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 Table of Contents  
Year : 2018  |  Volume : 4  |  Issue : 2  |  Page : 111-114

Genetic diversities of 23 Y-Chromosome short tandem repeat loci in a han population in the Beijing Region

Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education; Collaborative Innovation Center of Judicial Civilization, China

Date of Web Publication29-Jun-2018

Correspondence Address:
Dr. Di Lu
Key Laboratory for Evidence Science, CUPL, Beijing 100088
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/jfsm.jfsm_12_18

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We investigated the polymorphisms of 23 Y-short tandem repeat (STR) loci in a Han population in the Beijing region. Blood samples were collected from 255 unrelated Han males. DNA templates were amplified using the PowerPlex® Y23 system, and the amplification products were detected with a 3130 genetic analyzer. A total of 254 haplotypes were detected from the 255 unrelated Han males in the Beijing region. The gene diversity of these 23 Y-STR loci was 0.3952–0.9721. The haplotype diversity was 0.99996 and discrimination capacity (DC) was more than 99.6%. The 23 Y-STR loci used in this study are highly polymorphic in Han individuals in the Beijing region and are therefore suitable for paternal kinship identification. Studying allelic deletions such as DYS448 and DYS549 are important for examining Y-STR polymorphisms and forensic testing.

Keywords: Forensic biology, genetic polymorphism, Y-short tandem repeat

How to cite this article:
Hao S, Zhang X, Liu Y, Lu D. Genetic diversities of 23 Y-Chromosome short tandem repeat loci in a han population in the Beijing Region. J Forensic Sci Med 2018;4:111-4

How to cite this URL:
Hao S, Zhang X, Liu Y, Lu D. Genetic diversities of 23 Y-Chromosome short tandem repeat loci in a han population in the Beijing Region. J Forensic Sci Med [serial online] 2018 [cited 2022 Nov 26];4:111-4. Available from: https://www.jfsmonline.com/text.asp?2018/4/2/111/235440

  Introduction Top

Y-short tandem repeats (STRs) exhibit characteristics of paternal inheritance. Approximately 95% of the human Y chromosome is unpaired with the X chromosome and does not participate in recombination during meiosis; this region comprises multiple STR loci that are always passed down from father to son and are nearly unchanged as a specific haplotype. Y-STRs also have a supporting role in paternal paternity testing.[1] Establishing a Y-STR database is particularly important for mixed strain testing, pedigree investigation, and racial inference.[2] Twenty-three Y-STR loci (DYS576, DYS389I, DYS448, DYS389II, DYS19, DYS391, DYS481, DYS549, DYS533, DYS438, DYS437, DYS570, DYS635, DYS390, DYS439, DYS392, DYS643, DYS393, DYS458, DYS385a/b, DYS456, and Y-GATA-H4) included in the PowerPlex ® Y23 System were investigated in 255 unrelated Han males in the Beijing region. The investigation provides basic data for paternal kinship identification.

  Materials and Methods Top

Blood specimens

A total of 255 blood specimens were collected from unrelated individuals of the Han population in the Beijing region. These blood specimens were cases examined by Fada Forensic Institute. This study was approved by the institutional review boards and Ethics committee of China University of political science and law.


We extracted DNA from all blood samples using the Chelex method. Y-STR was typed using the PowerPlex ® Y23 System (Promega, Madison, WI, USA) with the GeneAmp PCR system 9700 (Applied Biosystems, Foster City, CA, USA). Amplified DNA was separated on an ABI3130 DNA Genetic Analyzer (Applied Biosystems) and analyzed using GeneMapper IDv3.2 software (Applied Biosystems, Foster City, CA, USA).

Statistical analysis

Allele frequency and haplotype frequency were calculated by the direct counting method. Gene diversity and haplotype diversity were calculated according to the formula: h = n (1− ΣPi2)/(n − 1) (n refers to the number of samples, Pi refers to allele frequency).[3] DC = Ndiff/N (Ndiff refers to the number of observed haplotypes, N refers to the number of samples).[4]

  Results and Discussion Top

The allele distribution and frequency of 23 Y-STR loci in a Han population in Beijing region are shown in [Table 1] and [Table 2], respectively. We found 202 different alleles and 254 different haplotypes by statistical analysis. The gene diversity of these 23 Y-STR loci was 0.3952–0.9721. The highest GD value was 0.9721 at DYS385a/b and the lowest was 0.3952 at DYS391. Haplotype diversity was 0.99996, and the DC was more than 99.6%, indicating a high level of polymorphisms. The genetic data in paternal kinship identification showed greater application value.
Table 1: The distribution of allelic frequencies of 21 single-copy Y-short tandem repeat loci in Beijing Han population (n=255)

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Table 2: The distribution of haplogroup frequencies of the multi-copy DYS385 locus in Beijing Han population (n=255)

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Four null alleles were observed at DYS448 and DYS549. Among the 255 unrelated Han males in Beijing, the probability of DYS448 allele deletion was 1.57%, and probability of DYS549 allele deletion was 0.39%. DYS448 allele deletion has been reported previously. Parkin et al.[5] tested blood samples from 769 normal Nepalese men, three of whom showed allelic deletion of DYS448. To assess polymorphisms for the 16 loci Y-Filer kit in a Spanish population, Sánchez et al.[6] tested blood samples from 247 unrelated males in Barcelona. One male showed allelic deletion of DYS448. Wang et al.[7] reported two cases of AZFb deletion with DYS549 allele deletion in 240 patients with nonobstructive azoospermia, severe oligozoospermia, or congenital bilateral absence of bilateral vas deferens.

Budowle et al.[8] suggested that null alleles in allelic deletions are divided into two types: “phenotype deletion” and “true deletion.” Phenotypic deletions are caused by a lack of hybridization of the amplification primer, resulting in the mutation of the primer binding site. True deletions are large deletions in the region of repeats and upstream and downstream repeats of the loci. Currently, studies on allelic deletion of DYS448 and DYS549 loci are difficult because of the lack of samples and limited input. Thus, studies on deletions remain in the exploratory stage.

In forensic analysis, combining multiple Y-STRs for both forensic individual identification and pedigree research plays an important role and has unique advantages. Genetic data obtained from studies of Y-STR polymorphisms can be used as objective criteria for assessing the value of the kit for use in a related region and can guide primer design and kit development. Allelic deletion clearly affects genotype analysis. Therefore, studies on allelic deletions such as DYS448 and DYS549 are important for examining Y-STR polymorphisms and forensic identification practice.

Financial support and sponsorship


Conflicts of interest

There are no conflicts of interest.

  References Top

Purps J, Siegert S, Willuweit S, Nagy M, Alves C, Salazar R, et al. Aglobal analysis of Y-chromosomal haplotype diversity for 23 STR loci. Forensic Sci Int Genet 2014;12:12-23.  Back to cited text no. 1
Yang X, Shi MS, Yuan L, Lu D. Application of multiple genetic markers in a case of determination of half sibling. Fa Yi Xue Za Zhi 2016;32:45-8.  Back to cited text no. 2
Nei M. Molecular Evolutionary Genetics. New York: Columbia University Press; 1987.  Back to cited text no. 3
Coble MD, Hill CR, Butler JM. Haplotype data for 23 Y-chromosome markers in four U.S. Population groups. Forensic Sci Int Genet 2013;7:e66-8.  Back to cited text no. 4
Parkin EJ, Kraayenbrink T, Opgenort JR, van Driem GL, Tuladhar NM, de Knijff P, et al. Diversity of 26-locus Y-STR haplotypes in a Nepalese population sample: Isolation and drift in the Himalayas. Forensic Sci Int 2007;166:176-81.  Back to cited text no. 5
Sánchez C, Barrot C, Xifró A, Ortega M, de Aranda IG, Huguet E, et al. Haplotype frequencies of 16 Y-chromosome STR loci in the Barcelona metropolitan area population using Y-filer kit. Forensic Sci Int 2007;172:211-7.  Back to cited text no. 6
Wang Y, Ye J, Li Z, Zheng S, Ma L, Guo H, et al. Identification of null and duplicated alleles for forensic DYS549, DYS527 and DYS459 in male infertility population. Yi Chuan 2014;36:786-92.  Back to cited text no. 7
Budowle B, Aranda XG, Lagace RE, Hennessy LK, Planz JV, Rodriguez M, et al. Null allele sequence structure at the DYS448 locus and implications for profile interpretation. Int J Legal Med 2008;122:421-7.  Back to cited text no. 8


  [Table 1], [Table 2]


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