This study analyzed Alu elements retrieved from the GenBank database and identified two new Alu subfamilies, Alu Yb9 and Alu Yc2, and further characterized Yc1 subfamily members.
Alu elements have been accumulating in the human genome throughout primate evolution, reaching a copy number of over a million per genome. Most of these Alu copies are not identical and can be classified into several subfamilies. The availability of large quantities of human genomic DNA sequence provided by the Human Genome Project facilitates genomic database mining for recently integrated Alu elements. Using this approach, the authors were able to identify the youngest Alu subfamily reported to date, termed Ya5a2, and they also determined that the majority of its members are Alu insertion polymorphisms. Computational analyses were expanded to identify other Alu subfamilies derived from the Alu Y and Yb8 subfamilies. This report describes the analysis of three of the most recently formed Alu subfamilies and demonstrates their use in the study of human genomic diversity. A PCR analysis was performed on a panel of human DNA samples in order to determine the levels of human diversity associated with the Alu elements from the new subfamilies, using oligonucleotide primers. The panel consisted of 20 individuals of European origin, African-Americans, Asians, and Egyptians. The authors were able to analyze 28 out of the 56 Yb9 elements, 97 out of 176 Yc1 elements, and 8 out of 17 Yc2 Alu elements. The descriptions of materials and methods address computation analyses, DNA sample sources, and oligonucleotide primer design and PCR amplification. 3 tables, 3 figures, and 33 references