Sequence polymorphism at the human apolipoprotein all gene (APOA2): Unexpected deficit of variation in an African-American sample

Human Genetics

Volumn 111, Issue 1, 2002, Pages 75-87

  Fullerton, Stephanie M ^a   Clark, Andrew G ^a   Weiss, Kenneth M ^a   Taylor, Scott L ^b   Stengård, Jari H ^c   Salomaa, Veikko ^c   Boerwinkle, Eric ^d   Nickerson, Deborah A ^b  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c NATIONAL PUBLIC HEALTH INSTITUTE   (Finland)

^d UNIVERSITY OF TEXAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APOLIPOPROTEIN A2;

ALLELE; ARTICLE; ASSAY; CHIMPANZEE; CHROMOSOME SEGREGATION; CONTROLLED STUDY; DNA FLANKING REGION; DNA SEQUENCE; EUROPE; FINLAND; GENE AMPLIFICATION; GENE LOCUS; GENE SEQUENCE; GENETIC POLYMORPHISM; GENETIC TRANSCRIPTION; GENOTYPE; GEOGRAPHICAL VARIATION (SPECIES); HAPLOTYPE; HETEROZYGOSITY; HUMAN; LIGATION; NEGRO; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN DOMAIN; RANDOM AMPLIFIED MICROSATELLITE; SINGLE NUCLEOTIDE POLYMORPHISM; UNITED STATES;

AFRICAN CONTINENTAL ANCESTRY GROUP; ALLELES; ANIMALS; APOLIPOPROTEIN A-II; CARDIOVASCULAR DISEASES; DEMOGRAPHY; EUROPEAN CONTINENTAL ANCESTRY GROUP; FINLAND; GENE FREQUENCY; GENETIC SCREENING; GENETICS, POPULATION; GENOTYPE; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; OLIGONUCLEOTIDES; PAN TROGLODYTES; POLYMORPHISM, GENETIC; UNITED STATES; VARIATION (GENETICS);

EID: 0036664926     PISSN: 03406717     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00439-002-0763-x     Document Type: Article

References (64)

1. Bandelt HJ, Forster P, Sykes BC, Richards MB (1995) Mitochondrial portraits of human populations using median networks. Genetics 141:743-753
2. Blanco-Vaca F, Escola-Gil JC, Martin-Campos JM, Julve J (2001) Role of apoA-II in lipid metabolism and atherosclerosis: Advances in the study of an enigmatic protein. J Lipid Res 42:1727-1739
3. Boisfer E, Lambert G, Atger V, Tran NQ, Pastier D, Benetollo C, Trottier JF, Beaucamps I, Antonucci M, Laplaud M, Griglio S, Chambaz J, Kalopissis AD (1999) Overexpression of human apolipoprotein A-II in mice induces hypertriglyceridemia due to defective very low density lipoprotein hydrolysis. J Biol Chem 274:11564-11572
4. Bu X, Warden CH, Xia YR, De Meester C, Puppione DL, Teruya S, Lokensgard B, Daneshmand S, Brown J, Gray RJ et al (1994) Linkage analysis of the genetic determinants of high density lipoprotein concentrations and composition: Evidence for involvement of the apolipoprotein A-II and cholesteryl ester transfer protein loci. Hum Genet 93:639-648
5. Cardot P, Chambaz J, Cladaras C, Zanni VI (1991) Regulation of the human ApoA-II gene by the synergistic action of factors binding to the proximal and distal regulatory elements. J Biol Chem 266:24460-24470
6. Cardot P, Pastier D, Lacorte JM, Mangeney M, Zannis VI, Chambaz J (1994) Purification and characterization of nuclear factors binding to the negative regulatory element D of human apolipoprotein A-II promoter: A negative regulatory effect is reversed by GABP, an Ets-related protein. Biochemistry 33:12139-12148
7. Castellani LW, Navab M, Lenten BJ, Hedrick CC, Hama SY, Goto AM, Fogelman AM, Lusis AJ (1997) Overexpression of apolipoprotein AII in transgenic mice converts high density lipoproteins to proinflammatory particles. J Clin Invest 100:464-474
8. Chambaz J, Cardot P, Pastier D, Zannis VI, Cladaras C (1991) Promoter elements and factors required for hepatic transcription of the human ApoA-II gene. J Biol Chem 266:11676-11685
9. Civeira F, Genest J, Pocovi M, Salem DN, Herbert PN, Wilson PW, Schaefer EJ, Ordovas JM (1992) The MspI restriction fragment length polymorphism 3′ to the apolipoprotein A-II gene: Relationships with lipids, apolipoproteins, an premature coronary artery disease. Atherosclerosis 92:165-176
10. Clark AG (1990) Inference of haplotypes from PCR-amplified samples of diploid populations. Mol Biol Evol 7:111-122
11. Clark AG, Weiss KM, Nickerson DA, Taylor SL, Buchanan A, Stengård J, Salomaa V, Vartiainen E, Perola M, Boerwinkle E, Sing CF (1998) Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. Am J Hum Genet 63:595-612
12. Deeb SS, Takata K, Peng RL, Kajiyama G, Albers JJ (1990) A splice-junction mutation responsible for familial apoliprotein A-II deficiency. Am J Hum Genet 46: 822-827
13. Delahunty C, Ankener W, Deng Q, Eng J, Nickerson DA (1996) Testing the feasibility of DNA typing for human identification by PCR and an oligonucleotide ligation assay. Am J Hum Genet 58:1239-1246
14. Dupuy-Gorce AM, Desmarais E, Vigneron S, Buresi C, Nicaud V, Evans A, Luc G, Arveiler D, Marques-Vidal P, Cambien F, Tiret L, De Crastes Paulet A, Roizes G (1996) DNA polymorphisms in linkage disequilibrium at the 3′ end of the human APO AII gene: Relationships with lipids, apolipoproteins and coronary heart disease. Clin Genet 50:191-198
15. Ewing B, Green P (1998) Base-calling of automated sequencer traces using Phred. Error probabilities. Genome Res 8:186-194
16. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res 8:175-185
17. Excoffier L, Slatkin M (1995) Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12:921-927
18. Fay JC, Wu CI (2000) Hitchhiking under positive Darwinian selection. Genetics 155:1405-1413
19. Ferns GA, Shelley CS, Stocks J, Rees A, Paul H, Baralle F, Galton DJ (1986) A DNA polymorphism of the apoprotein AII gene in hypertriglyceridaemia. Hum Genet 74:302-306
20. Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915-925
21. Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133:693-709
22. Fullerton SM, Clark AG, Weiss KM, Nickerson DA, Taylor SL, Stengård JH, Salomaa V, Vartiainen E, Perola M, Boerwinkle E, Sing CF. (2000) Apolipoprotein E variation at the sequence haplotype level: Implications for the origin and maintenance of a major human polymorphism. Am J Hum Genet 67:881-900
23. Hamblin MT, Di Renzo A (2000) Detection of the signature of natural selection in humans: Evidence from the Duffy blood group locus. Am J Hum Genet 66:1669-1679
24. Hamblin MT, Thompson EE, Di Rienzo A (2002) Complete signatures of natural selection at the Duffy blood group locus. Am J Hum Genet 70:369-383
25. Harding RM, Fullerton SM, Griffiths RC, Bond J, Cox MJ, Schneider JA, Moulin DS, Clegg JB (1997) Archaic African and Asian lineages in the genetic ancestry of modern humans. Am J Hum Genet 60:772-789
26. Harding RM, Healy E, Ray AJ, Ellis NS, Flanagan N, Todd C, Dixon C, Sajantila A, Jackson IJ, Birch-Machin MA, Rees JL (2000) Evidence for variable selective pressures at MC1R. Am J Hum Genet 66:1351-1361
27. Hong SH, Kang BY, Park WH, Kim JQ, Lee CC (1998) Association between apolipoprotein A2 MspI polymorphism and hypertriglyceridemia in Koreans. Hum Biol 70:41-46
28. Huang XQ, Hardison RC, Miller W (1990) A space-efficient algorithm for local similarities. Comput Appl Biosci 6:373-381
29. Huang Y, Von Eckardstein A, Wu S, Assmann G (1995) Cholesterol efflux, cholesterol esterification, and cholesteryl ester transfer by LpA-I and LpA-I/A-II in native plasma. Arterioscler Thromb Vasc Biol 15:1412-1418
30. Hudson RR, Kreitman M, Aguadé M (1987) A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-159
31. Hussain MM, Zannis VI (1990) Intracellular modification of human apolipoprotein AII (apoII) and sites of apoAII mRNA synthesis: Comparison of apoAII with apoCII and apoCIII isoproteins. Biochemistry 29:209-217
32. Ikewaki K, Zech LA, Kindt M, Brewer HB Jr, Rader DJ (1995) Apolipoprotein A-II production rate is a major factor regulating the distribution of apolipoprotein A-I among HDL subclasses LpA-I and LpA-I:A-II in normolipidemic humans. Arterioscler Thromb Vasc Biol 15:306-312
33. Ikewaki K, Zech LA, Brewer HB Jr, Rader DJ (1996) ApoA-II kinetics in humans using endogenous labeling with stable isotopes: Slower turnover of apoA-II compared with the exogenous radiotracer method. J Lipid Res 37:399-407
34. Johnson GC, Esposito L, Barratt BJ, Smith AN, Heward J, Di Genova G, Ueda H, Cordell HJ, Eaves IA, Dudbridge F, Twells RC, Payne F, Hughes W, Nutland S, Stevens H, Carr P, Tuomilehto-Wolf E, Tuomilehto J, Gough SC, Clayton DG, Todd JA (2001) Haplotype tagging for the identification of common disease genes. Nat Genet 29:233-237
35. Kessling AM, Rajput-Williams J, Bainton D, Scott J, Miller NE, Baker I, Humphries SE (1988) DNA polymorphisms of the apolipoprotein AII and AI-CIII-AIV genes: A study in men selected for differences in high-density-lipoprotein cholesterol concentration. Am J Hum Genet 42:458-467
36. Lautenberger JA, Stephens JC, O'Brien SJ, Smith MW (2000) Significant admixture linkage disequilibrium across 30 cM around the FY locus in African Americans. Am J Hum Genet 66:969-978
37. Nei M, Kumar S (2000) Molecular Evolution and Phylogenetics. Oxford University Press, Oxford
38. Nickerson DA, Tobe VO, Taylor SL (1997) PolyPhred: Automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res 25:2745-2751
39. Nickerson DA, Taylor SL, Weiss KM, Clark AG, Hutchinson RG, Stengård J, Salomaa V, Vartiainen E, Boerwinkle E, Sing CF (1998) DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene. Nat Genet 19:233-240
40. Nickerson DA, Taylor SL, Fullerton SM, Weiss KM, Clark AG, Stengärd JH, Salomaa V, Boerwinkle E, Sing CF (2000) Sequence diversity and large-scale typing of SNPs in the human apolipoprotein E gene. Genome Res 10:1532-1545
41. Przeworksi M, Hudson RR, Di Rienzo A (2000) Adjusting the focus on human variation. Trends Genet 16:296-302
42. Puchois P, Kandoussi A, Fievet P, Fourrier JL, Bertrand M, Koren E, Fruchart JC (1987) Apolipoprotein A-I containing lipoproteins in coronary artery disease. Atherosclerosis 68:35-40
43. Rajput-Williams J, Eyre J, Nanjee MN, Crook D, Scott J, Miller NE (1989) Plasma lipoprotein lipids in relation to the MspI polymorphism of the apolipoprotein AII gene in Caucasian men. Lack of association with plasma triglyceride concentration. Atherosclerosis 77:31-36
44. Rogne S, Myklebost O, Hoyheim B, Olaisen B, Gedde-Dahl T Jr (1989) The genes for apolipoprotein all (APOA2) and the Duffy blood group (FY) are linked on chromosome 1 in man. Genomics 4:169-173
45. Rozas J, Rozas R (1999) DnaSP version 3: An integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174-175
46. Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston RH, McPherson JD, Gilman B, Schaffner S, Van Etten WJ, Reich D, Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody MC, Linton L, Lander ES, Altshuler D (2001) A map of genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928-933
47. Saha N, Tan JA, Tay JS (1992) MspI polymorphism of the apolipoprotein A-II gene, serum lipids and apolipoproteins in Chinese from Singapore. Hum Hered 42:293-297
48. Salomaa V, Rasi V, Pekkanen J, Vahtera E, Jauhiainen M, Vartiainen E, Myllyla G, Ehnholm C (1994) Haemostatic factors and prevalent coronary heart disease; the FINRISK haemostasis study. Eur Heart J 15:1293-1299
49. Scott J, Knott TJ, Priestley LM, Robertson ME, Mann DV, Kostner G, Miller GJ, Miller NE (1985) High-density lipoprotein composition is altered by a common DNA polymorphism adjacent to apoprotein AII gene in man. Lancet I:771-773
50. Simonsen KL, Churchill GA, Aquadro CF (1995) Properties of statistical tests of neutrality for DNA polymorphism data. Genetics 141:413-429
51. Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, Stanley SE, Jiang R, Messer CJ, Chew A, Han JH, Duan J, Carr JL, Lee MS, Koshy B, Kumar AM, Zhang G, Newell WR Windemuth A, Xu C, Kalbfleisch TS, Shaner SL, Arnold K, Schulz V, Drysdale CM, Nandabahan K, Judson RS, Ruano G, Vovis GF (2001a) Haplotype variation and linkage disequilibrium in 313 human genes. Science 293:489-493
52. Stephens M, Smith NJ, Donnelly P. (2001b) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68:978-989
53. Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460
54. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595
55. Templeton AR, Clark AG, Weiss KM, Nickerson DA, Boerwinkle E, Sing CF (2000) Recombinational and mutational hotspots within the human lipoprotein lipase gene. Am J Hum Genet 66:69-83
56. Thorn JA, Stocks J, Reichl D, Alcolado JC, Chamberlain JC, Galton D (1993) Variability of plasma apolipoprotein (apo) A-II levels associated with an apo A-II gene polymorphism in monozygotic twin pairs. Biochim Biophys Acta 1180:299-303
57. Tobe VO, Taylor SL, Nickerson DA (1996) Single-well genotyping of diallelic sequence variations by a two-color ELISA-based oligonucleotide ligation assay. Nucleic Acids Res 24: 3728-3732
58. Turner ST, Weidman WH, Michels VV, Reed TJ, Ormson CL, Fuller T, Sing CF (1989) Distribution of sodium-lithium countertransport and blood pressure in Caucasians five to eigthy-nine years of age. Hypertension 13:378-391
59. Utermann G, Hees M, Steinmetz A (1977) Polymorphism of apolipoprotein E and occurrence of dysbetalipoproteinaemia in man. Nature 269:604-607
60. Vohl MC, Lamarche B, Bergeron J, Moorjani S, Prud'homme D, Nadeau A, Tremblay A, Lupien PJ, Bouchard C, Despres JP (1997) The MspI polymorphism of the apolipoprotein A-II gene as a modulator of the dyslipidemic state found in visceral obesity. Atherosclerosis 128:183-190
61. Warden CH, Daluiski A, Bu X, Purcell-Huynh DA, De Meester C, Shieh BH, Puppione DL, Gray RM, Reaven GM, Chen YD, et al (1993) Evidence for linkage of the apolipoprotein A-II locus to plasma apolipoprotein A-II and free fatty acid levels in mice and humans. Proc Natl Acad Sci USA 90:10886-10890
62. Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256-276
63. Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388-396
64. Weir BS (1996) Genetic Data Analysis II. Sinauer Associates, Sunderland, Mass., USA