Multiplex PCR-based Alu insertion polymorphisms genotyping for identifying individuals of Japanese ethnicity

Discrimination of Alu insertions is a useful tool for geographic ancestry analysis, and is usually performed by Alu element amplification and agarose gel electrophoresis. Here, we have developed a new fluorescence-based method for multiple Alu genotyping in forensic identification. Allele frequencies were determined in 70 Japanese individuals, and we selected 30 polymorphic Alu insertions. Three primers were designed for each Alu locus to discriminate alleles using the 3–6 bp differences in amplicon sizes. Furthermore, we classified the amplification primers for the 30 loci into three different sets, and PCR using each set of primers provided 10 loci fragments ranging from 50 to 137 bp. Based on population data, the probability of incorrectly assigning a match was 3.7 × 10− 13. Three independent amplifications and subsequent capillary electrophoresis enabled the sensitive genotyping of small amounts of DNA, indicating that this method is suitable for identifying individuals of Japanese ethnicity.

► We developed a new fluorescence-based method for multiple Alu genotyping.
► Thirty polymorphic Alu loci were selected using Japanese individuals.
► Multiplex PCR provided 10 loci fragments ranging from 50 to 137 bp.
► The probability of incorrectly assigning a match was 3.7 × 10(− 13).
► Our method is suitable for identifying individuals of Japanese ethnicity.