Skip to main content
Springer Nature Link
Log in

Estimating Allele Frequencies

  • Protocol
  • First Online:
Statistical Human Genetics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1666))

  • 3878 Accesses

Abstract

Methods of estimating allele frequencies from data on unrelated and related individuals are described in this chapter. For samples of unrelated individuals with simple codominant markers, the natural estimators of allele frequencies can be used. For genetic data on related individuals, maximum likelihood estimation (MLE) can be applied to compute allele frequencies. Factors that influence allele frequencies in populations are also explained.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

Similar content being viewed by others

References

  1. Ott J (1992) Strategies for characterizing highly polymorphic markers in human gene mapping. Am J Hum Genet 51:283–290

    PubMed  PubMed Central  CAS  Google Scholar 

  2. Lockwood JR, Roeder K, Devlin B (2001) A Bayesian hierarchical model for allele frequencies. Genet Epidemiol 20:17–33

    Article  CAS  PubMed  Google Scholar 

  3. Mandal DM, Sorant AJ, Atwood LD, Wilson AF, Bailey-Wilson JE (2006) Allele frequency misspecification: effect on power and type I error of model-dependent linkage analysis of quantitative traits under random ascertainment. BMC Genet 7:21

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Hoggart CJ, Shriver MD, Kittles RA, Clayton DG, McKeigue PM (2004) Design and analysis of admixture mapping studies. Am J Hum Genet 74:965–978

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Montana G, Pritchard JK (2004) Statistical tests for admixture mapping with case-control and cases-only data. Am J Hum Genet 75:771–789

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Ceppellini R, Siniscalco M, Smith CA (1955) The estimation of gene frequencies in a random-mating population. Ann Hum Genet 20:97–115

    Article  CAS  PubMed  Google Scholar 

  7. Smith CA (1957) Counting methods in genetical statistics. Ann Hum Genet 21:254–276

    Article  CAS  PubMed  Google Scholar 

  8. Boehnke M (1991) Allele frequency estimation from data on relatives. Am J Hum Genet 48:22–25

    PubMed  PubMed Central  CAS  Google Scholar 

  9. McPeek MS, Wu X, Ober C (2004) Best linear unbiased allele-frequency estimation in complex pedigrees. Biometrics 60:359–367

    Article  PubMed  Google Scholar 

  10. Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via Em algorithm. J R Stat Soc Series B Stat Methodol 39:1–38

    Google Scholar 

  11. Elston RC, Stewart J (1971) A general model for the genetic analysis of pedigree data. Hum Hered 21:523–542

    Article  CAS  PubMed  Google Scholar 

  12. Lange K, Boehnke M (1983) Extensions to pedigree analysis. V. Optimal calculation of Mendelian likelihoods. Hum Hered 33:291–301

    Article  CAS  PubMed  Google Scholar 

  13. Lange K, Weeks D, Boehnke M (1988) Programs for pedigree analysis: MENDEL, FISHER, and dGENE. Genet Epidemiol 5:471–472

    Article  CAS  PubMed  Google Scholar 

  14. Elston RC, Gray-McGuire C (2004) A review of the 'Statistical Analysis for Genetic Epidemiology' (S.A.G.E.) software package. Hum Genomics 1:456–459

    Article  PubMed  PubMed Central  Google Scholar 

  15. Broman KW (2001) Estimation of allele frequencies with data on sibships. Genet Epidemiol 20:307–315

    Article  CAS  PubMed  Google Scholar 

  16. Guo CY, DeStefano AL, Lunetta KL, Dupuis J, Cupples LA (2005) Expectation maximization algorithm based haplotype relative risk (EM-HRR): test of linkage disequilibrium using incomplete case-parents trios. Hum Hered 59:125–135

    Article  PubMed  Google Scholar 

  17. Allen AS, Satten GA (2007) Inference on haplotype/disease association using parent-affected-child data: the projection conditional on parental haplotypes method. Genet Epidemiol 31:211–223

    Article  PubMed  Google Scholar 

  18. Boyles AL, Scott WK, Martin ER et al (2005) Linkage disequilibrium inflates type I error rates in multipoint linkage analysis when parental genotypes are missing. Hum Hered 59:220–227

    Article  PubMed  PubMed Central  Google Scholar 

  19. Bergemann TL, Huang Z (2009) A new method to account for missing data in case-parent triad studies. Hum Hered 68:268–277

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Burrell AS, Disotell TR (2009) Panmixia postponed: ancestry-related assortative mating in contemporary human populations. Genome Biol 10:245

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Torche F (2010) Educational assortative mating and economic inequality: a comparative analysis of three Latin American countries. Demography 47:481–502

    Article  PubMed  PubMed Central  Google Scholar 

  22. Sebro R, Hoffman TJ, Lange C, Rogus JJ, Risch NJ (2010) Testing for non-random mating: evidence for ancestry-related assortative mating in the Framingham heart study. Genet Epidemiol 34:674–679

    Article  PubMed  PubMed Central  Google Scholar 

  23. Purcell S, Neale B, Todd-Brown K et al (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J hum Genet 81:559–575

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ (2015) Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4:7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Danecek P, Auton A, Abecasis G et al (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. S.A.G.E. (2016) Statistical analysis for genetic Epidemiology, Release 6.4.: http://darwin.cwru.edu/sage/.

Download references

Author information

Authors and Affiliations

  1. Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, 825 N.E. 13th Street, Oklahoma City, OK, USA

    Indra Adrianto & Courtney Montgomery

Authors
  1. Indra Adrianto
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Courtney Montgomery
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Courtney Montgomery .

Editor information

Editors and Affiliations

  1. Case Western Reserve University, Cleveland, OH, USA

    Robert C. Elston

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Adrianto, I., Montgomery, C. (2017). Estimating Allele Frequencies. In: Elston, R. (eds) Statistical Human Genetics. Methods in Molecular Biology, vol 1666. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7274-6_5

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7274-6_5

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7273-9

  • Online ISBN: 978-1-4939-7274-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics