Null alleles and sequence variations at primer binding sites of STR loci within multiplex typing systems. (January 2018)

• Record Type: Journal Article
• Authors: Yao, Yining; Yang, Qinrui; Shao, Chengchen; Liu, Baonian; Zhou, Yuxiang; Xu, Hongmei; Zhou, Yueqin; Tang, Qiqun; Xie, Jianhui
• Is Part Of: Legal medicine. Volume 30(2018)
• Page Start: 10
• Page End: 13
• Publication Date: 2018-01
• Subjects: Short tandem repeats -- Genotyping -- Null alleles -- Primer binding sites -- Sequence variations; Medical jurisprudence -- Periodicals; Forensic Medicine -- Periodicals; Médecine légale -- Périodiques; Medical jurisprudence; Periodicals; 614.1
• DOI: 10.1016/j.legalmed.2017.10.007
• Languages: English
• ISSNs: 1344-6223

Abstract

Highlights: Five null alleles were observed using PP21 at TH01, FGA, D5S818, D8S1179, and D16S539 due to single base variations at primer binding sites. Null alleles at D5S818 and D19S433 were frequently observed in population detected by PowerPlex® typing systems and AmpFℓSTR™ typing systems, respectively. The mutation C to T with G to A appears the most popular mutation type at primer binding sites. Abstract: Rare variants are widely observed in human genome and sequence variations at primer binding sites might impair the process of PCR amplification resulting in dropouts of alleles, named as null alleles. In this study, 5 cases from routine paternity testing using PowerPlex ® 21 System for STR genotyping were considered to harbor null alleles at TH01, FGA, D5S818, D8S1179, and D16S539, respectively. The dropout of alleles was confirmed by using alternative commercial kits AGCU Expressmarker 22 PCR amplification kit and AmpFℓSTR ® . Identifiler ® Plus Kit, and sequencing results revealed a single base variation at the primer binding site of each STR locus. Results from the collection of previous reports show that null alleles at D5S818 were frequently observed in population detected by two PowerPlex ® typing systems and null alleles at D19S433 were mostly observed in Japanese population detected by two AmpFℓSTR™ typing systems. Furthermore, the most popular mutation type appeared the transition from C to T with G to A, which might have a potential relationship with DNA methylation. Altogether, these results can provide helpful information in forensic practice to the elimination of genotyping discrepancy and the development of primer sets.