Real-time PCR-based detection of the Alu-mediated deletion of FUT2 (sedel2)

Secretor status of the ABH(O) histoblood group antigens is regulated by secretor type alpha(1,2)fucosyltransferase encoded by FUT2. The se(del2) allele is a complete deletion of the FUT2 coding region generated by Alu-mediated homologous recombination. This deletion seems to be exclusively encountered in certain Oceanian populations. From the perspective of forensic science, se(del2) is considered to be one of ancestry informative markers for these populations. Real-time PCR followed by melting curve analysis was employed to find primer set to specifically amplify se(del2). We designed primers which produced a 231-bp amplicon specific to se(del2). The specificity of these primers was also confirmed by gel electrophoresis and sequencing of the PCR product. Then, two real-time PCR methods based on melting curve analysis and a hydrolysis probe were designed to determine se(del2) zygosity by adding FUT2-specific primers. These two methods were validated by analyzing 24 Samoan subjects. The results obtained from 24 Samoan subjects by the two methods were fully in accordance with those obtained by a previous conventional PCR method that amplified a 2.7-kb fragment of se(del2). Therefore, these two methods seemed to accurately determine the zygosity of se(del2) and were useful for investigation of the distribution and origin of this deletion.