Estimating European admixture in African Americans by using microsatellites and a microsatellite haplotype (CD4/Alu)

Human Genetics

Volumn 104, Issue 2, 1999, Pages 149-157

  Destro Bisol, Giovanni ^a   Maviglia, Riccardo ^c   Caglià, Alessandra ^c   Boschi, Ilaria ^c   Spedini, Gabriella ^a   Pascali, Vincenzo ^c   Clark, Andrew ^b   Tishkoff, Sarah ^b  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

^c NONE

Author keywords

[No Author keywords available]

Indexed keywords

CD4 ANTIGEN; MICROSATELLITE DNA;

ARTICLE; DNA POLYMORPHISM; GENE DELETION; GENE FREQUENCY; GENE LOCUS; HAPLOTYPE; HETEROZYGOSITY; HUMAN; MAXIMUM LIKELIHOOD METHOD; NEGRO; PRIORITY JOURNAL; UNITED STATES;

AFRICAN AMERICANS; AFRICAN CONTINENTAL ANCESTRY GROUP; ALU ELEMENTS; ANTIGENS, CD4; EUROPE; EUROPEAN CONTINENTAL ANCESTRY GROUP; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MICROSATELLITE REPEATS;

EID: 0032973641     PISSN: 03406717     EISSN: None     Source Type: Journal    
DOI: 10.1007/s004390050928     Document Type: Article

References (66)

1. Anker RT, Steinbrueck M, Donis-Koeller H (1992) Tetranucleotide repeat polymorphism at the human thyroid peroxidase (hTPO) locus. Hum Mol Genet 1:137
2. Bengtsson BO, Thomson G (1981) Measuring the strength of associations between HLA antigens and diseases. Tissue Antigens 18:356-363
3. Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, Cavalli-Sforza LL (1994) High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368:455-457
4. Brinkmann B, Klintschar M, Neuhuber F, Hohne J, Rolf B (1998) Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat. Am J Hum Genet 62:1408-1415
5. Budowle B, Giusti AM, Waye JS, Baechtel FS, Fourney RM, Adams DE, Presley LA, Deadman HA, Monson KL (1991) Fixed-bin analysis for statistical evaluation of continuous distributions of allelic data from VNTR loci, for use in forensic comparisons. Am J Hum Genet 48:841-855
6. Budowle B, Smerick JB, Keys KM. Moretti TR (1997a) United States population data on the multiplex short tandem repeat loci -HUMTHOI, TPOX, and CSF1PO - and the variable number tandem repeat locus D1S80. J Forensic Sci 42:846-849
7. Budowle B, Nhari LT, Moretti TR, Kanoyangwa SB, Masuka E, Defenbaugh DA (1997b) Zimbabwe black population data on the six short tandem repeat loci - CSFIPO, TPOX, TH01, D3S1358, VWA and FGA. Forensic Sci Int 90:215-221
8. Calafell F, Shuster A, Speed WC, Kidd JR, Kidd K (1998) Short tandem repeat polymorphism evolution in humans. Eur J Hum Genet 6:38-49
9. n microsatellite markers. Am J Hum Genet 52:922-927
10. Chakraborty R (1986) Gene admixture in human populations: models and predictions. Yearbook Phys Anthropol 29:1-43
11. Chakraborty R, Jin L (1992) Heterozygote deficiency, population substructure and their implications in DNA fingerprinting. Hum Genet 88:267-272
12. Chakraborty R, Kidd KK (1991) The utility of DNA typing in forensic work. Science 254:1735-1739
13. Chakraborty R, Smouse PE (1988) Recombination of haplotypes leads to biased estimates of admixture proportions in human populations. Proc Natl Acad Sci USA 85:3071-3074
14. Chakraborty R, Kamboh MI, Nwankwo M, Ferrell RE (1992) Caucasians genes in American Blacks: new data. Am J Hum Genet 50:145-155
15. Chakraborty R, Kimmel M, Stivers DN, Davison LJ, Deka RM (1997) Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci. Proc Natl Acad Sci USA 94:1041-1046
16. Curtin PD (1969) The Atlantic slave trade. University of Wisconsin Press, Madison, Wis
17. n polymorphisms in world populations. Am J Hum Genet 56:461-474
18. Dib C, Faure S, Fizames C, Samson D, Drouot N, Vignal A, Millasseau P, Marc S (1996) A comprehensive genetic map of the human genome based on 5.624 microsatellites. Nature 380:152-154
19. Edwards MC, Gibbs RA (1992) A human dimorphism resulting from loss of an Alu. Genomics 14:590-597
20. Edwards MC, Clemens PR, Tristan M, Pizzuli A, Gibbs RA (1991a) Pentanucleotide repeat length polymorphism at the human CD4 locus. Nucleic Acids Res 19:4791
21. Edwards MC, Civitello AA, Hammond HA, Caskey CT (1991b) DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am J Hum Genet 49:746-756
22. Edwards A, Hammond HA, Jin L, Caskey CT, Chakraborty R (1992) Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups. Genomics 12:241-253
23. Elston RC (1971) The estimation of admixture in racial hybrids. Ann Hum Genet 35:9-17
24. Evett IW, Gill PD, Scranage JK. Weir BS (1996) Establishing the robustness of short-tandem-repeat statistics for forensic applications. Am J Hum Genet 58:398-407
25. Evett IW, Gill PD, Lambert JA, Oldroyd N, Frazier R, Watson S, Panchul S, Connolly A, Kimpton C (1997) Statistical analysis of data for three British ethnic groups form a new STR multiplex. Int J Legal Med 110:5-9
26. Felsenstein J (1989) Phylip-phylogeny inference package (version 3.2). Cladistics 5:164-166
27. Goldstein DB, Ruiz Linares A, Cavalli Sforza LL, Feldman MW (1995) An evaluation of genetic distances for use with microsatellite loci. Genetics 139:463-471
28. Guo SW, Thompson EA (1992) Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48:361-372
29. Hammond HA, Jin L, Zhong Y, Caskey CT, Chakraborty R (1994) Evaluation of 13 short tandem repeat loci for use in personal identification applications. Am J Hum Genet 55:175-189
30. Hawley ME, Kidd KK (1995) HAPLO: a program using the EM algorithm to estimate the frequencies of multi-site haplotypes. J Hered 86:409-411
31. Jin L, Chakraborty R (1995) Population structure, stepwise mutations, heterozygote deficiency and their implications in DNA forensics. Heredity 74:274-285
32. Jorde LB, Bamshad MJ, Watkins WS, Zenger R, Fraley AE, Krakowiak PA, Carpenter KD (1995) Origins and affinities of modern humans: a comparision of mitochondrial and nuclear genetic data. Am J Hum Genet 57:23-528
33. Jorde LB, Rogers AR, Bamshad MJ, Watkins WS, Krakowiak P, Sung S, Kere J, Harpending HC (1997) Microsatellite diversity and demographic history of modern humans. Proc Natl Acad Sci USA 94:3100-3103
34. Kidd KK, Morar B, Castiglione CM, Zhao H, Pakstis AJ, Speed WC, Bonne-Tamir B, Lu R-B, Goldman D, Lee C, Suk Nam Y, Grandy D, Jenkins T, Kidd JR (1998) A global survey of haplotype frequencies and linkage disequilibrium at the DRD2 locus. Hum Genet 103:211-227
35. Kimmel M, Chakraborty R, King JP, Bamshad MJ, Watkins WS, Jorde LB (1998) Signatures of population expansion in microsatellite repeat data. Genetics 148:1921-1930
36. Kimpton C, Walton A, Gill P (1992) A further tetranucleotide repeat polymorphism in the vWF gene. Hum Mol Genet 1:287
37. Kruskal JB (1964) Non-metric multidimensional scaling. Psychometrika 29:1-27
38. Lewontin RC, Hartl DL (1991) Population genetics in forensic DNA typing. Science 254:1745-1750
39. Li H, Schmidt L, Wei MH, Hustad T, Lerman MI, Zbar B, Tory K (1993) Three tetranucleotide polymorphisms for loci: D3S1352; D3S1358; D3S1359. Hum Mol Genet 2:1327
40. Lin Z, Cui X, Li H (1996) Multiplex genotype determination at a large number of gene loci. Proc Natl Acad Sci USA 93:2582-2587
41. Long JC (1991) The genetic structure of admixed populations. Genetics 127:417-428
42. Meyer E, Wiegand P, Brinkmann B (1995) Phenotype differences of STRs in 7 human populations. Int J Legal Med 107:314-322
43. Michalakis Y, Excoffier L (1996) A generic estimation of population subdivision using distances between alleles with special reference for microsatellite loci. Genetics 142:1061-1064
44. Moscetti A, Boschi I, Dobosz M, Destro-Bisol G, Pescarmona M, d' Aloja E, Pascali VL (1995) Fluorescence based classification of microsatellites using wavelength semiautomatic sequencer: genotype assignment and identity test by analysis of comigrating peak profiles. Electrophoresis 16:1875-1880
45. Nauta MJ. Weissing FJ (1996) Constraints on allele size at microsatellite loci: implications tor genetic differentiation. Genetics 143:1021-1032
46. Nei M (1987) Molecular evolutionary genetics. Columbia University press, New York
47. Perez-Lezaun A, Calafell F, Mateu E, Comas D, Ruiz-Pacheco R, Bertranpetit J (1997) Microsatellite variation and the differentiation of modern humans. Hum Genet 99:1-7
48. Polymeropoulos MH, Rath DS, Xiao H, Merril CR (1991a) Tetranucleotide repeat polymorphism at the human coagulation factor XIII subunit gene (F13A1). Nucleic Acids Res 19:4306
49. Polymeropoulos MH, Rath DS, Xiao H, Merril CR (1991b) Tetranucleotide repeat polymorphism at the human c-fes\fps proto-oncogene (FES). Nucleic Acids Res 19:4018
50. Raymond M, Roussel F (1995) An exact test for population differentiation. Evolution 49:1280-1283
51. Reed TE (1969) Caucasian genes in American Negroes. Science 165:762-768
52. Robertson JM, Sgueglia J, Badger CA, Juston AC, Ballantyne J (1995) Forensic applications of a rapid, sensitive, and precise multiplex analysis of the four short tandem repeat loci HUM-VWF31/A, HUMTH01, HUMF13A1, and HUMFES/FPS. Electrophoresis 16:1568-1576
53. Roussel F (1996) Equilibrium values of measures of population subdivision for stepwise mutation processes. Genetics 142:1357-1362
54. Roussel F, Raymond M (1995) Testing heterozygote excess and deficiency. Genetics 140:1413-1419
55. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
56. Sajantila A, Pacek P, Lukka M, Syvnen AC. Nokelainen P, Sistonen P, Peltonen L, Budowle B (1994) A microsatellite polymorphism in the von Willebrand factor gene: comparison of allele frequencies in different population samples and evaluation for forensic medicine. Forensic Sci Int 68:91-102
57. Sharma V, Litt M (1992) Tetranucleotide repeat polymorphism at the D21S11 locus. Hum Mol Genet 1:67
58. Shriver MD, Jin L, Boerwinkle E, Deka R, Ferrell RE, Chakraborty R (1995) A novel measure of genetic distance for highly polymorphic tandem repeat loci. Mol Biol Evol 12:914-920
59. Shriver MD, Jin L, Ferrell RE, Deka R (1997a) Microsatellite data support an early population expansion in Africa. Genome Res 7:586-591
60. Shriver MD, Smith MW, Jin L, Marcini A, Akey JM, Deka R, Ferrell RE (1997b) Ethnic-affiliation estimation by use of population-specific DNA markers. Am J Hum Genet 60:957-964
61. Slatkin M (1995) Hitchiking and associative overdominance at a microsatellite locus. Mol Biol Evol 12:473-480
62. Straub RE, Speer MC, Luo Y, Rojas K, Overhauser J, Ott J, Gilliam C (1993) A microsatellite genetic linkage map of human chromosome 18. Genomics 15:48-56
63. Tishkoff SA, Dietzsch E, Speed W, Pakstis AJ, Kidd J, Cheung K, Bonné-Tamir B, Santachiara-Benerecetti AS, Moral P, Krings M, Paabo S, Watson E, Risch N, Jenkins T, Kidd KK (1996) Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 271:1380-1387
64. Tishkoff SA, Goldman A, Calafell F, Speed WC, Deinard AS, Bonne-Tamir B, Kidd JR, Pakstis AJ, Jenkins T, Kidd KK (1998) A global haplotype analysis of the myotonic dystrophy locus: implications for the evolution of modern humans and for the origin of myotonic dystrophy mutations. Am J Hum Genet 62:1389-1402
65. Weber JL, Wong C (1993) Mutation of human short tandem repeats. Hum Mol Genet. 2:1123-1128
66. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370