Forensic Parameters of 41 Y-STR Loci in Shandong Han Individuals and Comparison with 42 other Populations

Chen, Anqi; Luo, Li; Tao, Ruiyang; Zhang, Suhua; Li, Chengtao

doi:10.1080/20961790.2021.1963397

Cited by 2 publications

(2 citation statements)

References 12 publications

(17 reference statements)

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“…At the same time, trialleles are found at two double-copy loci (DYS527 and DYF404S1) in the Guizhou Dong population. Similar results are found in individuals of the Shandong Han population, which may be related to the extra copies of these loci on the Y chromosome ( Chen et al, 2022 ). This needs to be verified by the Sanger sequencing.…”

Section: Discussionsupporting

confidence: 82%

Comprehensive analyses of genetic diversities and population structure of the Guizhou Dong group based on 44 Y-markers

Zhang,

Huang,

Jin

et al. 2023

PeerJ

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Background The non-recombining region of the human Y chromosome (NRY) is a strictly paternally inherited genetic marker and the best material to trace the paternal lineages of populations. Y chromosomal short tandem repeat (Y-STR) is characterized by high polymorphism and paternal inheritance pattern, so it has been widely used in forensic medicine and population genetic research. This study aims to understand the genetic distribution of Y-STRs in the Guizhou Dong population, provide reference data for forensic application, and explore the phylogenetic relationships between the Guizhou Dong population and other comparison populations. Methods Based on the allele profile of 44 Y-markers in the Guizhou Dong group, we estimate their allele frequencies and haplotype frequencies. In addition, we also compare the forensic application efficiency of different Y-STR sets in the Guizhou Dong group. Finally, genetic relationships among Guizhou Dong and other reference populations are dissected by the multi-dimensional scaling and the phylogenetic tree. Results A total of 393 alleles are observed in 312 Guizhou Dong individuals for these Y-markers, with allele frequencies ranging from 0.0032 to 0.9679. The haplotype diversity and discriminatory capacity for these Y-markers in the Guizhou Dong population are 0.99984 and 0.97440, respectively. The population genetic analyses of the Guizhou Dong group and other reference populations show that the Guizhou Dong group has the closest genetic relationship with the Hunan Dong population, and followed by the Guizhou Tujia population. Conclusions In conclusion, these 44 Y-markers can be used as an effective tool for male differentiation in the Guizhou Dong group. The haplotype data in this study not only enrich the Y-STR data of different ethnic groups in China, but also have important significance for population genetics and forensic research.

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Section: Discussionsupporting

confidence: 82%

Comprehensive analyses of genetic diversities and population structure of the Guizhou Dong group based on 44 Y-markers

Zhang,

Huang,

Jin

et al. 2023

PeerJ

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“…The amplitudes of increasing were mild or very slow when comparing with 25–29 Y-STRs. These improvements in haplotype resolution and forensic parameters are similar to those from Southeastern Han Chinese [ 31 ] and Shandong Han Chinese [ 32 ].…”

Section: Resultssupporting

confidence: 64%

Sequence-based mutation patterns at 41 Y chromosomal STRs in 2 548 father–son pairs

Liu

Long

Lang

et al. 2023

Forensic Sciences Research

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A total of 2548 unrelated healthy father-son pairs from a Northern Han Chinese population were genotyped at 41 Y-STRs including DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS444, DYS447, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS522, DYS549, DYS533, DYS557, DYS570, DYS576, DYS593, DYS596, DYS627, DYS635, DYS643, DYS645, Y-GATA-H4, DYF387S1a/b, DYF404S1a/b, DYS385a/b and DYS527a/b. In 2548 father samples, 2387 unique haplotypes were detected with the haplotype diversity (HD) and discrimination capacity (DC) values of 0.999956608 and 0.967410 07. The average gene diversity (GD) value was 0.6934 with a range from 0.1051 at DYS645 to 0.9657 at DYS385a/b. When comparing alleles at 24 overlapped Y-STRs between the ForenSeq™ DNA Signature Prep Kit on the MiSeq FGx® Forensic Genomics System and the Goldeneye® DNA ID Y Plus Kit on the Applied Biosystems™ 3730 DNA Analyzer from 308 father samples in mutational pairs, 258 alleles were detected by massively parallel sequencing (MPS) typing including 156 length-based alleles that could be obtained by capillary electrophoresis (CE) typing, 95 repeat region (RR) variant alleles and 7 flanking region (FR) variant alleles. Hereof, we found 16 novel RR variant alleles and firstly identified two SNPs (rs2016239814 at DYS19 and rs2089968964 at DYS448) and one 4-bp deletion (rs2053269960 at DYS439) that had been validated by the Database of Short Genetic Variation (dbSNP). Sanger sequencing or MPS was employed to confirm 356 mutations from 104 468 allele transfers generated from CE, where 96.63% resulted in one-step mutations, 2.25% in two-step and 1.12% in multi-step, and the overall ratio of repeat gains versus losses was balanced (173 gains v.s. 183 losses). In 308 father-son pairs, 268 pairs occurred mutations at a single locus, 33 pairs at two loci, 6 pairs at three loci and 1 pair at four loci. The average Y-STR mutation rate at 41 Y-STRs was approximately 3.4 × 10−3 (95% CIs: 3.1 × 10−3–3.8 × 10−3). The mutation rates at DYS576 and DYS627 were higher than 1 × 10−2 in Northern Han Chinese, while the mutation rates at DYF387S1a/b, DYF404S1a/b, DYS449, DYS518 and DYS570 were lower than initially-defined. In this study, the classical molecular factors (the longer STR region, the more complex motif and the order father) were confirmed to drive Y-STR mutation rates increased, but the length of repeat unit did not conform to the convention. Lastly, the interactive graphical and installable StatsY was developed to facilitate forensic scientists to automatically calculate allele and haplotype frequencies, forensic parameters and mutation rates at Y-STRs.

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Forensic Parameters of 41 Y-STR Loci in Shandong Han Individuals and Comparison with 42 other Populations

Cited by 2 publications

References 12 publications

Comprehensive analyses of genetic diversities and population structure of the Guizhou Dong group based on 44 Y-markers

Comprehensive analyses of genetic diversities and population structure of the Guizhou Dong group based on 44 Y-markers

Sequence-based mutation patterns at 41 Y chromosomal STRs in 2 548 father–son pairs

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