Practical population group assignment with selected informative markers: characteristics and properties of Bayesian clustering via STRUCTURE.

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  • Author(s): Yang BZ;Yang BZ; Zhao H; Kranzler HR; Gelernter J
  • Source:
    Genetic epidemiology [Genet Epidemiol] 2005 May; Vol. 28 (4), pp. 302-12.
  • Publication Type:
    Comparative Study; Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, U.S. Gov't, P.H.S.
  • Language:
    English
  • Additional Information
    • Source:
      Publisher: Wiley-Liss Country of Publication: United States NLM ID: 8411723 Publication Model: Print Cited Medium: Print ISSN: 0741-0395 (Print) Linking ISSN: 07410395 NLM ISO Abbreviation: Genet Epidemiol Subsets: MEDLINE
    • Publication Information:
      Publication: New York, NY : Wiley-Liss
      Original Publication: New York, N.Y. : Alan R. Liss, c1984-
    • Subject Terms:
      Genetics, Population*; Black or African American/*genetics ; White People/*genetics; Algorithms ; Bayes Theorem ; Cluster Analysis ; Genetic Markers ; Genotype ; Humans ; Models, Genetic ; Sample Size
    • Abstract:
      Population stratification, which is caused by population genetic substructure (PGS), is a critical issue for the design and interpretation of genetic association studies. Methods to address this problem have been devised, but little is known at this point about practical genotyping requirements for resolving PGS based on different marker characteristics. In this report, we seek to (1) identify a small, practical marker set to differentiate African Americans (AAs) from European Americans (EAs), and (2) assess the impact of marker efficiency and sample size on clustering individuals into subgroups by the methods of STRUCTURE (Pritchard et al., [2000a] Genetics 155:945-959). A panel of 37 markers was genotyped for 865 individuals (640 EAs and 225 AAs) from the Northeastern United States. Among EAs, the assignment accuracy reached >99% using only the 4 most efficient markers. Among AAs, the assignment accuracy exceeded 95% when using the 6 most informative markers. Smaller sample size increased the variance in population differentiation, rather than degrading the results consistently. We conclude that the use of marker-efficiency measures for marker selection yielded a relatively small set of STR markers that were effective at differentiating EA and AA populations. The number of markers required is much lower than has been suggested in previous studies.
      ((c) 2005 Wiley-Liss, Inc.)
    • Grant Information:
      MH14276 United States MH NIMH NIH HHS; GM59507 United States GM NIGMS NIH HHS; R01 DA012849 United States DA NIDA NIH HHS; AA12870 United States AA NIAAA NIH HHS; RR06192 United States RR NCRR NIH HHS; T32 MH014276 United States MH NIMH NIH HHS; R01 AA011330 United States AA NIAAA NIH HHS; AA03510 United States AA NIAAA NIH HHS; P50 AA012870 United States AA NIAAA NIH HHS; DA12849 United States DA NIDA NIH HHS; DA12468 United States DA NIDA NIH HHS; MH01387 United States MH NIMH NIH HHS; P50 AA003510 United States AA NIAAA NIH HHS; R01 DA012690 United States DA NIDA NIH HHS; K24 AA013736 United States AA NIAAA NIH HHS; M01 RR006192 United States RR NCRR NIH HHS; AA13736 United States AA NIAAA NIH HHS; DA12690 United States DA NIDA NIH HHS; AA11330 United States AA NIAAA NIH HHS; R01 GM059507 United States GM NIGMS NIH HHS
    • Accession Number:
      0 (Genetic Markers)
    • Publication Date:
      Date Created: 20050323 Date Completed: 20051208 Latest Revision: 20250104
    • Publication Date:
      20250104
    • Accession Number:
      10.1002/gepi.20070
    • Accession Number:
      15782414