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

• Published in: Legal medicine (Tokyo, Japan) Japan), 2022-02, Vol.54, p.101986-101986, Article 101986
• Main Authors: Soejima, Mikiko, Koda, Yoshiro
• Format: Article
• Language: English
• Subjects: ABO Blood-Group System; Alleles; Ancestry informative marker; Fucosyltransferases - genetics; FUT2; Humans; Nonsecretor allele; Oceanian populations; Real-Time Polymerase Chain Reaction; Sedel2
• ISSN: 1344-6223; 1873-4162
• DOI: 10.1016/j.legalmed.2021.101986

•The sedel2 of FUT2 is a complete deletion of the coding region generated by an Alu-mediated recombination.•We designed primers for amplification of 231-bp amplicon specific to sedel2.•We developed two real-time PCR methods based on melting curve analysis and hydrolysis probe to determine sedel2 zygosity. Secretor status of the ABH(O) histoblood group antigens is regulated by secretor type α(1,2)fucosyltransferase encoded by FUT2. The sedel2 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, sedel2 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 sedel2. We designed primers which produced a 231-bp amplicon specific to sedel2. 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 sedel2 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 sedel2. Therefore, these two methods seemed to accurately determine the zygosity of sedel2 and were useful for investigation of the distribution and origin of this deletion.