Login to MyKarger

New to MyKarger? Click here to sign up.

Login with Facebook

Forgot Password? Reset your password

Authors, Editors, Reviewers

For Manuscript Submission, Check or Review Login please go to Submission Websites List.

Submission Websites List

Institutional Login (Shibboleth)

For the academic login, please select your country in the dropdown list. You will be redirected to verify your credentials.

Table of Contents
Vol. 73, No. 2, 2012
Issue release date: May 2012
Section title: Original Paper
Free Access
Hum Hered 2012;73:73–83

Improved Eigenanalysis of Discrete Subpopulations and Admixture Using the Minimum Average Partial Test

Shriner D.
Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Md., USA
email Corresponding Author

Daniel Shriner

Center for Research on Genomics and Global Health

National Human Genome Research Institute

Building 12A, Room 4047, 12 South Dr., MSC 5635, Bethesda, MD 20892-5635 (USA)

Tel. +1 301 435 0068, E-Mail shrinerda@mail.nih.gov


  1. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D: Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 2006;38:904–909.
  2. Patterson N, Price AL, Reich D: Population structure and eigenanalysis. PLoS Genet 2006;2:e190.
  3. Basilevsky A: Statistical Factor Analysis and Related Methods: Theory and Applications. New York, John Wiley & Sons, Inc., 1994.
  4. McVean G: A genealogical interpretation of principal components analysis. PLoS Genet 2009;5:e1000686.
    External Resources
  5. Johnstone I: On the distribution of the largest eigenvalue in principal components analysis. Ann Stat 2001;29:295–327.
    External Resources
  6. Shriner D: Investigating population stratification and admixture using eigenanalysis of dense genotypes. Heredity 2011;107:413–420.
  7. Baik J, Ben Arous G, Péché S: Phase transition of the largest eigenvalue for nonnull complex sample covariance matrices. Ann Probab 2005;33:1643–1697.
    External Resources
  8. Baik J, Silverstein JW: Eigenvalues of large sample covariance matrices of spiked population models. J Multivariate Anal 2006;97:1382–1408.
    External Resources
  9. The International HapMap 3 Consortium: Integrating common and rare genetic variation in diverse human populations. Nature 2010;467:52–58.
  10. R Development Core Team: R: a language and environment for statistical computing. Vienna, The R Foundation for Statistical Computing, 2009.
  11. Johnstone IM, Perry PO, Ma Z, Shahram M: RMTstat: distributions, statistics, and tests derived from random matrix theory, version 0.2, 2009.
  12. Bretherton CS, Widmann M, Dymnikov VP, Wallace JM, Bladé I: The effective number of spatial degrees of freedom of a time-varying field. J Climate 1999;12:1990–2009.
  13. Velicer WF: Determining the number of components from the matrix of partial correlations. Psychometrika 1976;41:321–327.
    External Resources
  14. O’Connor BP: SSS and SAS programs for determining the number of components using parallel analysis and Velicer’s MAP test. Behav Res Methods Instrum Comput 2000;32:396–402.
  15. Chen G, Shriner D, Zhou J, Doumatey A, Huang H, Gerry NP, Herbert A, Christman MF, Chen Y, Dunston GM, Faruque MU, Rotimi CN, Adeyemo A: Development of admixture mapping panels for African Americans from commercial high-density SNP arrays. BMC Genomics 2010;11:417.
  16. Martinez-Marignac VL, Valladares A, Cameron E, Chan A, Perera A, Globus-Goldberg R, Wacher N, Kumate J, McKeigue P, O’Donnell D, Shriver MD, Cruz M, Parra EJ: Admixture in Mexico City: implications for admixture mapping of type 2 diabetes genetic risk factors. Hum Genet 2007;120:807–819.
    External Resources
  17. Price AL, Patterson N, Yu F, Cox DR, Waliszewska A, McDonald GJ, Tandon A, Schirmer C, Neubauer J, Bedoya G, Duque C, Villegas A, Bortolini MC, Salzano FM, Gallo C, Mazzotti G, Tello-Ruiz M, Riba L, Aguilar-Salinas CA, Canizales-Quinteros S, Menjivar M, Klitz W, Henderson B, Haiman CA, Winkler C, Tusie-Luna T, Ruiz-Linares A, Reich D: A genomewide admixture map for Latino populations. Am J Hum Genet 2007;80:1024–1036.
  18. The International HapMap Consortium: A second generation human haplotype map of over 3.1 million SNPs. Nature 2007;449:851–861.