The allelic architecture of human disease genes: Common disease - Common variant... or not?

Human Molecular Genetics

Volumn 11, Issue 20, 2002, Pages 2417-2423

  Pritchard, Jonathan K ^a   Cox, Nancy J ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; CONTROLLED STUDY; GENE FREQUENCY; GENE FUNCTION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENE MUTATION; GENE STRUCTURE; GENETIC DISORDER; GENETIC HETEROGENEITY; GENETIC SELECTION; GENETIC SUSCEPTIBILITY; GENETIC TRAIT; HUMAN; HUMAN GENETICS; HUMAN GENOME; MUTATION RATE; PRIORITY JOURNAL; REVIEW; THEORETICAL MODEL;

EID: 0036799545     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/11.20.2417     Document Type: Review

References (41)

1. Collins, F.S. and Guttmacher, A.E. (2001) Genetics moves into the medical mainstream. JAMA, 286, 2322-2324.
2. Cooper, D.N., Ball, E.V. and Krawczak, M. (1998) The human gene mutation database. Nucleic Acids Res., 26, 285-287.
3. Risch, N. (2000) Searching for genetic determinants in the new millennium. Nature, 405, 847-856.
4. Altmüller, J., Palmer, L.J., Fischer, G., Scherb, H. and Wjst, M. (2001) Genomewide scans of complex human diseases: true linkage is hard to find. Am. J. Hum. Genet., 69, 936-950.
5. Fajans, S.S., Bell, G.I. and Polonsky, K.S. (2001) Molecular mechanisms and clinical pathophysiology of maturity-onset diabetes of the young. N. Engl. J. Med., 345, 971-980.
6. Risch, N. and Merikangas, K. (1996) The future of genetic studies of complex human diseases. Science, 273, 1516-1517.
7. Pritchard, J.K. (2001) Are rare variants responsible for susceptibility to common diseases? Am. J. Hum. Genet., 69, 124-137.
8. Reich, D.E. and Lander, E.S. (2001) On the allelic spectrum of human disease. Trends Genet., 17, 502-510.
9. Hartl, D.L. and Campbell, R.B. (1982) Allele multiplicity in simple Mendelian disorders. Am. J. Hum. Genet., 34, 866-873.
10. Lander, E.S. (1996) The new genomics: global views of biology Science, 274, 536-539.
11. Chakravarti, A. (1999) Population genetics - making sense out of sequence. Nat. Genet., 21, 56-60.
12. Gabriel, S.B., Schaffner, S.F., Nguyen, H., Moore, J.M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M. et al. (2002) The structure of haplotype blocks in the human genome. Science, 296, 2225-2229.
13. Slager, S.L., Huang, J. and Vieland, V.J. (2000) Effect of allelic heterogeneity on the power of the transmission disequilibrium test. Genet. Epidemiol., 18, 143-156.
14. Wright, A.F., Carothers, A.D. and Pirastu, M. (1999) Population choice in mapping genes for complex diseases. Nat. Genet., 23, 397-404.
15. Hartl, D.L. and Clark, A.G. (2000) Principles of Population Genetics. Sinauer, Sunderland, MA.
16. Green, P.M., Saad, S., Lewis, C.M. and Giannelli, F. (1999) Mutation rates in humans. I. Overall and sex-specific rates obtained from a population study of hemophilia B. Am. J. Hum. Genet., 65, 1572-1579.
17. Estivill, X., Bancells, C. and Ramos, C. (1997) Geographic distribution and regional origin of 272 cystic fibrosis mutations in European populations. Hum. Mutat., 10, 135-154.
18. Gabriel, S.E., Brigman, K.N., Koller, B.H., Boucher, R.C. and Stutts, M.J. (1994) Cystic fibrosis heterozygote resistance to cholera toxin in the cystic fibrosis mouse model. Science, 266, 107-109.
19. Wiuf, C. (2001) Do ΔF508 heterozygotes have a selective advantage? Genet. Res., 78, 41-47.
20. Corder, E.H., Saunders, A.M., Strittmatter, W.J., Schmechel, D.E., Gaskell, P.C., Small, G.W., Roses, A.D. Haines, J.L. and Pericak-Vance, M.A. (1993) Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late onset families. Science, 261, 921-923.
21. Fullerton, S.M., Clark, A.G., Weiss, K.M., Nickerson, D.A., Taylor, S.L., Stengard, J.H., Salomaa, V., Vartiainen, E., Perola, M., Boerwinkle, E. and Sing, C.F. (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.
22. Altshuler, D., Hirschhorn, J.N., Klannemark, M., Lindgren, C.M., Vohl, M.C., Nemesh, J., Lane, C.R., Schaffner, S.F., Bolk, S., Brewer, C. et al. (2000) The common PPARγ Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes. Nat. Genet., 26, 76-80.
23. Bell, G.I., Horita, S. and Karam, J.H. (1984) A polymorphic locus near the human insulin gene is associated with insulin-dependent diabetes mellitus. Diabetes, 33, 176-183.
24. Hugot, J.P., Chamaillard, M., Zouali, H., Lesage, S., Cezard, J.P., Belaiche, J., Almer, S., Tysk, C., O'Morain, C.A., Gassull, M. et al. (2001) Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature, 411, 599-603.
25. Ogura, Y., Bonen, D.K., Inohara, N., Nicolae, D.L., Chen, F.F., Ramos, R., Britton, H., Moran, T., Karaliuskas, R., Duerr, R.H. et al. (2001) A frameshift mutation in NOD2 is associated with susceptibility to Crohn's disease. Nature, 411, 603-606.
26. Horikawa, Y., Oda, N., Cox, N.J., Li, X., Orho-Melander, M., Hara, M., Hinokio, Y., Lindner, T.H., Mashima, H., Schwarz, P.E. et al. (2000) Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus. Nat. Genet., 26, 163-175.
27. Neel, J.V. (1962) Diabetes mellitus: a 'thrifty' genotype rendered detrimental by progress? Am. J. Hum. Genet., 14, 353-362.
28. Slatkin, M. and Rannala, B. (1997) The sampling distribution of disease-associated alleles. Genetics, 147, 1855-1861.
29. Sherry, S.T., Rogers, A.R., Harpending, H., Soodyall, H., Jenkins, T. and Stoneking, M. (1994) Mismatch distributions of mtDNA reveal recent human population expansions. Hum. Biol., 66, 761-775.
30. Kimmel, M., Chakraborty, R., King, J.P., Bamshad, M., Watkins, W.S. and Jorde, L.B. (1998) Signatures of population expansion in microsatellite repeat data. Genetics, 148, 1921-1930.
31. Reich, D.E. and Goldstein, D.B. (1998) Genetic evidence for a Paleolithic human population expansion in Africa. Proc. Natl Acad. Sci. USA, 95, 8119-8123.
32. Pritchard, J.K., Seielstad, M.T., Perez-Lezaun, A. and Feldman, M.W. (1999) Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Mol. Biol. Evol., 16, 1791-1798.
33. Wall, J.D. and Przeworski, M. (2000) When did the human population start increasing? Genetics, 155, 1865-1874.
34. Pritchard, J.K. and Przeworski, M. (2001) Linkage disequilibrium in humans: models and data. Am. J. Hum. Genet., 69, 1-14.
35. Reich, D.E., Cargill, M., Bolk, S., Ireland, J., Sabeti, P.C., Richter, D.J., Lavery, T., Kouyoumjian, R., Farhadian, S.F., Ward, R. and Lander, E.S. (2001) Linkage disequilibrium in the human genome. Nature, 411, 199-204.
36. Ewens, W.J. (1979) Mathematical Population Genetics. Springer-Verlag, New York.
37. Wright, S. (1949) Adaptation and selection. In Jepson, G.I., Simpson, G.G. and Mayr, E. (eds), Genetics, Palaeontology and Evolution. Princeton University Press, Princeton, pp. 365-389.
38. Slatkin, M. and Bertorelle, G. (2001) The use of intraallelic variability for testing neutrality and estimating population growth rate. Genetics, 158, 865-874.
39. Spielman, R.S., McGinnis, R.E. and Ewens, W.J. (1993) Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am. J. Hum. Genet., 52, 506-513.
40. Cox, N.J., Wapelhorst, B., Morrison, V.A., Johnson, L., Pinchuk, L., Spielman, R.S., Todd, J.A. and Concannon, P. (2001) Seven regions of the genome show evidence of linkage to type 1 diabetes in a consensus analysis of 767 multiplex families. Am. J. Hum. Genet., 69, 820-830.
41. Hanis, C.L., Boerwinkle, E., Chakraborty, R., Ellsworth, D.L., Concannon, P., Stirling, B., Morrison, V.A., Wapelhorst, B., Spielman, R.S., Gogolin-Ewens, K.J. et al. A genome-wide search for human noninsulin-dependent (type 2) diabetes genes reveals a major susceptibility locus on chromosome 2. Nat. Genet., 13, 161-166.