CHARACTERIZATION AND POPULATION DIVERSITY OF INTERSPERSED REPEAT SEQUENCE VARIANTS (IRS-MORPHS)

Inter-Alu PCR is increasingly useful in human genome mapping studies. One use is the generation of alumorphs, polymorphisms resulting from t he presence or absence of inter-Aln PCR products. In this study, we ha ve increased the proportion of the genome that can be analyzed by this technique with the use of long interspersed elements (LINEs). The set of polymorphisms detected by both Alu and LINE primers are referred t o as interspersed repetitive sequence variants or TRS-morphs. Since a presence-absence variant may have been the result of a recent Alu or L INE insertion, we analyzed 7 isolated IRS-morphs that were generated, in pare, with a primer derived from either a consensus LINE or a young Alu subfamily specific sequence, and observed by Southern blot analys is that these variants resulted from other types of genomic alteration s. The use of these primers, however, reduces background from the nume rous LINEs and Alu elements in the genome, providing sharp DNA fingerp rint profiles. We have demonstrated the potential usefulness of these IRS-morph profiles in human population studies. We compared 12 IRS-mor phs from a single amplification reaction from five distinct population groups (Caucasian (northern European descent), Hispanic (Mexican-Amer ican), Hindu-Indian, Papua New Guinean, and Greenland Eskimo) and obse rved that most have variable allelic frequencies among populations, Th e utilization of additional IRS-morph profiles will perpetuate this te chnique as a tool for DNA fingerprinting and for the analysis of human populations.