MBE Advance Access originally published online on July 13, 2007
Molecular Biology and Evolution 2007 24(9):2049-2058; doi:10.1093/molbev/msm135
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Research Articles |
Dissecting Linkage Disequilibrium in African-American Genomes: Roles of Markers and Individuals
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* MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
Chinese Academy of Science–Max-Planck-Gesellschaft Partner Institute for Computational Biology, Shanghai Institutes for Biological Science, CAS, Shanghai, China
Chinese National Human Genome Center at Shanghai, China
Rui Jin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
|| Human Genetics Center, School of Public Health, University of Texas-Health Science Center at Houston
E-mail: ljin007{at}gmail.com.
Accepted for publication June 25, 2007.
Substantial increases of linkage disequilibrium (LD) both in magnitude and in range have been observed in recently admixed populations such as African-American (AfA). On the other hand, it has also been shown that LD in AfAs was very similar to that of African. In this study, we attempted to resolve these contradicting observations by conducting a systematic examination of the LD structure in AfAs by genotyping a sample of AfA individuals at 24,341 single nucleotide polymorphisms (SNPs) spanning almost the entire chromosome 21, with an average density of 1.5 kb/SNP. The overall LD in AfAs is similar to that in African populations and much less than that in European populations. Even when the ancestry-informative markers (AIMs) were used, extended LD in AfA was found to be limited to certain magnitude range (0.2 
r2 0.8) and certain distance range, that is, between-marker distance more than 200 kb. Furthermore, the inclusion of AfA individuals with predominant African ancestry was found to reduce the overall magnitude of LD. Elevation of LD in the AfA population, compared with its parental populations, can only be observed at the markers with large allele frequency differences between 2 parental populations at limited scenario. AfA individuals of wholly African ancestry contribute little to the extended LD in the AfA population, and further genotyping or association analysis conducted using only admixed individuals may lead to higher statistical power and possibly reduced cost.
Key Words: African-American • linkage disequilibrium • single nucleotide polymorphism • ancestry-informative markers • admixture population
1 Present address Institute of Genetics, School of Life Sciences at Fudan University, Shanghai, China.