Alu elements undergo amplification through retroposition and integration in
to new locations throughout primate genomes. Over 500,000 Alu elements resi
de in the human genome, making the identification of newly inserted Alu rep
eats the genomic equivalent of finding needles in the haystack. Here, we pr
esent two complementary methods for rapid detection of newly integrated Alu
elements. In the first approach we employ computational biology to mine th
e human genomic DNA sequence databases in order to identify recently integr
ated Alu elements. The second method is based on an anchor-PCR technique wh
ich we term Allele-Specific Alu PCR (ASAP). In this approach, Alu elements
are selectively amplified from anchored DNA generating a display or 'finger
print' of recently integrated Alu elements. Alu insertion polymorphisms are
then detected by comparison of the DNA fingerprints generated from differe
nt samples. Here, we explore the utility of these methods by applying them
to the identification of members of the smallest previously identified subf
amily of Alu repeats in the human genome termed Ya8. This subfamily of Alu
repeats is composed of about 50 elements within the human genome. Approxima
tely 50% of the Ya8 Alu family members have inserted in the human genome so
recently that they are polymorphic, making them useful markers for the stu
dy of human evolution.