Abstract
Four single nucleotide polymorphisms (SNPs) and a variable number of tandem repeats (VNTR) polymorphism located within disease associated/causing genes were typed in four populations of different tribal and ethnic affiliation from the Sudan. The genotype and allele frequencies were compared with those of other groups from published and unpublished data of world populations. The combined Sudanese sample conformed with Hardy–Weinberg equilibrium (HWE) expectation. However, population sub-structuring according to ethnic/linguistic group indicated at least two SNPs in departure from HWE. Differences in allele frequencies and genotype distribution between groups was also noted in three of the four SNPs. The other loci were distributed homogeneously within the populations studied with genotype frequencies in agreement with HWE expectation. These results highlight the importance of inter-population stratification for polymorphic markers, as well as the potential influence of evolutionary history and ethnic variation of loci, in the general distribution of SNPs and other polymorphisms.
Similar content being viewed by others
References
Bayoumi, R.A., T.S. Taha & N. Saha, 1985. A study of some genetic characteristics of the Fur and Baggara tribes of the Sudan. Am. J. Phys. Anthro. 67: 363–370
Beckman, G., R. Birgander, A. Sjalander, N. Saha, P.A. Holmberg, A. Kivela & L. Beckman, 1994. Is p53 polymorphism maintained by natural selection? Hum. Hered. 44: 266–270
Bonafe, M., F. Olivieri, D. Mari, G. Baggio, R. Mattace, M. Beradelli, P. Sansoni et al., 1999. p53 codon 72 polymorphism and longevity: additional data on centenarians from continental Italy and Sardinia. Am. J. Hum. Genet. 65: 1782–1785
Brinkman, B.M., M.J. Giphart, A. Verhoef, E.L. Kaijzel, A.M. Naipal, M.R. Daha, F.C. Breedveld & C.L. Verweij, 1994. Tumor necrosis alpha –308 gene variants in relation to major histocompatibility complex alleles and Felty's syndrome. Hum. Immunol. 41: 259–266
Brookes, J.B., 1999. The essence of SNPs. Gene 234: 177–186.
Cabrera, M., M.A. Shaw, C. Sharples, H. Williams, M. Castes, J. Convit & J.M. Blackwell, 1995. Polymorphism in tumor necrosis factor genes associated with mucocutaneous leishmaniasis. J. Exp. Med. 180: 1741–1752
Caggana, M., K. Walker, A.A. Reilly, J.M. Conroy, S. Duva & A.C. Walsh, 1999. Population based studies reveal differences in the allelic frequencies of two functionally significant human interleukin-4 receptor polymorphisms in several ethnic groups. Genet. Med. 1: 267–271
Cavalli-Sforza, L.L., 1998. The DNA revolution in population genetic. Trends Genet. 14: 60–65
Cavalli-Sforza, L.L., P. Menozzi & A. Piazza, 1996. Africa. In: The History and Geography of Human Genes. Princeton University Press, New York, pp. 169–171
Chapman, N.H. & E.M. Wijsman, 1998. Genome screen using linkage disequilibrium tests: optimal marker characteristics. Am. J. Hum. Genet. 63: 1875–1885
Conway, D.J., M.J. Holland, R.L. Bailey, A.E. Campbell, O.S. Mahdi, R. Jennings, E. Mbena & D.C.W. Mabey, 1997. Scaring trachoma is associated with polymorphism in the tumor necrosis factor alpha gene promoter and with elevated TNF-levels in tear fluid. Infect. Immun. 65: 1003–1006
Cox, A., A.M. Gonzalez, A.G. Wilson, R.M. Wilson, J.D. Ward, C.M. Artlett, K. Welsh & G.W. Duff, 1994. Comparative analysis of the genetic association of HLA-DR3 and tumor necrosis factor alpha with human IDDM. Diabetologia 37: 500–503
Goddard, K.A.B., P.J. Hopkins, J.M. Hall & J.S. Witte, 2000. Linkage disequilibrium and allele-frequency distribution for single nucleotide polymorphisms in five populations. Am. J. Hum. Genet. 66: 216–234.
Grimes, B.F., 1988. Ethnologue. Vol. 11, Summer Institute of Linguistics, Dallas, pp. 306–317.
Healey, C.S., A.M. Dunning, M.D. Teare, D. Chase, L. Parker, J. Burn, J. Chang-Claude, A. Mannermaa, V. Kataja, D.G. Huntsman, P.D. Pharoah, R.N. Luben, D.F. Easton & B.A. Ponder, 2000. A common variant in BRCA2 is associated with both breast cancer risk and prenatal viability. Nature Genet. 3: 362–364.
Helland, A., A. Langerod, H. Johnsen, A.O. Olsen, E. Skovlund & A.L. Borresen-Dale, 1998. p53 Polymorphism and risk of cervical cancer. Nature 396: 530–531.
Hildesheim, A., M. Schiffman, L.A. Brinton, J.F. Fraumeni Jr., R. Herrero, M.C. Bratti, P. Schwartz, R. Mortel, W. Barnes, M. Greenberg, L. McGowan, D.R. Scott, M. Martin, J.E. Herrera & M. Carrington, 1998. p53 polymorphism and risk of cervical cancer. Nature 396: 531–532.
Josefsson, A.M., P.K. Magnusson, N. Ylitalo, P. Quarforth-Tubbin, J. Ponten, H.O. Adami, U.B. Gyllensten, N. Ylitalo et al., 1998. p53 polymorphism and risk of cervical cancer. Nature 396: 531.
Knight, J.C. & D. Kwiatkowski, 1999. Inherited variability of tumor necrosis factor production and susceptibility to infectious disease. Proc. Assoc. Am. Phys. 111: 290–298.
Kruglyak, L., 1997. The use of a genetic map of biallelic markers in linkage studies. Nature Genet. 17: 21–24.
Liu, J., T.M. Fujiwara, N.T. Buu, F.O. Sanchez, M. Cellier, A.J. Paradis, D. Frappier, E. Skamene, P. Gros, K. Morgan et al., 1995. Identification of polymorphisms and sequence variants in the human homologue of the mouse natural resistance-associated macrophage protein gene. Am. J. Hum. Genet. 56: 845–853.
Messer, G., U. Spengler, M.C. Jung, G. Honold, K. Bulmer, G.R. Pape, G. Riethmuller & E.H. Weiss, 1991. Polymorphic structure of the tumor necrosis factor (TNF) locus: an NcoI polymorphism in the first intron of the human TNF-β gene correlates with a variant amino acid in position 26 and a reduced level of TNF-α production. J. Exp. Med. 173: 209–219.
Mout, R., R. Willemze & J.E. Landegent, 1991. Repeat polymorphisms in the interleukin-4 gene (IL4). Nucl. Acids Res. 19: 3763.
Perea, W.A., A. Moren, T. Ancelle & E. Soundrope, 1989. Epdemic of visceral leishmaniasis in southern Sudan. Lancet 2(8673): 1222–1225.
Ramel, C., 1992. Evolutionary aspects of human cancer. Pharmacogenetics 6: 344–353.
Reich, D.E., M. Cargill & S. Bolk, 2001. Linkage disequilibrium in the human genome. Nature 411: 199–203.
Ring, H.Z. & D.L. Kroetz, 2002. Candidate gene approach for pharmacogenetic studies. Pharmacogenomics 3: 47–56.
Seaman, J., A.J. Mercer & E. Sondorp, 1996. The epidemic of visceral leishmaniasis in western Upper Nile, southern Sudan: course and impact from 1984 to 1994. Int. J. Epidemiol. 25: 862–871.
Ibrahim, M.E., B. Lambson, A.O. Yousif, N.S. Deifalla, D.A. Alnaiem, A. Ismail, H. Yousif, H.W. Ghalib, E.A. Khalil, A. Kadaro, D.C. Barker & A.M. El Hassan, 1999. Kala-Azar in a high transmission focus: an ethnic and geographic dimension. Am. J. Trop. Med. Hyg. 61: 941–944.
Simigielski, E.M., K. Sirthin, M. Ward & S.T. Sherry, 2000. dbSNP: a database of single nucleotide polymorphisms. Nucl. Acids Res. 28: 352–355.
Storey, A., M. Thomas, A. Kalita et al., 1998. Role of a p53 polymorphism in the development of human papilloma virusassociated cancer. Nature 393: 229–233.
Warnich, L., H.F. Waso, I.M. Groenewald, A.E. Bester, J.N. de Villiers, M.J. Kotze, A.G. Lynch & J.H. Louw, 2001. Single nucleotide polymorphisms of the protoporphyrinogen oxidase gene: inter-population heterogeneity of allelic variation. Mol. Cell Probes 15: 217–221.
Wilson, A.G., F.S. Glovine, A.F. Blakemore & G.W. Duff, 1992. Single base polymorphism in the human tumor necrosis factor alpha gene detectable by NcoI restriction of PCR products. Hum. Mol. Genet. 1: 353.
Xiong, M. & L. Jin, 1999. Comparison of the power and accuracy of biallelic and microsatellite makers in population-based gene mapping methods. Am. J. Hum. Genet. 64: 629–640.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Bereir, R., Mohamed, H., Seielstad, M. et al. Allele Frequency and Genotype Distribution of Polymorphisms within Disease-Related Genes is Influenced by Ethnic Population Sub-Structuring in Sudan. Genetica 119, 57–63 (2003). https://doi.org/10.1023/A:1024486716497
Issue Date:
DOI: https://doi.org/10.1023/A:1024486716497