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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Comparison of genome-wide variation between Malawians and African ancestry HapMap populations
Journal of Human Genetics, Volume 55, No. 6, Year 2010
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Description
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 r2=0.97), Luhya in Webuye, Kenya (r2=0.97), African Americans in the southwest United States (r2=0.94) and Maasai in Kinyawa, Kenya (r2=0.91). This correlation was much lower between Malawians and other ancestry populations (r2<0.52). LD correlations between Malawians and HapMap populations were strongest for the populations of AFA (AFA r2>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 × 10-33). © 2010 The Japan Society of Human Genetics All rights reserved.
Authors & Co-Authors
Joubert, Bonnie R.
United States, Chapel Hill
The University of North Carolina at Chapel Hill
North, Kari E.
United States, Chapel Hill
The University of North Carolina at Chapel Hill
Wang, Yunfei
United States, Chapel Hill
Unc School of Medicine
United States, Chapel Hill
The University of North Carolina at Chapel Hill
Mwapasa, Victor
Malawi, Zomba
University of Malawi
Franceschini, Nora
United States, Chapel Hill
The University of North Carolina at Chapel Hill
Meshnick, Steven Richard
United States, Chapel Hill
The University of North Carolina at Chapel Hill
Lange, Ethan Mather
United States, Chapel Hill
The University of North Carolina at Chapel Hill
United States, Chapel Hill
Unc School of Medicine
Statistics
Citations: 13
Authors: 7
Affiliations: 3
Identifiers
Doi:
10.1038/jhg.2010.41
ISSN:
14345161
Research Areas
Genetics And Genomics
Study Design
Cross Sectional Study
Study Locations
Kenya
Malawi
Nigeria