Human Population Stratification and its Assessment by Microarray Genotyping

Marc Bauchet, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

Published online: March 2008

DOI: 10.1002/9780470015902.a0020797

Population stratification is an important phenomenon in biomedical research and anthropology. The recent microarray technology allows genome-wide assessment of this structure and opens new avenues for understanding and using the rich diversity of the human genome across populations.

Keywords: population stratification; population structure; microarray genotyping; SNP; genetic ancestry

Figure 1. Two main scenarios resulting in population stratification. (a) Two populations of different allele frequencies at many loci contribute different proportions of individuals to cases and controls. (b) Two populations of different allele frequencies at many loci contribute different admixture proportions to cases and controls.
Figure 2. Individual panels of European-derived ancestry in the context of European stratification. (a) The Coriell Caucasian panel (n=42), based on 9114 genome-wide SNPs. (b) CEPH Utah individuals (n=74), using 6207 genome-wide SNPs. (c) STRUCTURE runs of the Coriell Caucasian individuals based on all available SNPs (bottom) and sets of SNPs most informative for the north-southeast European axis of ancestry (mainly reflected in PC1). Redrawn from Bauchet et al. (2007).
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 References
    Bauchet M, McEvoy B, Pearson LN et al. (2007) Measuring European population stratification using microarray genotype data. American Journal of Human Genetics 80(May): 948–956.
    Clark AG, Hubisz MJ, Bustamante CD, Williamson SH and Nielsen R (2005) Ascertainment bias in studies of human genome-wide polymorphism. Genome Research 15(11): 1496–1502.
    Conrad DF, Jakobsson M, Coop G et al. (2006) A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nature Genetics 38(11): 1251–1260.
    Devlin B and Roeder K (1999) Genomic control for association studies. Biometrics 55(4): 997–1004.
    McKeigue PM (2005) Prospects for admixture mapping of complex traits. American Journal of Human Genetics 76(1): 1–7.
    Patterson N, Price AL and Reich D (2006) Population structure and eigenanalysis. PLoS Genetics 2(12): 2074–2093.
    Pfaff CL, Kittles RA and Shriver MD (2002) Adjusting for population structure in admixed populations. Genetic Epidemiology 22(2): 196–198.
    Pritchard JK, Stephens M, Rosenberg NA and Donnelly P (2000) Association mapping in structured populations. American Journal of Human Genetics 67(1): 170–181.
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    Seldin MF, Shigeta R, Villoslada P et al. (2006) European population substructure: clustering of Northern and Southern populations. PLoS Genetics 2(9): e143.
    Shriver MD and Kittles RA (2004) Genetic ancestry and the search for personalized genetic histories. Nature Reviews. Genetics 5(8): 611–613.
    Shriver MD, Mei R, Parra EJ et al. (2005) Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation. Human Genomics 2(2): 81–89.
 Further Reading
    other Jobling M, Hurles M and Tyler-Smith C (2004) Human Evolutionary Genetics: Origins, People and Diseases. Garland Science.
    book Reardon J (2005) Race to the Finish: Identity and Governance in an Age of Genomics. Princeton: Princeton University Press.
 Recent developments in correcting population structure in association studies:
    Cheng KF and Lin WJ (2007) Simultaneously correcting for population stratification and genotyping error in case-control association studies. American Journal of Human Genetics 81(4): 726–743.
    Gorroochurn P, Hodge SE, Heiman GA and Greenberg DA (2007) A unified approach for quantifying, testing and correcting population stratification in case-control association studies. Human Heredity 64(3): 149–159.
    Hinds DA, Stokowski RP, Patil N et al. (2004) Matching strategies for genetic association studies in structured populations. American Journal of Human Genetics 74(2): 317–325.
    Hoggart CJ, Shriver MD, Kittles RA, Clayton DG and McKeigue PM (2004) Design and analysis of admixture mapping studies. Genetic Epidemiology 74(5): 965–978.
    Kimmel G, Jordan MI, Halperin E, Shamir R and Karp RM (2007) A randomization test for controlling population stratification in whole-genome association studies. American Journal of Human Genetics 81(5): 895–905.
    Price AL, Patterson NJ, Plenge RM et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics 38(8): 904–909.
    Setakis E, Stirnadel H and Balding DJ (2006) Logistic regression protects against population structure in genetic association studies. Genome Research 16(2): 290–296.
    Yu JM, Pressoir G, Briggs WH et al. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics 38(2): 203–208.
 Web Links
 Databases
    ePath dbSNP http://www.ncbi.nlm.nih.gov/projects/SNP/
    ePath HapMap http://www.hapmap.org/
    ePath OMIM http://www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM
 Tools
    ePath ADMIXMAP: Detect and controlling for population structure (variation in individual admixture) in genetic association studies (and much more) http://www.ucd.ie/genepi/admixmap/
    ePath EIGENSOFT 1.0: detect and correct for population stratification and eigenanalysis http://genepath.med.harvard.edu/~reich/Software.htm
    ePath PLINK: Genome association analysis toolset, designed to perform a range of basic, large-scale analyses http://pngu.mgh.harvard.edu/~purcell/plink
    ePath STRAT (structured association method) and STRUCTURE 2.2 (explore population structure using Bayesian method and MCMC algorithm) http://pritch.bsd.uchicago.edu/structure.html
    ePath TESS 1.1: Bayesian Clustering using tessellations and Markov models for spatial population genetics http://www-timc.imag.fr/Olivier.Francois/tess.html

Related Sub-Topics:

Evolutionary Genomics | Human Evolution | Population Structure and Genetics
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Article Title: Human Population Stratification and its Assessment by Microarray Genotyping
 
How to Cite close
Bauchet, Marc(Mar 2008) Human Population Stratification and its Assessment by Microarray Genotyping. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020797]