Developmental validation of the AGCU YNFS Y Kit: A new 6-dye multiplex system with 44 Y-STRs and 5 Y-InDels for forensic application

• Published in: PloS one 2024-08, Vol.19 (8), p.e0308535
• Main Authors: Sun, Chaoran, Wang, Xindi, Wang, Shuangshuang, Zhou, Yuxiang, Jiang, Lanrui, Wang, Zefei, Yao, Hewen, Zhang, Zhirui, Zha, Lagabaiyila, Luo, Haibo, Song, Feng
• Format: Article
• Language: English
• Subjects: Blood; Chromosomes, Human, Y - genetics; Deoxyribonucleic acid; DNA; Female; Forensic Genetics - methods; Forensic science; Forensic sciences; Genetic testing; Genetics; Genotyping; Haplotypes; Humans; Humic acid; Humic acids; INDEL Mutation; Male; Males; Microsatellite Repeats - genetics; Mixtures; Mutation; Mutation rates; Parameter sensitivity; Performance evaluation; Photodegradation; Polymerase chain reaction; Polymerase Chain Reaction - methods; Population (statistical); Population studies; Saliva; Semen; Short tandem repeats; Statistical analysis; Tannic acid; Thermal cycling; Ultraviolet radiation; Y chromosomes
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0308535

With the widespread use of the Y chromosome in genetics, a lot of commercially available Y chromosome kits were developed, validated, and applied to forensic science practice. The AGCU YNFS Y Kit is a new Y chromosome system containing forty-four preferred Y short tandem repeats (Y-STRs) and five common Y-InDels. In this study, the AGCU YNFS Y system was validated to verify its performance by following the guidelines of the Scientific Working Group on DNA Analysis Methods (SWGDAM). A series of validation experiments included the following parameters: PCR-based studies, sensitivity studies, species specificity studies, stability studies, mixture studies, precision studies, stutter calculation, mutation and statistical analysis, population study, and case samples and degradation studies. The results suggested that appropriately changing PCR amplification conditions did not affect genotyping; the kit had good sensitivity for trace amounts of DNA (0.0625 ng), mixtures of multiple male individuals (minor: major = 1: 9), and three PCR inhibitors (more than 250 μM hematin, 250 ng/μL humic acid and 50 ng/μL tannic acid). The maximum standard deviation of allele size did not exceed 0.1552 reflecting the high accuracy of the system. By this, 87 DNA-confirmed pairs of father-son pairs were also analyzed for mutations. A total of 18 loci were mutated, with mutation rates ranging from 11.5×10-3 to 34.5×10-3 (95% CI 7.2×10-3-97.5×10-3, DYS627 and DYF404S1). In the population study, the haplotype diversity of 87 unrelated individuals was 0.9997, and discrimination capacity was 0.9885. Degradation studies have demonstrated that UV-C light exposure for up to 120 hours has no effect on male blood and semen-vaginal secretion mixtures. However, complete typing could no longer be obtained after 48 hours of UV exposure in single male saliva and in male saliva and female blood mixed samples. Collectively, the AGCU YNFS Y Kit is sensitive and accurate and can play its application value in forensic science practice.