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3 - Population genetics and disease

Published online by Cambridge University Press:  17 August 2009

Alan Wright
Affiliation:
MRC Human Genetics Unit, Edinburgh
Nicholas Hastie
Affiliation:
MRC Human Genetics Unit, Edinburgh
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Summary

Introduction

The field of population genetics may be broadly defined as the study of the generation and maintenance of genetic variation within populations. Population genetic theory plays an important role in shaping our understanding of human genetic variation in general, and the genetic basis of common disease in particular. It also plays a central role in association- and linkage disequilibrium-based approaches to disease mapping, as these can only be properly understood within a population genetic framework.

One way to think about the role of population genetics in the study of complex disease is as follows. If it were possible to sequence every base pair of every person in a study population, conventional statistical methods would, arguably, be sufficient to make inferences about which sequence variants are associated with disease. Population genetics provides an analytical framework for predicting the nature of unobserved variation that lies between genotyped sites, or in unsampled individuals. Similarly, population genetic approaches are used to explore plausible models of complex disease, as there are at present few empirical data on the genetic basis of complex diseases. Lastly, population genetics allows us to measure the effect of genetic variation on health in an indirect way, by detecting selective effects that may be too subtle to observe directly in prospective data, or that may have affected humans during our evolutionary history. In short, biological properties of a species which we cannot directly observe are illuminated by population genetics.

Type
Chapter
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Genes and Common Diseases
Genetics in Modern Medicine
, pp. 44 - 58
Publisher: Cambridge University Press
Print publication year: 2007

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References

Altshuler, D., Brooks, L. D., Chakravarti, A.et al.; International HapMap Consortium. (2005). A haplotype map of the human genome. Nature, 437, 1299–320.Google Scholar
Baird, P. A., Anderson, T. W., Newcombe, H. B. and Lowry, R. B. (1988). Genetic disorders in children and young adults: a population study. Am J Hum Genet, 42, 677–93.Google Scholar
Botstein, D. and Risch, N. (2003). Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet, 33 Suppl, 228–37.CrossRefGoogle ScholarPubMed
Carlson, C. S., Eberle, M. A., Rieder, M. J.et al. (2003). Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat Genet, 33, 518–21.CrossRefGoogle ScholarPubMed
Chakravarti, A. (1999). Population genetics–making sense out of sequence. Nat Genet, 21, 56–60.CrossRefGoogle ScholarPubMed
Charlesworth, B., Morgan, M. T. and Charlesworth, D. (1993). The effects of deleterious mutations on neutral variation. Genetics, 134, 1289–303.Google Scholar
Cohen, J. C., Pertsemlidis, A., Fahmi, S.et al. (2006). Multiple rare variants in NPC1L1 associated with reduced sterol absorption and plasma low-density lipoprotein levels. Proc Natl Acad Sci USA, 103, 1810–15.CrossRefGoogle ScholarPubMed
Cohen, J. C., Kiss, R. S., Pertsemlidis, A.et al. (2004). Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science, 305, 869–72.CrossRefGoogle ScholarPubMed
Conrad, D. F., Andrews, T. D., Carter, N. P., Hurles, M. E. and Pritchard, J. K. (2006). A high-resolution survey of deletion polymorphism in the human genome. Nat Genet, 38, 75–81.CrossRefGoogle ScholarPubMed
Crow, J. F. (2000). The origins, patterns and implications of human spontaneous mutation. Nat Rev Genet, 1, 40–7.CrossRefGoogle ScholarPubMed
Crow, J. F. and Kimura, M. (1970). An introduction to population genetics theory. New York: Harper and Row.Google Scholar
Devlin, B. and Risch, N. (1995). A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics, 29, 311–22.CrossRefGoogle ScholarPubMed
Dilda, C. L. and Mackay, T. F. (2002). The genetic architecture of Drosophila sensory bristle number. Genetics, 162, 1655–74.Google ScholarPubMed
Estivill, X., Bancells, C. and Ramos, C. (1997). Mutations in European populations. The Biomed CF Mutation Analysis Consortium. Hum Mutat, 10, 135–54.3.0.CO;2-J>CrossRefGoogle ScholarPubMed
Ewens, W. J. (1972). The sampling theory of selectively neutral alleles. Theor Pop Gen, 3, 87–112.CrossRefGoogle ScholarPubMed
Falconer, D. S. and Mackay, T. F. C. (1996). Introduction to quantitative genetics. Essex, UK: Longman Group Ltd.Google Scholar
Fay, J. C., Wyckoff, G. J. and Wu, C. I. (2001). Positive and negative selection on the human genome. Genetics, 158, 1227–34.Google ScholarPubMed
Gabriel, S. B., Schaffner, S. F., Nguyen, H.et al. (2002). The structure of haplotype blocks in the human genome. Science, 296, 2225–9.CrossRefGoogle ScholarPubMed
Garrigan, D. and Hedrick, P. W. (2003). Perspective: detecting adaptive molecular polymorphism: lessons from the MHC. Evolution, 57, 1707–22.CrossRefGoogle ScholarPubMed
Gillespie, J. (2004). Population genetics, a concise guide, 2nd edn. Baltimore, MD: Johns Hopkins University Press.Google Scholar
Gomes, I., Collins, A., Lonjou, C.et al. (1999). Hardy-Weinberg quality control. Ann Hum Genet, 63, 535–8.CrossRefGoogle ScholarPubMed
Haldane, J. B. S. (1947). The mutation rate of the gene for hemophelia and its segregation ratios in males and females. Ann Eugen, 13, 262–71.CrossRefGoogle Scholar
Hardy, G. H. (1908). Mendelian proportions in a mixed population. Science, 28, 49–50.CrossRefGoogle Scholar
Hartl, D. and Clark, A. G. (1997). Principles of population genetics, 3rd edition Sunderland, MA: Sinauer Associates Inc.Google Scholar
Hartl, D. L. and Campbell, R. B. (1982). Allele multiplicity in simple Mendelian disorders. Am J Hum Genet, 34, 866–73.Google ScholarPubMed
Hayes, B. and Goddard, M. E. (2001). The distribution of the effects of genes affecting quantitative traits in livestock. Genet Sel Evol, 33, 209–29.CrossRefGoogle ScholarPubMed
Hein, J., Schierup, M. K. and Wiuf, C. (2005). Gene genealogies, variation and evolution: a primer in coalescent theory. New York, USA: Oxford University Press.Google Scholar
Hudson, R. R. (1983). Properties of a neutral allele model with intragenic recombination. Theor Popul Biol, 23, 183–201.CrossRefGoogle ScholarPubMed
Hudson, R. R. (1990). Gene genealogies and the coalescent process., volume 7. Oxford, UK: Oxford University Press, pp. 1–43.Google Scholar
Hudson, R. R. (2001). Linkage disequilibrium and recombination. In Balding, D., Bishop, M. and Cannings, C. eds., Handbook of statistical genetics. Wiley, pp. 309–24.Google Scholar
Hugot, J. P., Chamaillard, M., Zouali, H.et al. (2001). Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature, 411, 599–603.CrossRefGoogle ScholarPubMed
Iafrate, A. J., Feuk, L., Rivera, M. N.et al. (2004). Detection of large-scale variation in the human genome. Nat Genet, 36, 949–51.CrossRefGoogle ScholarPubMed
Kingman, J. F. C. (1982). On the genealogy of large populations. J Appl Probab, 19A, 27–43.CrossRefGoogle Scholar
Kondrashov, A. S. (1995). Contamination of the genomes by very slightly deleterious mutations. why have we not died 100 times over?J Theor Biol, 175, 583–94.CrossRefGoogle Scholar
Kondrashov, A. S. (2003). Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases. Hum Mutat, 21, 12–27.CrossRefGoogle ScholarPubMed
Kreitman, M. (2000). Methods to detect selection in populations with applications to the human. Ann Rev Genomics Hum Genet, 1, 539–59.CrossRefGoogle ScholarPubMed
Kruglyak, L. (1999). Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet, 22, 139–44.CrossRefGoogle ScholarPubMed
Lander, E. S. (1996). The new genomics: global views of biology. Science, 274, 536–9.CrossRefGoogle ScholarPubMed
Lohmueller, K. E., Pearce, C. L., Pike, M., Lander, E. S. and Hirschhorn, J. N. (2003). Metaanalysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat Genet, 33, 177–82.CrossRefGoogle Scholar
Nachman, M. W. and Crowell, S. L. (2000). Estimate of the mutation rate per nucleotide in humans. Genetics, 156, 297–304.Google ScholarPubMed
Nielsen, D. M., Ehm, M. G. and Weir, B. S. (1998). Detecting marker-disease association by testing for Hardy-Weinberg disequilibrium at a marker locus. Am J Hum Genet, 63, 1531–40.CrossRefGoogle Scholar
Nordborg, M. (2001). Coalescent theory. In Balding, D., Bishop, M. and Cannings, C. eds., Handbook of statistical genetics. Chichester, England: Wiley, pp. 179–212.Google Scholar
Orr, H. A. (1998). The population genetics of adaptation: the distribution of factors fixed during evolution. Evolution, 52, 935–49.CrossRefGoogle ScholarPubMed
Pritchard, J. K. (2001). Are rare variants responsible for susceptibility to complex diseases?Am J Hum Genet, 69, 124–37.CrossRefGoogle ScholarPubMed
Pritchard, J. K. and Cox, N. J. (2002). The allelic architecture of human disease genes: common disease-common variant … or not?Hum Mol Genet, 11, 2417–23.CrossRefGoogle ScholarPubMed
Pritchard, J. K. and Przeworski, M. (2001). Linkage disequilibrium in humans: models and data. Am J Hum Genet, 69, 1–14.CrossRefGoogle ScholarPubMed
Reich, D. E., Cargill, M., Bolk, S.et al. (2001). Linkage disequilibrium in the human genome. Nature, 411, 199–204.CrossRefGoogle ScholarPubMed
Reich, D. E. and Lander, E. S. (2001). On the allelic spectrum of human disease. Trends Genet, 17, 502–10.CrossRefGoogle ScholarPubMed
Rimoin, D. L., Connor, J. M. and Pyeritz, R. E. (1997). Nature and frequency of genetic disease. 3rd edn. Edinburgh: Churchill Livingstone, pp. 31–4.Google Scholar
Risch, N. (1990). Linkage strategies for genetically complex traits I. Multilocus models. Am J Hum Genet, 46, 222–8.Google ScholarPubMed
Risch, N. and Merikangas, K. (1996). The future of genetic studies of complex human diseases. Science, 273, 1516–17.CrossRefGoogle ScholarPubMed
Risch, N., Tang, H., Katzenstein, H. and Eckstein, J. (2003). Geographic distribution of disease mutations in the Ashkenazi Jewish population supports genetic drift over selection. Am J Hum Genet, 72, 812–22.CrossRefGoogle ScholarPubMed
Robertson, A. (1967). The nature of quantitative genetic variation. In Brink, A. ed., Heritage from Mendel. Madison, WI: The University of Wisconsin Press, pp. 265–80.Google Scholar
Rosenberg, N. A. and Nordborg, M. (2002). Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat Rev Genet, 3, 380–90.CrossRefGoogle ScholarPubMed
Sabeti, P. C., Reich, D. E., Higgins, J. M.et al. (2002). Detecting recent positive selection in the human genome from haplotype structure. Nature, 419, 832–7.CrossRefGoogle ScholarPubMed
Sachidanandam, R., Weissman, D., Schmidt, S. C.et al. (2001). A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature, 409, 928–33.CrossRefGoogle ScholarPubMed
Salisbury, B. A., Pungliya, M., Choi, J. Y.et al. (2003). SNP and haplotype variation in the human genome. Mutat Res, 526, 53–61.CrossRefGoogle ScholarPubMed
Sebat, J., Lakshmi, B., Troge, J.et al. (2004). Large-scale copy number polymorphism in the human genome. Science, 305, 525–8.CrossRefGoogle ScholarPubMed
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, 143–56.3.0.CO;2-5>CrossRefGoogle ScholarPubMed
Slatkin, M. and Bertorelle, G. (2001). The use of intraallelic variability for testing neutrality and estimating population growth rate. Genetics, 158, 865–74.Google ScholarPubMed
Stenson, P. D., Ball, E. V., Mort, M.et al. (2003). Human gene mutation database (HGMD): 2003 update. Hum Mutat, 21, 577–81.CrossRefGoogle ScholarPubMed
Stephens, J. C., Briscoe, D. and O'Brien, S. J. (1994). Mapping by admixture disequilibrium in human populations: limits and guidelines. Am J Hum Genet, 55, 809–24.Google ScholarPubMed
Tajima, F. (1983). Evolutionary relationships of DNA sequences in finite populations. Genetics, 105, 437–60.Google Scholar
Terwilliger, J. D. and Weiss, K. M. (1998). Linkage disequilibrium mapping of complex disease: fantasy or reality?Curr Opin Biotechnol, 9, 578–94.CrossRefGoogle ScholarPubMed
Tishkoff, S. A., Varkonyi, R., Cahinhinan, N.et al. (2001). Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance. Science, 293, 455–62.CrossRefGoogle ScholarPubMed
Tuzun, E., Sharp, A. J., Bailey, J. A.et al. (2005). Fine-scale structural variation of the human genome. Nat Genet, 37, 727–32.CrossRefGoogle ScholarPubMed
Voight, B. F., Kudaravalli, S., Wen, X. and Pritchard, J. K. (2006). A map of recent positive selection in the human genome. PLoS Biol, 4, e72.CrossRefGoogle ScholarPubMed
Wade, M. J. (2001). Epistasis, complex traits, and mapping genes. Genetica, 112, 59–69.CrossRefGoogle ScholarPubMed
Weinberg, W. (1908). Ueber den Nachweis der Vererbung beim Menschen. Jh Ver Vaterl Naturk Wurttemb, 64, 368–82.Google Scholar
Wittke-Thompson, J. K., Pluzhnikov, A. and Cox, N. J. (2005). Rational inferences about departures from Hardy-Weinberg equilibrium. Am J Hum Genet, 76, 967–86.CrossRefGoogle ScholarPubMed
Wright, A., Charlesworth, B., Rudan, I., Carothers, A. and Campbell, H. (2003). A polygenic basis for late-onset disease. Trends Genet, 19, 97–106.CrossRefGoogle ScholarPubMed
Xu, J., Turner, A., Little, J., Bleecker, E. R. and Meyers, D. A. (2002). Positive results in association studies are associated with departure from Hardy-Weinberg equilibrium: hint for genotyping error?Hum Genet, 111, 573–4.CrossRefGoogle ScholarPubMed

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