Alu insertion polymorphisms for the study of human genomic diversity

Genomic database mining has been a very useful aid in the identification an d retrieval of recently integrated Alu elements from the human genome. We a nalyzed Alu elements retrieved from the GenBank database and identified two new Alu subfamilies, Alu Yb9 and Alu Yc2, and further characterized Yc1 su bfamily members. Some members of each of the three subfamilies have inserte d in the human genome so recently that about a one-third of the analyzed el ements are polymorphic for the presence/absence of the Alu repeat in divers e human populations. These newly identified Alu insertion polymorph isms wi ll serve as identical-by-descent genetic markers for the study of human evo lution and forensics. Three previously classified Alu Y elements linked wit h disease belong to the Yc1 subfamily, supporting the retroposition potenti al of this subfamily and demonstrating that the Alu Y subfamily currently h as a very low amplification rate in the human genome.