ALU-PCR COMBINED WITH NON-ALU PRIMERS REVEALS MULTIPLE POLYMORPHIC LOCI

A marker suitable for genetic mapping and genomic fingerprinting is ch aracterized by high polymorphic information content (PIC) and high ''m ultiplex ratio'' (defined as the number of loci that can be simultaneo usly typed). Towards this goal, we combined an Alu-specific with a non -Alu primer in a single PCR amplification targeting genomic regions wh ere length polymorphisms are abundant. Three loci were revealed with t he variable number of (AAT), (TAAA), (AG), and/or (AAAGG) motifs, and PIC values between 0.7 and >0.94. Their location on Chromosomes (Chrs) 19q12, 17q12-q24, and 5q31.2-33.3 was determined by multipoint analys is with markers from CEPH database. The most common genotype for this three-locus marker, estimated from the occurrence of the most frequent alleles, is of the order of 2 x 10(-4), while the combined PIC value of a single typing experiment is 2.37. The use of a similar primer pai r, as well as examples from the literature, indicates the general natu re of this approach when a non-Alu oligonucleotide, presumably with '' random'' priming sites downstream of Alu repeats, is combined with an Alu-specific one. Clustering of DNA length variants in the regions adj acent to interspersed repeats provides opportunity to develop other hi ghly informative multiple-locus markers similar to that described here .