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. 2004 Nov;1(6):399-409.
doi: 10.1186/1479-7364-1-6-399.

Geographic Stratification of Linkage Disequilibrium: A Worldwide Population Study in a Region of Chromosome 22

Free PMC article

Geographic Stratification of Linkage Disequilibrium: A Worldwide Population Study in a Region of Chromosome 22

Anna González-Neira et al. Hum Genomics. .
Free PMC article


Recent studies of haplotype diversity in a number of genomic regions have suggested that long stretches of DNA are preserved in the same chromosome, with little evidence of recombination events. The knowledge of the extent and strength of these haplotypes could become a powerful tool for future genetic analysis of complex traits. Different patterns of linkage disequilibrium (LD) have been found when comparing individuals of African and European descent, but there is scarce knowledge about the worldwide population stratification. Thus, the study of haplotype composition and the pattern of LD from a global perspective are relevant for elucidating their geographical stratification, as it may have implications in the future analysis of complex traits. We have typed 12 single nucleotide polymorphisms in a chromosome 22 region--previously described as having high LD levels in European populations--in 39 different world populations. Haplotype structure has a clear continental structure with marked heterogeneity within some continents (Africa, America). The pattern of LD among neighbouring markers exhibits a strong clustering of all East Asian populations on the one hand and of Western Eurasian populations (including Europe) on the other, revealing only two major LD patterns, but with some very specific outliers due to specific demographic histories. Moreover, it should be taken into account that African populations are highly heterogeneous. The present results support the existence of a wide (but not total) communality in LD patterns in human populations from different continental regions, despite differences in their demographic histories, as population factors seem to be less relevant compared with genomic forces in shaping the patterns of LD.


Figure 1
Figure 1
Plot of first three dimensions obtained in the correspondence analysis based on the 182 shared haplotypes found in 40 populations (English population included). The first dimension separates the six African populations from the rest. Native Americans are clearly differentiated in the second dimension and East Asians and Oceanians are separated from the rest of Eurasian populations by the third dimension.
Figure 2
Figure 2
Principal components analysis plots based on the r2 values obtained for neighbouring markers. Populations with more than three missing r2 values were excluded in the analysis (Surui, San, Non-Austronesian (NAN) Melanesian, Colombian, Karitiana, Pima and Papuan). 42.1% and 18.9% of the variance is explained by the first and second components, respectively. The plot of the two first components pools the populations into two groups: East Asia and European/Western Eurasians. African populations are scattered due their lack of a single linkage disequilibrium pattern. Note that four Native American populations were excluded from the analysis and only one such population (Mayans, from Mexico) could be included.

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