Hartiala J, Lawrence JM, et al. Variation in IGF2BP2 interacts with adiposity to alter insulin sensitivity in Mexican Americans. Obesity (Silver Spring). 2009; 17(4):729-36. Epub 2009/01/17. doi: 10.1038/oby.2008.593 oby2008593 [pii]. PMID: 19148120.
34. Shu YH, Hartiala J, Xiang AH, Trigo E, Lawrence JM, Allayee H, et al. Evidence for sex-specific associations between variation in acid phosphatase locus 1 (ACP1) and insulin sensitivity in Mexican-Americans. J Clin Endocrinol Metab. 2009; 94(10):4094-102. Epub 2009/07/23. doi: 10.1210/jc.2008-2751 jc.2008-2751 [pii]. PMID: 19622628; PubMed Central PMCID: PMC2758733.
35. Buchanan TA, Xiang AH, Peters RK, Kjos SL, Marroquin A, Goico J, et al. Preservation of pancreatic beta-cell function and prevention of type 2 diabetes by pharmacological treatment of insulin resistance in high-risk hispanic women. Diabetes. 2002; 51(9):2796-803. Epub 2002/08/28. PMID: 12196473.
36. Buchanan TA, Xiang AH, Peters RK, Kjos SL, Berkowitz K, Marroquin A, et al. Response of pancreatic beta-cells to improved insulin sensitivity in women at high risk for type 2 diabetes. Diabetes. 2000; 49 (5):782-8. Epub 2000/07/25. PMID: 10905487.
37. Xiang AH, Azen SP, Raffel LJ, Tan S, Cheng LS, Diaz J, et al. Evidence for joint genetic control of insulin sensitivity and systolic blood pressure in hispanic families with a hypertensive proband. Circulation. 2001; 103(1):78-83. Epub 2001/01/04. PMID: 11136689.
38. Cheng LS, Davis RC, Raffel LJ, Xiang AH, Wang N, Quinones M, et al. Coincident linkage of fasting plasma insulin and blood pressure to chromosome 7q in hypertensive hispanic families. Circulation. 2001; 104(11):1255-60. Epub 2001/09/12. PMID: 11551876.
39. Goodarzi MO, Guo X, Taylor KD, Quinones MJ, Samayoa C, Yang H, et al. Determination and use of haplotypes: ethnic comparison and association of the lipoprotein lipase gene and coronary artery disease in Mexican-Americans. Genet Med. 2003; 5(4):322-7. Epub 2003/07/17. doi: 10.1097/01.GIM. 0000076971.55421.AD PMID: 12865761.
40. Goodarzi MO, Guo X, Taylor KD, Quinones MJ, Saad MF, Yang H, et al. Lipoprotein lipase is a gene for insulin resistance in Mexican Americans. Diabetes. 2004; 53(1):214-20. Epub 2003/12/25. PMID: 14693718.
41. Goodarzi MO, Taylor KD, Guo X, Quinones MJ, Cui J, Li X, et al. Variation in the gene for muscle-specific AMP deaminase is associated with insulin clearance, a highly heritable trait. Diabetes. 2005; 54 (4):1222-7. Epub 2005/03/29. doi: 54/4/1222 [pii]. PMID: 15793265.
42. Wang Y-P, Kandeel F, Taylor KD, Hernandez D, Saad MF, Nadler JL, et al. Insulin and blood pressure are linked to the LDL receptor-related protein locus on chromosome 12q (Abstract). Diabetes. 2000; 49 (Supp 1):A204.
43. Han B, Eskin E. Random-effects model aimed at discovering associations in meta-analysis of genomewide association studies. Am J Hum Genet. 2011; 88(5):586-98. Epub 2011/05/14. doi: 10.1016/j.ajhg. 2011.04.014 S0002-9297(11)00155-8 [pii]. PMID: 21565292; PubMed Central PMCID: PMC3146723.
44. Johnson AD, Handsaker RE, Pulit SL, Nizzari MM, O'Donnell CJ, de Bakker PI. SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. Bioinformatics. 2008; 24(24):2938-9. Epub 2008/11/01. doi: 10.1093/bioinformatics/btn564 btn564 [pii]. PMID: 18974171; PubMed Central PMCID: PMC2720775.
45. Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 2009; 5(6):e1000529. Epub 2009/06/23. doi: 10.1371/journal.pgen.1000529 PMID: 19543373; PubMed Central PMCID: PMC2689936.
46. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010; 7(4):248-9. Epub 2010/04/01. doi: 10.1038/nmeth0410-248 nmeth0410-248 [pii]. PMID: 20354512; PubMed Central PMCID: PMC2855889.
47. Kapushesky M, Emam I, Holloway E, Kurnosov P, Zorin A, Malone J, et al. Gene Expression Atlas at the European Bioinformatics Institute. Nucleic Acids Research. 2010; 38:D690-D8. doi: 10.1093/Nar/Gkp936 ISI:000276399100109. PMID: 19906730
48. Yang J, Loos RJ, Powell JE, Medland SE, Speliotes EK, Chasman DI, et al. FTO genotype is associated with phenotypic variability of body mass index. Nature. 2012; 490(7419):267-72. Epub 2012/09/18 doi: 10.1038/nature11401 nature11401 [pii]. PMID: 22982992; PubMed Central PMCID: PMC3564953.
49. Bradfield JP, Taal HR, Timpson NJ, Scherag A, Lecoeur C, Warrington NM, et al. A genome-wide association meta-analysis identifies new childhood obesity loci. Nat Genet. 2012; 44(5):526-31. Epub 2012/04/10. doi: 10.1038/ng.2247 ng.2247 [pii]. PMID: 22484627; PubMed Central PMCID: PMC3370100.
50. Heng JI, Nguyen L, Castro DS, Zimmer C, Wildner H, Armant O, et al. Neurogenin 2 controls cortical neuron migration through regulation of Rnd2. Nature. 2008; 455(7209):114-8. Epub 2008/08/12. doi: 10.1038/nature07198 nature07198 [pii]. PMID: 18690213.
51. Nam WS, Park KM, Park JW. RNA interference targeting cytosolic NADP(+)-dependent isocitrate dehydrogenase exerts anti-obesity effect in vitro and in vivo. Biochim Biophys Acta. 2012; 1822(8):1181-8. Epub 2012/05/01. doi: 10.1016/j.bbadis.2012.04.003 S0925-4439(12)00090-7 [pii]. PMID: 22542506.
52. Reitman ZJ, Yan H. Isocitrate dehydrogenase 1 and 2 mutations in cancer: alterations at a crossroads of cellular metabolism. J Natl Cancer Inst. 2010; 102(13):932-41. Epub 2010/06/02. doi: 10.1093/jnci/djq187 djq187 [pii]. PMID: 20513808; PubMed Central PMCID: PMC2897878.
53. Koh HJ, Lee SM, Son BG, Lee SH, Ryoo ZY, Chang KT, et al. Cytosolic NADP+-dependent isocitrate dehydrogenase plays a key role in lipid metabolism. J Biol Chem. 2004; 279(38):39968-74. Epub 2004/07/16. doi: 10.1074/jbc.M402260200 M402260200 [pii]. PMID: 15254034.