Significant admixture linkage disequilibrium across 30 cM around the FY locus in African Americans

American Journal of Human Genetics

Volumn 66, Issue 3, 2000, Pages 969-978

  Lautenberger, James A ^a   Stephens, J Claiborne ^a,c   O'Brien, Stephen J ^a   Smith, Michael W ^a,b  

^a NATIONAL CANCER INSTITUTE   (United States)

^b SAIC FREDERICK INC   (United States)

^c Clinical Data Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; GENE DELETION; GENE INSERTION; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC POLYMORPHISM; HUMAN; NEGRO; PRIORITY JOURNAL; TANDEM REPEAT;

EID: 0033912677     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/302820     Document Type: Article

References (50)

1. Altshuler D, Kruglyak L, Lander E (1998) Genetic polymorphisms and disease. N Engl J Med 338:1626
2. Bock SC, Levitan DJ (1983) Characterization of an unusual DNA length polymorphism 5′ to the human antithrombin III gene. Nucleic Acids Res 11:8569-8582
3. Bodmer WF (1986) Human genetics: the molecular challenge. Cold Spring Harb Symp Quant Biol 51:1-13
4. Briscoe D, Stephens JC, O'Brien SJ (1994) Linkage disequilibrium in admixed populations: applications in gene mapping. J Hered 85:59-63
5. Chakraborty R, Kamboh MI, Ferrell RE (1991) "Unique" alleles in admixed populations: a strategy for determining "hereditary" population differences of disease frequencies. Ethn Dis 1:245-256
6. Chakraborty R, Kamboh MI, Nwankwo M, Ferrell RE (1992) Caucasian genes in American blacks: new data. Am J Hum Genet 50:145-155
7. Chakraborty R, Weiss KM (1988) Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci. Proc Natl Acad Sci USA 85: 9119-9123
8. Chaudhuri A, Polyakova J, Zbrzezna V, Pogo AO (1995) The coding sequence of Duffy blood group gene in humans and simians: restriction fragment length polymorphism, antibody and malarial parasite specificities, and expression in nonerythroid tissues in Duffy-negative individuals. Blood 85:615-621
9. Deloukas P, Schuler GD, Gyapay G, Beasley EM, Soderlund C, Rodriguez-Tome P, Hui L, et al (1998) A physical map of 30,000 human genes. Science 282:744-746
10. Destro-Bisol G, Maviglia R, Caglia A, Boschi I, Spedini G, Pascali V, Clark A, et al (1999) Estimating European admixture in African Americans by using microsatellites and a microsatellite haplotype (CD4/Alu). Hum Genet 104: 149-157
11. Dib C, Faure S, Fizames C, Samson D, Drouot N, Vignal A, Millasseau P, et al (1996) A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380:152-154
12. Ginzburg HM, Fleming PL, Miller KD (1988) Selected public health observations derived from Multicenter AIDS Cohort Study. J Acquir Immune Defic Syndr 1:2-7
13. Goedert JJ, Biggar RJ, Melbye M, Mann DL, Wilson S, Gail MH, Grossman RJ, et al (1987) Effect of T4 count and cofactors on the incidence of AIDS in homosexual men infected with human immunodeficiency virus. JAMA 257: 331-334
14. Goedert JJ, Kessler CM, Aledort LM, Biggar RJ, Andes WA, White GCD, Drummond JE, et al (1989) A prospective study of human immunodeficiency virus type 1 infection and the development of AIDS in subjects with hemophilia. N Engl JMed 321:1141-1148
15. Hadley TJ, Peiper SC (1997) From malaria to chemokine receptor: the emerging physiologic role of the Duffy blood group antigen. Blood 89:3077-3091
16. Hentati A, Hu P, Asgharzadeh S, Siddique T (1992) Dinucleotide repeat polymorphism at the human erythroid alpha spectrin (SPTA1) locus. Hum Mol Genet 1:218
17. Holm S (1979) A simple sequentially rejective multiple test procedure. Scand J Stat 6:65-70
18. Horuk R, Chitnis CE, Darbonne WC, Colby TJ, Rybicki A, Hadley TJ, Miller LH (1993) A receptor for the malarial parasite Plasmodium vivax: the erythrocyte chemokine receptor. Science 261:1182-1184
19. Hudson TJ, Stein LD, Gerety SS, Ma J, Castle AB, Silva J, Slonim DK, et al (1995) An STS-based map of the human genome. Science 270:1945-1954
20. Huttley GA, Smith MW, Carrington M, O'Brien SJ (1999) A scan for linkage disequilibrium across the human genome. Genetics 152:1711-1722
21. Iwamoto S, Li J, Sugimoto N, Okuda H, Kajii E (1996) Characterization of the Duffy gene promoter: evidence for tissue-specific abolishment of expression in Fy(a-b-)of black individuals. Biochem Biophys Res Commun 222:852-859
22. Jaffe HW, Darrow WW, Echenberg DF, O'Malley PM, Getchell JP, Kalyanaraman VS, Byers RH, et al (1985) The acquired immunodeficiency syndrome in a cohort of homosexual men: a six-year follow-up study. Ann Intern Med 103: 210-214
23. Kaplan NL, Martin ER, Morris RW, Weir BS (1998) Marker selection for the transmission/disequilibrium test, in recently admixed populations. Am J Hum Genet 62:703-712
24. Laan M, Pääbo S (1997) Demographic history and linkage disequilibrium in human populations. Nat Genet 17:435-438
25. Lander ES, Schork NJ (1994) Genetic dissection of complex traits. Science 265:2037-2048
26. Lewontin RC (1964) The interaction of selection and linkage. I. General considerations: heterotic models. Genetics 49: 49-67
27. Lincoln SE, Daly MJ, Lander ES (1991) PRIMER: a computer program for automatically selecting PCR primers. MIT Center for Genome Research, Cambridge, MA
28. Long JC (1991) The genetic structure of admixed populations. Genetics 127:417-428
29. Long JC, Williams RC, Urbanek M (1995) An E-M algorithm and testing strategy for multiple-locus haplotypes. Am J Hum Genet 56:799-810
30. Loveland KA, Stehbens J, Contant C, Bordeaux JD, Sirois P, Bell TS, Hill S, et al (1994) Hemophilia growth and development study: baseline neurodevelopmental findings. J Pediatr Psychol 19:223-239
31. Ludbrook J (1998) Multiple comparison procedures updated. Clin Exp Pharmacol Physiol 25:1032-1037
32. McKeigue PM (1997) Mapping genes underlying ethnic differences in disease risk by linkage disequilibrium in recently admixed populations. Am J Hum Genet 60:188-196
33. _ (1998) Mapping genes that underlie ethnic differences in disease risk: methods for detecting linkage in admixed populations, by conditioning on parental admixture. Am J Hum Genet 63:241-251
34. Miller LH, Mason SJ, Clyde DF, McGinniss MH (1976) The resistance factor to Plasmodium vivax in blacks: the Duffy-blood-group genotype, FyFy. N Engl J Med 295:302-304
35. Parra EJ, Marcini A, Akey J, Martinson J, Batzer MA, Cooper R, Forrester T, et al (1998) Estimating African American admixture proportions by use of population-specific alleles. Am J Hum Genet 63:1839-1851
36. Peterson AC, Di Rienzo A, Lehesjoki AE, de la Chapelle A, Slatkin M, Freimer NB (1995) The distribution of linkage disequilibrium over anonymous genome regions. Hum Mol Genet 4:887-894
37. Rabinowitz D (1997) A transmission disequilibrium test for quantitative trait loci. Hum Hered 47:342-350
38. Roychoudhury AK, Nei M (1988) Human polymorphic genes: world distribution. Oxford University Press, New York
39. Shriver MD, Smith MW, Jin L, Marcini A, Akey JM, Deka R, Ferrell RE (1997) Ethnic-affiliation estimation by use of population-specific DNA markers. Am J Hum Genet 60: 957-964
40. Sidak Z (1967) Rectangular confidence regions for the means of multivariate normal distributions. J Am Stat Assoc 62: 626-633
41. Smith MW, Dean M, Carrington M, Winkler C, Huttley GA, Lomb DA, Goedert JJ, et al (1997) Contrasting genetic influence of CCR2 and CCR5 variants on HIV-1 infection and disease progression. Science 277:959-965
42. Sokal RR, Rohlf FJ (1995) Biometry: the principles and practice of statistics in biological research. WH Freeman, New York
43. Spielman RS, McGinnis RE, Ewens WJ (1993) Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes melltius (IDDM). Am J Hum Genet 52:506-516
44. Stephens JC, Briscoe D, O'Brien SJ (1994) Mapping by ad mixture linkage disequilibrium in human populations: limits and guidelines. Am J Hum Genet 55:809-824
45. Stephens JC, Smith MW, Shin HD, O'Brien SJ (1999) Tracking linkage disequilibrium in admixed populations with MALD using microsatellite loci. In: Goldstein DB, Schlötterer C (eds) Microsatellites evolution and applications. Oxford University Press, Oxford, pp 211-224
46. Tournamille C, Colin Y, Cartron JP, Le Van Kim C (1995) Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-negative individuals. Nat Genet 10:224-228
47. Vlahov D, Anthony JC, Munoz A, Margolick J, Nelson KE, Celentano DD, Solomon L, et al (1991) The ALIVE study, a longitudinal study of HIV-1 infection in intravenous drug users: description of methods and characteristics of participants. NIDA Res Monogr 109:75-100
48. Weir BS (1996) Genetic data analysis. II. Methods for discrete population genetic data. Sinauer Associates, Sunderland, MA
49. Wu S, Seino S, Bell GI (1989) Human antithrombin II (AT3) gene length polymorphism revealed by the polymerase chain reaction. Nucleic Acids Res 17:6433
50. Zheng C, Elston RC (1999) Multipoint linkage disequilibrium mapping with particular reference to the African-American population. Genet Epidemiol 17:79-101