|
|
The Hardy-Weinberg principle and its applications
in modern population genetics |
John J. CHEN, |
Department of Preventive
Medicine, State University of New York at Stony Brook, Stony Brook,
NY 11794-8036, USA; |
|
|
Abstract The discovery of the Hardy-Weinberg principle marked the beginning of the field of population genetics. Over the past hundred years, it has provided a starting point for many population genetic investigations. In this review, the Hardy-Weinberg principle, its statistical testing, and several of its applications in various modern population genetic research areas, including allelic variability and selection in the human leukocyte antigen region, microsatellite genotyping error detection, and accuracy of haplotype estimation, are discussed.
|
Keywords
the Hardy-Weinberg principle
statistical testing
population genetics
human leukocyte antigens
microsatellite genotyping
haplotype estimation
|
Issue Date: 01 August 2010
|
|
|
Chen J J, Duan T, Single R, Mather K, Thomson G(2005). Hardy-Weinbergtesting of a single homozygous genotype. Genetics, 170(3): 1439―1442
doi: 10.1534/genetics.105.043190
|
|
Chen J J, Hollenbach J A, Trachtenberg E A, Just J J, Carrington M, R?nningen K S, Begovich A, King M C, McWeeney S, Mack S J, Erlich H A, Thomson G(1999). Hardy-Weinberg testing for HLA class II (DRB1, DQA1,DQB1, and DPB1) loci in 26 human ethnic groups. Tissue Antigens, 54(6): 533―542
doi: 10.1034/j.1399-0039.1999.540601.x
|
|
Chen J J, Thomson G(1999). The variancefor the disequilibrium coefficient in the individual Hardy-Weinbergtest. Biometrics, 55(4): 1269―1272
doi: 10.1111/j.0006-341X.1999.01269.x
|
|
Crow J F(1988). Eighty years ago: the beginnings of population genetics. Genetics, 119(3): 473―476
|
|
Demers D B, Curry E T, Egholm M, Sozer A C(1995). Enhanced PCR amplification of VNTR locus D1S80 using peptide nucleicacid (PNA). Nucl Acids Res, 23(15): 3050―3055
doi: 10.1093/nar/23.15.3050
|
|
Dempster A P, Laird N M, Rubin D B(1977). Maximum likelihood from incompletedata via EM algorithm. J R Stat Soc, B, 39: 1―38
|
|
Ellegren H(2000). Heterogeneous mutation processes in human microsatelliteDNA sequences. Nat Genet, 24(4): 400―402
doi: 10.1038/74249
|
|
Ellegren H(2004). Microsatellites: simple sequences with complex evolution. Nat Rev Genet, 5(6): 435―445
doi: 10.1038/nrg1348
|
|
Elston R C, Forthofer R(1977). Testingfor Hardy-Weinberg equilibrium in small samples. Biometrics, 33(3): 536―542
doi: 10.2307/2529370
|
|
Emigh T H(1980). A comparison of tests for Hardy-Weinberg equilibrium. Biometrics, 36(4): 627―642
doi: 10.2307/2556115
|
|
Epstein M P, Satten G A(2003). Inferenceon haplotype effects in case-control studies using unphased genotypedata. Am J Hum Genet, 73(6): 1316―1329
doi: 10.1086/380204
|
|
Excoffier L, Laval G, Schneider S(2005). Arlequin (version 3.0): an integratedsoftware package for population genetics data analysis. Evol Bioinform Online, 1: 47―50
|
|
Excoffier L, Slatkin M(1995). Maximum-likelihoodestimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol, 12(5): 921―927
|
|
Fallin D, Schork N J(2000). Accuracyof haplotype frequency estimation for biallelic loci, via the expectation-maximizationalgorithm for unphased diploid genotype data. Am J Hum Genet, 67(4): 947―959
doi: 10.1086/303069
|
|
Gomes I, Collins A, Lonjou C, Thomas N S, Wilkinson J, Watson M, Morton N(1999). Hardy-Weinberg quality control. Ann Hum Genet, 63(Pt 6): 535―538
doi: 10.1046/j.1469-1809.1999.6360535.x
|
|
Guo S W, Thompson E A(1992). Performingthe exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics, 48(2): 361―372
doi: 10.2307/2532296
|
|
Hardy G H(1908). Mendelian proportions in a mixed population. Science, 28(706): 49―50
doi: 10.1126/science.28.706.49
|
|
Hearne C M, Ghosh S, Todd J A(1992). Microsatellites for linkage analysisof genetic traits. Trends Genet, 8(8): 288―294
doi: 10.1016/0168-9525(92)90256-4
|
|
Hernández J L, Weir B S(1989). A disequilibriumcoefficient approach to Hardy-Weinberg testing. Biometrics, 45(1): 53―70
doi: 10.2307/2532034
|
|
Hosking L, Lumsden S, Lewis K, Yeo A, McCarthy L, Bansal A, Riley J, Purvis I, Xu C F(2004). Detection of genotyping errors by Hardy-Weinberg equilibrium testing. Eur J Hum Genet, 12(5): 395―399
doi: 10.1038/sj.ejhg.5201164
|
|
Lancaster A K, Single R M, Solberg O D, Nelson M P, Thomson G(2007). PyPopupdate—a software pipeline for large-scale multilocus populationgenomics. Tissue Antigens, 69(Suppl 1): 192―197
doi: 10.1111/j.1399-0039.2006.00769.x
|
|
Li C C(1955). Population Genetics. Chicago: University of Chicago Press
|
|
Louis E J, Dempster E R(1987). An exacttest for Hardy-Weinberg and multiple alleles. Biometrics, 43(4): 805―811
doi: 10.2307/2531534
|
|
Meng X L, Rubin D B(1993). Mximum-likelihoodestimation via the ECM algorithm – a general framework. Biometrika, 80(2): 267―278
doi: 10.1093/biomet/80.2.267
|
|
Miller K M, Kaukinen K H, Beacham T D, Withler R E(2001). Geographic heterogeneity in natural selection on anMHC locus in sockeye salmon. Genetica, 111(1―3): 237―257
doi: 10.1023/A:1013716020351
|
|
Morin P A, Leduc R G, Archer F I, Martien K K, Huebinger R, Bickham J W, Taylor B L(2009). Significant deviations from Hardy–Weinberg equilibriumcaused by low levels of microsatellite genotyping errors. Molecular Ecology Resources, 9(2): 498―504
|
|
Parham P(2005). MHC class I molecules and KIRs in human history, healthand survival. Nat Rev Immunol, 5(3): 201―214
doi: 10.1038/nri1570
|
|
Robinson J, Waller M J, Fail S C, McWilliam H, Lopez R, Parham P, Marsh S G E(2009). The IMGT/HLA database. NuclAcids Res, 37 (SI): D1013―D1017
|
|
Rodríguez S, Visedo G, Zapata C(2001). Detection of errors in dinucleotiderepeat typing by nondenaturing electrophoresis. Electrophoresis, 22(13): 2656―2664
doi: 10.1002/1522-2683(200108)22:13<2656::AID-ELPS2656>3.0.CO;2-6
|
|
Rousset F, Raymond M(1995). Testingheterozygote excess and deficiency. Genetics, 140(4): 1413―1419
|
|
Schaid D J(2004). Evaluating associations of haplotypes with traits. Genet Epidemiol, 27(4): 348―364
doi: 10.1002/gepi.20037
|
|
Shoemaker J, Painter I, Weir B S(1998). A Bayesian characterization of Hardy-Weinbergdisequilibrium. Genetics, 149(4): 2079―2088
|
|
Single R M, Meyer D, Hollenbach J, Nelson M, Noble J A, Erlich H A, Thomson G(2002). Haplotype frequency estimation in patient populations:an example from the HLA region. Genet Epidemiol, 22: 186―195
doi: 10.1002/gepi.0163
|
|
Smith C A B(1986). Chi-squared tests with small numbers. Ann Hum Genet, 50(Pt 2): 163―167
doi: 10.1111/j.1469-1809.1986.tb01035.x
|
|
Solberg O D, Mack S J, Lancaster A K, Single R M, Tsai Y, Sanchez-Mazas A, Thomson G(2008). Balancing selection and heterogeneity across the classicalhuman leukocyte antigen loci: a meta-analytic review of 497 populationstudies. Hum Immunol, 69(7): 443―464
doi: 10.1016/j.humimm.2008.05.001
|
|
Takahata N, Satta Y, Klein J(1992). Polymorphism and balancing selectionat major histocompatibility complex loci. Genetics, 130(4): 925―938
|
|
Trachtenberg E, Korber B, Sollars C, Kepler T B, Hraber P T, Hayes E, Funkhouser R, Fugate M, Theiler J, Hsu Y S, Kunstman K, Wu S, Phair J, Erlich H, Wolinsky S(2003). Advantage of rare HLA supertype in HIV disease progression. Nat Med, 9(7): 928―935
doi: 10.1038/nm893
|
|
Traherne J A(2008). Human MHC architecture and evolution: implications fordisease association studies. Int J Immunogenet, 35(3): 179―192
doi: 10.1111/j.1744-313X.2008.00765.x
|
|
Weinberg W(1908). über den Nachweis der Vererbung beim Menschen. Jahresh. Ver. Vaterl. Naturkd. Württemb, 64: 369―382. On the demonstrationof heredity in man (Translated by S.H. Boyer, 1963)
|
|
Westfall P H, Young S S(1993). Resampling-basedmultiple testing. New York: Wiley
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
|
Shared |
|
|
|
|
|
Discussed |
|
|
|
|