Incorporation of Flanking Single Nucleotide Polymorphisms Advances the Use of a Yb8 Alu Dimorphism in Assessing the Ethnicity or Geographic Location from a DNA Sample

Abstract

Alu elements represent a group of nonautonomous retrotransposons with over one million copies contained in the human genome. Roughly 1,500–2,000 elements have more recently integrated and are therefore not fixed among human genomes yielding dimorphic variants based on the presence or absence of the element. Although these have been highly useful as DNA markers in human population studies, incorporating the use of internal single nucleotide polymorphisms (SNPs) markers to extend beyond a two-allele system has notably enriched its usefulness. To advance this strategy, we analyzed an additional intermediate-frequency Alu of the young Yb8 subfamily but alternatively used SNPs closely upstream of the integration site. We developed a simple assay involving the polymerase chain reaction and restriction endonuclease digests leading to the identification of four haplotypes in which the evolutionary order of alleles can be determined. One haplotype was found at significantly higher levels in western and central African and African American populations, and another haplotype was found at exceedingly higher levels among Pacific groups. This further demonstrates the improved resolution of incorporating adjacent SNP markers to Alu dimorphisms for human population studies, particularly in potentially determining the ethnicity and/or geographic location of origin from a DNA sample.