Forensic characteristics and genetic analysis of both 27 Y-STRs and 143 Y-SNPs in Eastern Han Chinese population

Lang, Min; Liu, Hai; Song, Feng; Qiao, Xianhua; Ye, Yi; Ren, He; Li, Jienan; Huang, Jian; Xie, Mingkun; Chen, Shengjie; Song, Mengyuan; Zhang, Youfang; Qian, Xiaoqin; Yuan, Taoxiu; Wang, Zheng; Liu, Yuming; Wang, Mengge; Liu, Yacheng; Liu, Jing; Hou, Yiping

doi:10.1016/j.fsigen.2019.07.011

Cited by 67 publications

(65 citation statements)

References 32 publications

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“…Albeit it has been concluded that the QR haplogroup is not a major haplogroup of the East Asian population [65], 92.2% of the reported "DYS518~.2" mutations were found in Chinese samples in the YHRD database. Additionally, Lang et al found a relationship between the "DYS518~.2" alleles and the haplogroup Q [66]. In order to define the evolutionary history of the "DYS518~.2" allele, the median-joining network was utilized to construct the inner structure of the QR-M45 haplogroup (Figure 4).…”

Section: Y-str Allele Variantsmentioning

confidence: 99%

Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs

Yin

et al. 2020

Genes

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Y chromosomal short tandem repeats (Y-STRs) have been widely harnessed for forensic applications, such as pedigree source searching from public security databases and male identification from male–female mixed samples. For various populations, databases composed of Y-STR haplotypes have been built to provide investigating leads for solving difficult or cold cases. Recently, the supplementary application of Y chromosomal haplogroup-determining single-nucleotide polymorphisms (SNPs) for forensic purposes was under heated debate. This study provides Y-STR haplotypes for 27 markers typed by the Yfiler™ Plus kit and Y-SNP haplogroups defined by 24 loci within the Y-SNP Pedigree Tagging System for Shandong Han (n = 305) and Yunnan Han (n = 565) populations. The genetic backgrounds of these two populations were explicitly characterized by the analysis of molecular variance (AMOVA) and multi-dimensional scaling (MDS) plots based on 27 Y-STRs. Then, population comparisons were conducted by observing Y-SNP allelic frequencies and Y-SNP haplogroups distribution, estimating forensic parameters, and depicting distribution spectrums of Y-STR alleles in sub-haplogroups. The Y-STR variants, including null alleles, intermedia alleles, and copy number variations (CNVs), were co-listed, and a strong correlation between Y-STR allele variants (“DYS518~.2” alleles) and the Y-SNP haplogroup QR-M45 was observed. A network was reconstructed to illustrate the evolutionary pathway and to figure out the ancestral mutation event. Also, a phylogenetic tree on the individual level was constructed to observe the relevance of the Y-STR haplotypes to the Y-SNP haplogroups. This study provides the evidence that basic genetic backgrounds, which were revealed by both Y-STR and Y-SNP loci, would be useful for uncovering detailed population differences and, more importantly, demonstrates the contributing role of Y-SNPs in population differentiation and male pedigree discrimination.

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Section: Y-str Allele Variantsmentioning

confidence: 99%

Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs

Yin

et al. 2020

Genes

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“…As shown in Figure 2b, a heatmap of the pairwise Rst values for 23 Y-STRs indicated the genetic relationships of Kyrgyz group and 13 reference populations. These 13 reference populations included East Asian populations: Beijing Han [33][34][35], Guangdong Han [36], Southern Han [37], Asian American [38], Japanese [39][40][41][42], and Qiemo Uygur and Xinjiang Uygur in northwest China [43][44][45]; European populations: Estonian [46], Italian [47][48][49][50][51][52], Norwegian [53,54], European American, and Hispanic American [38]; and African population: African American [38]. According to the Rst values, the Kyrgyz group had the closest distances to the northwest Chinese populations, Qiemo Uygur (Rst = 0.0831) and Xinjiang Uygur (Rst = 0.0840), followed by the European populations with Rst ranging from 0.1177 to 0.1639, and then by other populations from East Asia (the Rst values were in the range of 0.2199 to 0.2957).…”

Section: Population Genetic Differentiation Analyses For Y-strsmentioning

confidence: 99%

Joint Genetic Analyses of Mitochondrial and Y-Chromosome Molecular Markers for a Population from Northwest China

Guo

Xia

Cui

et al. 2020

Genes

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The genetic markers on mitochondria DNA (mtDNA) and Y-chromosome can be applied as a powerful tool in population genetics. We present a study to reveal the genetic background of Kyrgyz group, a Chinese ethnic group living in northwest China, and genetic polymorphisms of 60 loci on maternal inherited mtDNA and 24 loci on paternal inherited Y-chromosome short tandem repeats (Y-STRs) were investigated. The relationship between the two systems was tested, and the result indicated that they were statistically independent from each other. The genetic distances between Kyrgyz group and 11 reference populations for mtDNA, and 13 reference populations for Y-STRs were also calculated, respectively. The present results demonstrated that the Kyrgyz group was genetically closer to East Asian populations than European populations based on the mtDNA loci but the other way around for the Y-STRs. The genetic analyses could largely strengthen the understanding for the genetic background of the Kyrgyz group.

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“…pyrosequencing (26,28,29). The study received the approval of the Ethics Committee at the Institute of Forensic Medicine, Sichuan University (K2019018) and the data were analyzed anonymously due to privacy concerns.…”

Section: Datasetsmentioning

confidence: 99%

YHP: Y-chromosome Haplogroup Predictor for predicting male lineages based on Y-STRs

Song

Zhao

et al. 2021

Preprint

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Human Y chromosome reflects the evolutionary process of males. Male lineage tracing by Y chromosome is of great use in evolutionary, forensic, and anthropological studies when male samples exist or especially when the biological sample is a mixture of male and female individuals. Identifying the male lineage based on the specific distribution of Y haplogroups narrows down the investigation scope. Integrating previously published datasets with genotypes of Y chromosome short tandem repeats (Y-STRs) and high-resolution haplogroups (122 haplogroups in total), we developed YHP (Y Haplogroup Predictor), an open-access and userfriendly software package to predict haplogroups, compare the similarity, and conduct mismatch analysis of samples with Y-STR profiles. The software is available at Github (https://github.com/cissy123/YHP-Y-Haplogroup-Predictor-).Author SummaryFamilial searching has been used in forensic, anthropologic, and personalized scenarios. Software packages have been developed to assist in male familial searching, such as predicting Y-SNP haplogroups by Y-STRs. However, these software packages, in general, achieve this goal with a rough resolution. In this study, we developed a software package to conduct high-resolution haplogroup inference to help familial searching and at the same time reduce the cost, since it does not require tiresome Y-SNP sequencing.

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Forensic characteristics and genetic analysis of both 27 Y-STRs and 143 Y-SNPs in Eastern Han Chinese population

Cited by 67 publications

References 32 publications

Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs

Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs

Joint Genetic Analyses of Mitochondrial and Y-Chromosome Molecular Markers for a Population from Northwest China

YHP: Y-chromosome Haplogroup Predictor for predicting male lineages based on Y-STRs

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