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Comparative Study
. 2010 Jun;55(6):366-74.
doi: 10.1038/jhg.2010.41. Epub 2010 May 20.

Comparison of genome-wide variation between Malawians and African ancestry HapMap populations

Bonnie R Joubert  1 , Kari E North, Yunfei Wang, Victor Mwapasa, Nora Franceschini, Steven R Meshnick, Ethan M Lange
Affiliations
Comparative Study

Comparison of genome-wide variation between Malawians and African ancestry HapMap populations

Bonnie R Joubert et al. J Hum Genet. 2010 Jun.

Abstract

Understanding genetic variation between populations is important because it affects the portability of human genome-wide analytical methods. We compared genetic variation and substructure between Malawians and other African and non-African HapMap populations. Allele frequencies and adjacent linkage disequilibrium (LD) were measured for 617 715 single nucleotide polymorphisms (SNPs) across subject genomes. Allele frequencies in the Malawian population (N=226) were highly correlated with allele frequencies in HapMap populations of African ancestry (AFA, N=376), namely Yoruban in Ibadan, Nigeria (Spearman's r(2)=0.97), Luhya in Webuye, Kenya (r(2)=0.97), African Americans in the southwest United States (r(2)=0.94) and Maasai in Kinyawa, Kenya (r(2)=0.91). This correlation was much lower between Malawians and other ancestry populations (r(2)<0.52). LD correlations between Malawians and HapMap populations were strongest for the populations of AFA (AFA r(2)>0.82, other ancestries r(2)<0.57). Principal components analyses revealed little population substructure within our Malawi sample but provided clear distinction between Malawians, AFA populations and two European populations. Five SNPs within the lactase gene (LCT) had substantially different allele frequencies between the Malawi population and Maasai in Kenyawa, Kenya (rs3769013, rs730005, rs3769012, rs2304370; P-values <1 x 10(-33)).

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Figures

Figure 1
Figure 1
SNP Associations with population membership. Individuals in Blantyre, Malawi (BMW) were compared to each African ancestry HapMap population: Individuals of African ancestry in the Southwest USA (ASW), Luhya in Webuye, Kenya (LWK), Maasai in Kinyawa, Kenya (MKK), and Yoruban of Ibadan, Nigeria (YRI).
Figure 2
Figure 2
Lactase gene SNP frequencies by African ancestry population
Figure 3
Figure 3
No evidence of population substructure in Malawi population: Component 1 vs. 2. Analyses performed in EIGENSOFT software using 23,612 SNPs.
Figure 4
Figure 4
Separation of BMW and African ancestry HapMap populations: Component 1 vs. 2. Analyses performed in EIGENSOFT software using 18,481 SNPs.
See this image and copyright information in PMC

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