Title: Developmental validation of Y-SNP pedigree tagging system: A panel via quick ARMS PCR

Caiyong Yin; Yijie Ren; Atif Adnan; Junzhe Tian; Kejian Guo; Mingying Xia; Ziwei He; Dian Zhai; Xueyun Chen; Lei Wang; Xin Li; Xingjun Qin; Shilin Li; Li Jin

doi:10.1016/j.fsigen.2020.102271

Title: Developmental validation of Y-SNP pedigree tagging system: A panel via quick ARMS PCR

Forensic Sci Int Genet. 2020 May:46:102271. doi: 10.1016/j.fsigen.2020.102271. Epub 2020 Mar 4.

Authors

Caiyong Yin¹, Yijie Ren², Atif Adnan³, Junzhe Tian², Kejian Guo⁴, Mingying Xia⁵, Ziwei He², Dian Zhai⁶, Xueyun Chen⁶, Lei Wang⁷, Xin Li⁷, Xingjun Qin⁸, Shilin Li⁹, Li Jin²

Affiliations

¹ MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China; Human Phenome Institute, Fudan University, Shanghai, 200438, China; Fudan University Taizhou Institute of Health Sciences, Taizhou, 225300, Jiangsu, China. Electronic address: cyyin18@fudan.edu.cn.
² MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China; Human Phenome Institute, Fudan University, Shanghai, 200438, China; Fudan University Taizhou Institute of Health Sciences, Taizhou, 225300, Jiangsu, China.
³ Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, 110122, China.
⁴ MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China; Public Security Bureau of Zibo City, Zibo, 255000, Shandong, China.
⁵ MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China.
⁶ Criminal Investigation Department of Yunnan Province, Kunming, 650021, Yunnan, China.
⁷ Department of Oral & Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
⁸ Department of Oral & Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China. Electronic address: qinxj1989@sina.com.
⁹ MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China; Human Phenome Institute, Fudan University, Shanghai, 200438, China; Fudan University Taizhou Institute of Health Sciences, Taizhou, 225300, Jiangsu, China. Electronic address: lishilin@fudan.edu.cn.

PMID: 32169809
DOI: 10.1016/j.fsigen.2020.102271

Abstract

The Y chromosomal short tandem repeats (Y-STRs) have been used widely to establish paternal relatedness and examine sub-structures in different geographical regions. However, the applications of Y-STRs showed their limitations when it comes to resolving the complicated relationships within close relatives or among unrelated individuals from different geographic areas. Here, we overcome these limitations by introducing a new strategy for Y-SNP multiplex typing using rapid ARMS (amplification-refractory mutation system) PCR. Newly developed Y-SNP Pedigree Tagging System is able to profile 24 Y-SNPs in a single reaction while the whole process takes 4-5 hours. The panel precisely defines the 11 haplogroups (E-M96, D-JST021355, N-M231, C-M130, O-P186, I-M170, IJ-M429, K-M9, QR-M45, G-M201, and IJK-M522) and 13 sub-haplogroups (D1a1a1-N1, D1a2a-P47, C2-M217, N1a1-M46, O1a-M119, O1b-M268, O1b2-M176, O2-M122, O2a1-KL1, O2a2-P201, O2a2b-P164, O2a2a1a2-M7 and O2a2b1a1-M117). This system could contribute to providing the haplogroup affiliation of unknown pedigree and resolving the sub-structures of East Asian populations. In this study, the multiplex system was validated for: ability to detect degraded DNA, sensitivity, species specificity, reproducibility/repeatability, stability, performance in different scenarios, mixture studies, PCR amplification conditions, and population surveys. The Y-SNP information showed a consistent pattern within 40 father-son or brother-brother pairs. The results of this multiplex system showed the different distribution patterns of male donors from two Chinese Han populations. In this study, we try to discriminate the suspect's pedigree on the level of Y-SNP haplogroups. These results show that Y-SNP Pedigree Tagging System is a robust and reliable amplification kit which can be used for male haplogroup determination.

Keywords: Amplification-refractory mutation system; Developmental validation; Pedigree discrimination; Population substructures; Y chromosome database.

Publication types

Research Support, Non-U.S. Gov't
Validation Study

MeSH terms

China
Chromosomes, Human, Y*
Ethnicity / genetics
Forensic Genetics / methods
Humans
Male
Multiplex Polymerase Chain Reaction / methods*
Pedigree*
Polymorphism, Single Nucleotide*
Reproducibility of Results
Sensitivity and Specificity
Species Specificity