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.

Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

Original Publication: San Francisco, CA : Public Library of Science

Chromosomes, Human, Y*/genetics ; Microsatellite Repeats*/genetics; Humans ; Male ; INDEL Mutation ; Forensic Genetics/methods ; Female ; Haplotypes ; Polymerase Chain Reaction/methods

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.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2024 Sun et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Forensic Sci Int Genet. 2016 Nov;25:45-51. (PMID: 27497645)
Front Genet. 2021 Mar 11;12:610540. (PMID: 33777093)
Emerg Top Life Sci. 2021 Sep 24;5(3):427-441. (PMID: 34533187)
Mol Genet Genomic Med. 2020 Sep;8(9):e1419. (PMID: 32677357)
Forensic Sci Int Genet. 2017 Mar;27:67-73. (PMID: 27992828)
PLoS One. 2016 Nov 1;11(11):e0165678. (PMID: 27802306)
Biotechniques. 1996 Oct;21(4):700-9. (PMID: 8891224)
Forensic Sci Int Genet. 2012 Jul;6(4):e99-102. (PMID: 22005117)
Forensic Sci Res. 2023 May 31;8(2):152-162. (PMID: 37621447)
Forensic Sci Int Genet. 2021 Nov;55:102595. (PMID: 34543845)
Forensic Sci Int Genet. 2019 May;40:64-73. (PMID: 30776773)
Forensic Sci Med Pathol. 2024 Jun;20(2):400-411. (PMID: 37266863)
Forensic Sci Int Genet. 2016 Mar;21:5-9. (PMID: 26619377)
Biotechniques. 1991 Apr;10(4):506-13. (PMID: 1867860)
Anal Bioanal Chem. 2018 Jan;410(1):235-245. (PMID: 29188309)
Forensic Sci Int Genet. 2015 Nov;19:238-242. (PMID: 26280567)
Am J Hum Genet. 2002 Oct;71(4):854-62. (PMID: 12205564)
Nature. 2003 Jun 19;423(6942):825-37. (PMID: 12815422)
Forensic Sci Int Genet. 2013 Feb;7(2):296-304. (PMID: 23317914)
Hum Mutat. 2020 Sep;41(9):1680-1696. (PMID: 32579758)
Int J Legal Med. 2020 Jan;134(1):177-183. (PMID: 31713677)
Mol Biol Evol. 2015 Mar;32(3):661-73. (PMID: 25468874)
Nucleic Acids Res. 1992 Jan 25;20(2):211-5. (PMID: 1741246)
Forensic Sci Int Genet. 2017 May;28:155-177. (PMID: 28273508)
Forensic Sci Int Genet. 2023 Jul;65:102865. (PMID: 37004371)
Anal Bioanal Chem. 2020 Apr;412(9):2009-2023. (PMID: 32052066)
Electrophoresis. 2019 Dec;40(23-24):3099-3107. (PMID: 31596501)
Forensic Sci Med Pathol. 2015 Sep;11(3):326-38. (PMID: 25999132)
Anal Bioanal Chem. 2018 Apr;410(10):2569-2583. (PMID: 29504082)
Am J Hum Genet. 2010 Sep 10;87(3):341-53. (PMID: 20817138)

Date Created: 20240809 Date Completed: 20240809 Latest Revision: 20240811

20240812

PMC11315348

10.1371/journal.pone.0308535

39121067