Molecular evolution of 5′ flanking regions of 87 candidate genes for atherosclerotic cardiovascular disease

Genetic Epidemiology

Volumn 30, Issue 7, 2006, Pages 557-569

  Ding, Keyue ^a   Kullo, Iftikhar J ^a  

^a MAYO CLINIC   (United States)

Author keywords

5 flanking regions; Atherosclerosis; Evolution; Neutrality tests; Selection

Indexed keywords

AFRICAN AMERICAN; ARTICLE; ATHEROSCLEROSIS; CARDIOVASCULAR DISEASE; CHIMPANZEE; CLINICAL ARTICLE; DEMOGRAPHY; DISEASE PREDISPOSITION; DNA FLANKING REGION; DNA POLYMORPHISM; EUROPEAN AMERICAN; GENE EXPRESSION; GENE LOCUS; GENE SEQUENCE; GENETIC SELECTION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; HUMAN VERSUS ANIMAL COMPARISON; INTRASPECIFIC VARIATION; MOLECULAR EVOLUTION; NONHUMAN; POPULATION STRUCTURE; QUANTITATIVE TRAIT; SIMULATION; SPECIES COMPARISON; SPECIES DIFFERENCE; STATISTICAL ANALYSIS;

5' FLANKING REGION; AFRICAN AMERICANS; ANIMALS; ARTERIOSCLEROSIS; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETIC PREDISPOSITION TO DISEASE; HAPLOTYPES; HUMANS; PAN TROGLODYTES; POLYMORPHISM, GENETIC; SELECTION (GENETICS); VARIATION (GENETICS);

PAN TROGLODYTES;

EID: 33750373150     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20169     Document Type: Article

References (67)

1. Akey JM, Eberle MA, Rieder MJ, Carlson CS, Shriver MD, Nickerson DA, Kruglyak L. 2004. Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol 2:e286.
2. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD. 2002. Interrogating a high-density SNP map for signatures of natural selection. Genome Res 12:1805-1814.
3. Bamshad M, Wooding SP. 2003. Signatures of natural selection in the human genome. Nat Rev Genet 4:99-111.
4. Braun A, Kammerer S, Maier E, Bohme E, Roscher AA. 1996. Polymorphisms in the gene for the human B2-bradykinin receptor. New tools in assessing a genetic risk for bradykinin-associated diseases. Immunopharmacology 33:32-35.
5. Brouwers GJ, Leebeek FW, Tanck MW, Wouter Jukema J, Kluft C, de Maat MP. 2003. Association between thrombin-activatable fibrinolysis inhibitor (TAFI) and clinical outcome in patients with unstable angina pectoris. Thromb Haemost 90:92-100.
6. Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA. 2004. Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 74:106-120.
7. Cavalli-Sforza LL, Feldman MW. 1981. Cultural Transmission and Evolution. Princeton, NJ: Princeton University Press.
8. Chakraborty R, Kamboh MI, Nwankwo M, Ferrell RE. 1992. Caucasian genes in American blacks: new data. Am J Hum Genet 50:145-155.
9. Crawford DC, Carlson CS, Rieder MJ, Carrington DP, Yi Q, Smith JD, Eberle MA, Kruglyak L, Nickerson DA. 2004. Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations. Am J Hum Genet 74:610-622.
10. Depaulis F, Veuille M. 1998. Neutrality tests based on the distribution of haplotypes under an infinite-site model. Mol Biol Evol 15:1788-1790.
11. Di Rienzo A, Hudson RR. 2005. An evolutionary framework for common diseases: the ancestral-susceptibility model. Trends Genet 21:596-601.
12. Eriksson P, Kallin B, Hooft F, Bavenholm P, Hamsten A. 1995. Allele-specific increase in basal transcription of the plasminogen-activator inhibitor 1 gene is associated with myocardial infarction. Proc Natl Acad Sci USA 92:1851-1855.
13. Fay JC, Wu CI. 2000. Hitchhiking under positive Darwinian selection. Genetics 155:1405-1413.
14. Fuster V, Badimon L, Badimon JJ, Chesebro JH. 1992. The pathogenesis of coronary artery disease and the acute coronary syndromes (1). N Engl J Med 326:242-250.
15. Gainer JV, Brown NJ, Bachvarova M, Bastien L, Maltais I, Marceau F, Bachvarov DR. 2000. Altered frequency of a promoter polymorphism of the kinin B2 receptor gene in hypertensive African-Americans. Am J Hypertens 13:1268-1273.
16. Hahn MW, Rausher MD, Cunningham CW. 2002. Distinguishing between selection and population expansion in an experimental lineage of bacteriophage T7. Genetics 161:11-20.
17. Hahn MW, Rockman MV, Soranzo N, Goldstein DB, Wray GA. 2004. Population genetic and phylogenetic evidence for positive selection on regulatory mutations at the factor VII locus in humans. Genetics 167:867-877.
18. Hanchard NA, Rockett KA, Spencer C, Coop G, Pinder M, Jallow M, Kimber M, McVean G, Mott R, Kwiatkowski DP. 2006. Screening for recently selected alleles by analysis of human haplotype similarity. Am J Hum Genet 78:153-159.
19. Hirschhorn JN, Daly MJ. 2005. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6:95-108.
20. Hoh J, Ott J. 2003. Mathematical multi-locus approaches to localizing complex human trait genes. Nat Rev Genet 4:701-709.
21. Hudson RR. 1983. Properties of a neutral allele model with intragenic recombination. Theor Popul Biol 23:183-201.
22. Hudson RR. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18:337-338.
23. Hudson RR, Bailey K, Skarecky D, Kwiatowski J, Ayala FJ. 1994. Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster. Genetics 136:1329-1340.
24. Innan H, Zhang K, Marjoram P, Tavare S, Rosenberg NA. 2005. Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites. Genetics 169:1763-1777.
25. Jordan IK, McDonald JF. 1998. Interelement selection in the regulatory region of the copia retrotransposon. J Mol Evol 47:670-676.
26. Jorde LB, Watkins WS, Bamshad MJ. 2001. Population genomics: a bridge from evolutionary history to genetic medicine. Hum Mol Genet 10:2199-2207.
27. Kanehisa M, Goto S, Kawashima S, Nakaya A. 2002. The KEGG databases at GenomeNet. Nucl Acids Res 30:42-46.
28. Kong A, Gudbjartsson DF, Sainz J, Jonsdottir GM, Gudjonsson SA, Richardsson B, Sigurdardottir S, Barnard J, Hallbeck B, Masson G, et al. 2002. A high-resolution recombination map of the human genome. Nat Genet 31:241-247.
29. Kreitman M. 2000. Methods to detect selection in populations with applications to the human. Annu Rev Genomics Hum Genet 1:539-559.
30. Marth G, Schuler G, Yeh R, Davenport R, Agarwala R, Church D, Wheelan S, Baker J, Ward M, Kholodov M, et al. 2003. Sequence variations in the public human genome data reflect a bottlenecked population history. Proc Natl Acad Sci USA 100:376-381.
31. McDonald JH, Kreitman M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654.
32. Medley TL, Cole TJ, Dart AM, Gatzka CD, Kingwell BA. 2004. Matrix metalloproteinase-9 genotype influences large artery stiffness through effects on aortic gene and protein expression. Arterioscler Thromb Vasc Biol 24:1479-1484.
33. Mehrabian M, Allayee H, Wong J, Shi W, Wang XP, Shaposhnik Z, Funk CD, Lusis AJ. 2002. Identification of 5-lipoxygenase as a major gene contributing to atherosclerosis susceptibility in mice. Circ Res 91:120-126.
34. Nachman MW, Crowell SL. 2000. Estimate of the mutation rate per nucleotide in humans. Genetics 156:297-304.
35. Nakajima T, Wooding S, Sakagami T, Emi M, Tokunaga K, Tamiya G, Ishigami T, Umemura S, Munkhbat B, Jin F, et al. 2004. Natural selection and population history in the human angiotensinogen gene (AGT): 736 complete AGT sequences in chromosomes from around the world. Am J Hum Genet 74:898-916.
36. Neel JV. 1962. Diabetes mellitus: a "thrifty" genotype rendered detrimental by "progress"? Am J Hum Genet 14:353-362.
37. Nielsen R. 2001. Statistical tests of selective neutrality in the age of genomics. Heredity 86:641-647.
38. Otto SP. 2000. Detecting the form of selection from DNA sequence data. Trends Genet 16:526-529.
39. Parra EJ, Marcini A, Akey J, Martinson J, Batzer MA, Cooper R, Forrester T, Allison DB, Deka R, Ferrell RE, et al. 1998. Estimating African American admixture proportions by use of population-specific alleles. Am J Hum Genet 63:1839-1851.
40. Pastinen T, Hudson TJ. 2004. Cis-acting regulatory variation in the human genome. Science 306:647-650.
41. Przeworski M. 2002. The signature of positive selection at randomly chosen loci. Genetics 160:1179-1189.
42. Reich DE, Goldstein DB. 1998. Genetic evidence for a Paleolithic human population expansion in Africa. Proc Natl Acad Sci USA 95:8119-8123.
43. Reny JL, Laurendeau I, Fontana P, Bieche I, Dupont A, Remones V, Emmerich J, Vidaud M, Aiach M, Gaussem P. 2004. The TF-603A/G gene promoter polymorphism and circulating monocyte tissue factor gene expression in healthy volunteers. Thromb Haemost 91:248-254.
44. Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16:276-277.
45. Rockman MV, Hahn MW, Soranzo N, Loisel DA, Goldstein DB, Wray GA. 2004. Positive selection on MMP3 regulation has shaped heart disease risk. Curr Biol 14:1531-1539.
46. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. 2002. Genetic structure of human populations. Science 298:2381-2385.
47. Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, et al. 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature 419:832-837.
48. Saposnik B, Reny J-L, Gaussem P, Emmerich J, Aiach M, Gandrille S. 2004. A haplotype of the EPCR gene is associated with increased plasma levels of sEPCR and is a candidate risk factor for thrombosis. Blood 103:1311-1318.
49. Schneiderman J, Sawdey M, Keeton M, Bordin G, Bernstein E, Dilley R, Loskutoff D. 1992. Increased type 1 plasminogen activator inhibitor gene expression in atherosclerotic human arteries. Proc Natl Acad Sci USA 89:6998-7002.
50. Schork NJ, Cardon LR, Xu X. 1998. The future of genetic epidemiology. Trends Genet 14:266-272.
51. Simonsen KL, Churchill GA, Aquadro CF. 1995. Properties of statistical tests of neutrality for DNA polymorphism data. Genetics 141:413-429.
52. Stajich JE, Hahn MW. 2005. Disentangling the effects of demography and selection in human history. Mol Biol Evol 22:63-73.
53. Stephens M, Smith NJ, Donnelly P. 2001. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68:978-989.
54. Storey JD, Tibshirani R. 2003. Statistical significance for genome-wide studies. Proc Natl Acad Sci USA 100:9440-9445.
55. Tajima F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460.
56. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
57. Thompson EE, Kuttab-Boulos H, Witonsky D, Yang L, Roe BA, Di Rienzo A. 2004. CYP3A variation and the evolution of salt-sensitivity variants. Am J Hum Genet 75:1059-1069.
58. Thompson EE, Kuttab-Boulos H, Krasowski MD, Di Rienzo A. 2005. Functional constraints on the constitutive androstane receptor inferred from human sequence variation and cross-species comparisons. Hum Genomics 2:168-178.
59. Thornton K. 2003. Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19:2325-2327.
60. Vander Molen J, Frisse LM, Fullerton SM, Qian Y, Del Bosque-Plata L, Hudson RR, Di Rienzo A. 2005. Population genetics of CAPN10 and GPR35: implications for the evolution of type 2 diabetes variants. Am J Hum Genet 76:548-560.
61. Voight BF, Kudaravalli S, Wen X, Pritchard JK. 2006. A map of recent positive selection in the human genome. PLoS Biol 4:e72.
62. Wall JD. 1999. Recombination and the power of statistical tests of neutrality. Genet Res 74:65-79.
63. Watterson GA. 1975. On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256-276.
64. Wilson AG, Symons JA, McDowell TL, McDevitt HO, Duff GW. 1997. Effects of a polymorphism in the human tumor necrosis factor alpha promoter on transcriptional activation. Proc Natl Acad Sci USA 94:3195-3199.
65. Wingender E, Dietze P, Karas H, Knuppel R. 1996. TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res 24:238-241.
66. Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, Rockman MV, Romano LA. 2003. The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 20:1377-1419.
67. Yan H, Yuan W, Velculescu VE, Vogelstein B, Kinzler KW. 2002. Allelic variation in human gene expression. Science 297:1143.