Patterns of linkage disequilibrium in different populations: Implications and opportunities for lipid-associated loci identified from genome-wide association studies

Current Opinion in Lipidology

Volumn 21, Issue 2, 2010, Pages 104-115

  Teo, Yik Ying ^a   Sim, Xueling ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Fine mapping; Genome wide association study; Linkage disequilibrium; Meta analysis; Replication study

Indexed keywords

ABC TRANSPORTER G1; ABC TRANSPORTER G5; ANGIOPOIETIN; ANGIOPOIETIN LIKE 3; APOLIPOPROTEIN A1; APOLIPOPROTEIN A4; APOLIPOPROTEIN A5; APOLIPOPROTEIN B; APOLIPOPROTEIN C2; APOLIPOPROTEIN E; AXONEMAL DYNEIN; CARBOHYDRATE RESPONSE ELEMENT BINDING PROTEIN; CARRIER PROTEIN; CHOLESTEROL ESTER TRANSFER PROTEIN; DYNEIN HEAVY CHAIN 11; HEPATOCYTE NUCLEAR FACTOR 1ALPHA; HIGH DENSITY LIPOPROTEIN CHOLESTEROL; LIPOPROTEIN; LIVER X RECEPTOR; LOW DENSITY LIPOPROTEIN CHOLESTEROL; LOW DENSITY LIPOPROTEIN RECEPTOR; MEMBRANE PROTEIN; PROTEIN DOCK7; PROTEIN GCKR; REGULATOR PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR MAFB; TRANSCRIPTION FACTOR PBX4; TRIACYLGLYCEROL; TRIBBLE 1; UNCLASSIFIED DRUG; LIPID;

AFRICAN AMERICAN; ARTICLE; ETHNICITY; GENE CLUSTER; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOTYPE; HUMAN; LIPID METABOLISM; PHENOTYPIC VARIATION; PRIORITY JOURNAL; QUANTITATIVE TRAIT; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; GENETICS; HAPLOTYPE; REVIEW;

ANIMALS; GENETIC LOCI; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; LIPIDS;

EID: 77957357607     PISSN: 09579672     EISSN: 14736535     Source Type: Journal    
DOI: 10.1097/MOL.0b013e3283369e5b     Document Type: Article

References (50)

1. McCarthy MI, Abecasis GR, Cardon LR, et al. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 2008; 9:356-369. (Pubitemid 351556063)
2. Manolio TA, Brooks LD, Collins FS. A HapMap harvest of insights into the genetics of common disease. J Clin Invest 2008; 118:1590-1605. (Pubitemid 351632361)
3. Donnelly P. Progress and challenges in genome-wide association studies in humans. Nature 2008; 456:728-731.
4. Saxena R, Voight BF, Lyssenko V, et al. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 2007; 316:1331-1336. (Pubitemid 46871653)
5. Kooner JS, Chambers JC, Aguilar-Salinas CA, et al. Genome-wide scan identifies variation in MLXIPL associated with plasma triglycerides. Nat Genet 2008; 40:149-151. (Pubitemid 351171393)
6. Kathiresan S, Melander O, Guiducci C, et al. Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. Nat Genet 2008; 40:189-197. (Pubitemid 351171402)
7. Willer CJ, Sanna S, Jackson AU, et al. Newly identified loci that influence lipid concentrations and risk of coronary artery disease. Nat Genet 2008; 40:161-169. (Pubitemid 351171403)
8. Aulchenko YS, Ripatti S, Lindqvist I, et al. Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. Nat Genet 2009; 41:47-55.
9. Kathiresan S, Willer CJ, Peloso GM, et al. Common variants at 30 loci contribute to polygenic dyslipidemia. Nat Genet 2009; 41:56-65.
10. Carlson CS, Eberle MA, Rieder MJ, et al. Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat Genet 2003; 33:518-521. (Pubitemid 36390016)
11. Barrett JC, Cardon LR. Evaluating coverage of genome-wide association studies. Nat Genet 2006; 38:659-662. (Pubitemid 43927307)
12. Pe'er I, de Bakker PI, Maller J, et al. Evaluating and improving power in whole-genome association studies using fixed marker sets. Nat Genet 2006; 38:663-667. (Pubitemid 43927308)
13. de Bakker PI, Burtt NP, Graham RR, et al. Transferability of tag SNPs in genetic association studies in multiple populations. Nat Genet 2006; 38:1298-1303. (Pubitemid 44646292)
14. Pritchard JK, Przeworski M. Linkage disequilibrium in humans: models and data. Am J Hum Genet 2001; 69:1-14. (Pubitemid 32614013)
15. Teo YY, Fry AE, Bhattacharya K, et al. Genome-wide comparisons of variation in linkage disequilibrium. Genome Res 2009; 19:1849-1860.
16. Sabeti PC, Varilly P, Fry B, et al. Genome-wide detection and characterization of positive selection in human populations. Nature 2007; 449:913-918. (Pubitemid 47598625)
17. Voight BF, Kudaravalli S, Wen X, et al. A map of recent positive selection in the human genome. PLoS Biol 2006; 4:e72.
18. International HapMap Consortium. A haplotype map of the human genome. Nature 2005; 437:1299-1320.
19. International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 2007; 449:851-861.
20. Teo YY, Sim X, Ong RTH, et al. Singapore Genome Variation project: a haplotype map of three southeast Asian populations. Genome Res 2009; 19:2154-2162.
21. Brown MS, Goldstein JL. Receptor-mediated endocytosis: insights from the lipoprotein receptor system. Proc Natl Acad Sci U S A 1979; 76:3330-3337. (Pubitemid 9233955)
22. Sing CF, Davignon J. Role of the apolipoprotein E polymorphism in determining normal plasma lipid and lipoprotein variation. Am J Hum Genet 1985; 37:268-285. (Pubitemid 15053161)
23. Kingsley DM, Kozarsky KF, Hobbie L, Krieger M. Reversible defects in O-linked glycosylation and LDL receptor expression in a UDP-Gal/UDP-GalNAc 4-epimerase deficient mutant. Cell 1986; 44:749-759. (Pubitemid 16073971)
24. Guerra R, Wang J, Grundy SM, Cohen JC. A hepatic lipase (LIPC) allele associated with high plasma concentrations of high density lipoprotein cholesterol. Proc Natl Acad Sci USA 1997; 94:4532-4537. (Pubitemid 27194276)
25. Frikke-Schmidt R, Nordestgaard BG, Jensen GB, Tybjaerg-Hansen A. Genetic variation in ABC transporter A1 contributes to HDL cholesterol in the general population. J Clin Invest 2004; 114:1343-1353. (Pubitemid 40385306)
26. Kajinami K, Brousseau ME, Nartsupha C, et al. ATP binding cassette transporter G5 and G8 genotypes and plasma lipoprotein levels before and after treatment with atorvastatin. J Lipid Res 2004; 45:653-656. (Pubitemid 38405671)
27. Benn M, Nordestgaard BG, Jensen JS, et al. Polymorphism in APOB associated with increased low-density lipoprotein levels in both genders in the general population. J Clin Endocrinol Metab 2005; 90:5797-5803. (Pubitemid 41415494)
28. Boekholdt SM, Sacks FM, Jukema JW, et al. Cholesteryl ester transfer protein TaqIB variant, high-density lipoprotein cholesterol levels, cardiovascular risk, and efficacy of pravastatin treatment: individual patient meta-analysis of 13, 677 subjects. Circulation 2005; 111:278-287. (Pubitemid 40165333)
29. Ek J, Rose CS, Jensen DP, et al. The functional Thr130Ile and Val255Met polymorphisms of the hepatocyte nuclear factor-4alpha (HNF4A): gene associations with type 2 diabetes or altered beta-cell function among Danes. J Clin Endocrinol Metab 2005; 90:3054-3059. (Pubitemid 40686363)
30. Schaeffer L, Gohlke H, Muller M, et al. Common genetic variants of the FADS1 FADS2 gene cluster and their reconstructed haplotypes are associated with the fatty acid composition in phospholipids. Hum Mol Genet 2006; 15:1745-1756. (Pubitemid 43821765)
31. Rip J, Nierman MC, Ross CJ, et al. Lipoprotein lipase S447X: a naturally occurring gain-of-function mutation. Arterioscler Thromb Vasc Biol 2006; 26:1236-1245. (Pubitemid 44305366)
32. Kotowski IK, Pertsemlidis A, Luke A, et al. A spectrum of PCSK9 alleles contributes to plasma levels of low-density lipoprotein cholesterol. Am J Hum Genet 2006; 78:410-422. (Pubitemid 43291224)
33. Pare G, Serre D, Brisson D, et al. Genetic analysis of 103 candidate genes for coronary artery disease and associated phenotypes in a founder population reveals a new association between endothelin-1 and high-density lipoprotein cholesterol. Am J Hum Genet 2007; 80:673-682. (Pubitemid 46564404)
34. Romeo S, Pennacchio LA, Fu Y, et al. Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. Nat Genet 2007; 39:513-516. (Pubitemid 46514768)
35. Spirin V, Schmidt S, Pertsemlidis A, et al. Common single-nucleotide polymorphisms act in concert to affect plasma levels of high-density lipoprotein cholesterol. Am J Hum Genet 2007; 81:1298-1303. (Pubitemid 350211459)
36. Sabatti C, Service SK, Hartikainen AL, et al. Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Nat Genet 2009; 41:35-46.
37. Tai ES, Sim XL, Ong TH, et al. Polymorphisms at newly identified lipid-associated loci are associated with blood lipids and cardiovascular disease in an Asian Malay population. J Lipid Res 2009; 50:514-520.
38. Nakayama K, Bayasgalan T, Yamanaka K, et al. Large scale replication analysis of loci associated with lipid concentrations in a Japanese population. J Med Genet 2009; 46:370-374.
39. Chanock SJ, Manolio T, Boehnke M, et al. Replicating genotype-phenotype associations. Nature 2007; 447:655-660. (Pubitemid 46889722)
40. Teo YY, Small KS, Fry AE, et al. Power consequences of linkage dis-equilibrium variation between populations. Genet Epidemiol 2009; 33: 128-135.
41. Jallow M, Teo YY, Small KS, et al. Genome-wide and fine-resolution association analysis of malaria in west Africa. Nat Genet 2010. [Epub ahead of print]
42. Conrad DF, Jakobsson M, Coop G, et al. A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat Genet 2006; 38:1251-1260. (Pubitemid 44646287)
43. de Bakker PI, Yelensky R, Pe'er I, et al. Efficiency and power in genetic association studies. Nat Genet 2005; 37:1217-1223. (Pubitemid 41568704)
44. Conrad DF, Pinto D, Redon R, et al. Origins and functional impact of copy number variation in the human genome. Nature 2010. [Epub ahead of print]
45. Rosenberg NA, Pritchard JK, Weber JL, et al. Genetic structure of human populations. Science 2002; 298:2381-2385. (Pubitemid 36014209)
46. Jakobsson M, Scholz SW, Scheet P, et al. Genotype, haplotype and copy-number variation in worldwide human populations. Nature 2008; 451:998-1003. (Pubitemid 351301742)
47. Li JZ, Absher DM, Tang H, et al. Worldwide human relationships inferred from genome-wide patterns of variation. Science 2008; 319:1100-1104. (Pubitemid 351300793)
48. Malaria Genomic Epidemiology Network. A global network for investigating the genomic epidemiology of malaria. Nature 2008; 456:732-737.
49. Tishkoff SA, Reed FA, Friedaender FR, et al. The genetic structure and history of Africans and African Americans. Science 2009; 324:1035-1044.
50. Reich D, Thangaraj K, Patterson N, et al. Reconstructing Indian population history. Nature 2009; 461:489-495.