IDENTIFYING MARKER LOCI FOR DEFINING HUMAN POPULATION HISTORY: HLA MICROSATELLITES VS. GENOME WIDE MICROSATELLITES.
JA Hollenbach1, K Mather1, D Meyer,1W Klitz2, L Louie2, LF Barcellos3, G Thomson1. Department of Integrative Biology, University of California, Berkeley1, School of Public Health, University of California, Berkeley2, Department of Neurology, University of California, San Francisco3.
Six human populations (three Amerindian from Southern Mexico, one Chinese, one African, one North American Caucasian) native to four continents were typed for 20 microsatellite markers in the HLA region and 200 microsatellite markers outside chromosome 6. A DNA pooling strategy and automated typing with fluorescent-labeled markers has been utilized to allow rapid and efficient typing on a large number of markers. These markers are being studied in these populations as part of a pilot project for the Human Genome Diversity Project (HGDP). The markers were assessed for heterozygosity and PIC values, which give a general picture of the relative polymorphism of these loci inside and outside the HLA region. Fst values were calculated for each marker to measure population differentiation at that locus. Fst and AMOVA values were also averaged over the markers within the HLA region and compared to those outside the HLA region. Phylogenetic methods were applied to assess the relative abilities of HLA versus non-HLA markers to describe the relationships between the populations. Preliminary analyses suggest that markers within the HLA region are more polymorphic on average than those on other chromosomes. Additionally, markers within the HLA region appear to give an accurate reconstruction of the relationships between these populations.