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j.fsigss.2017.09.047

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Forensic Science International: Genetics Supplement Series xxx (xxxx) xxx–xxx
Contents lists available at ScienceDirect
Forensic Science International: Genetics Supplement Series
journal homepage: www.elsevier.com/locate/fsigss
A study of the genetic diversity in the Heze Han population using a novel
genotyping system based on 24 Y-chromosomal STR loci
Min Lia,b,1, Tingzhi Queb,1, Lei Huangc,1, Yuling Chenb,d, Yanan Lib,e, Lei Jiangb, Ruxin Zhub,
⁎
⁎
Wei Zhouf, Yingnan Biana,b, , Chengtao Lia,b,
a
Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Higher Education District, Wenzhou, 325035, Zhejiang Province, China
Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063,
China
c
The Institute of Criminal Science and Technology, Shandong Public Security Department, China
d
State Key Laboratory of Bioreactor Engineering, College Of Biology Engineering, East China University of Science and Technology, No.130, Meilong Road, Xuhui District,
200237, Shanghai, China
e
Department of Forensic Medical, School of Basic Medical Sciences, Inner Mongolia Medical University, Hohhot 010020, the Inner Mongolia Autonomous Region, China
f
The Jackson Laboratory For Genomic Medicine, 10 Discovery Dr., Farmington, CT, 06032, USA
b
A R T I C L E I N F O
A B S T R A C T
Keywords:
Y-STR loci
Forensic genetics
Han population
We established a 24-plex Y-STR typing system by including the 13 Y-STR loci used in AmpFLSTR® Yfiler® PCR
Amplification Kit (Applied Biosystems, Foster City, CA) and 11 additionally selected Y-STR loci that significantly
increased power of discrimiation. We applied the system to genotype 195 unrelated Chinese Han males, resulting
in 195 distinct haplotypes. The diversity observed across loci ranged from 0.0885 (DYS645) to 0.9646
(DYS385a/b)., while the haplotype diversity was 1 based on the 24 Y-STR loci. The ultra-high differentiation
power of the genotyping system has great potential in forensic applications.
1. Introduction
Y chromosome contains the largest non-recombining block in
human genome and is useful in inferring evolutionary history [1].
Within the Y chromosome, short tandem repeats (Y-STRs) are widely
used in forensic investigations, including mixture identification in
sexual assault cases and patrilineal relationship evaluation in kinship
testing [2]. However, existing Y-STR-based genotyping systems have
relatively low power of discrimination or high rate of mutation when
applied to subjects in a same population[3–5]. To overcome this limitation, we sought to select a set of Y-STR loci that have high power of
discrimination of unrelated males within Han population and relatively
low rate of mutation. In this study, we developed a new 24-plex STR
typing system and demonstrated its ultra-high power of discrimination
by characterizing the genetic diversity of the Han population from the
Heze City in China.
2. Materials and methods
Blood samples on FTA card were collected from 195 unrelated Heze
Han males, with informed consents, using the 1.2 mm of Micro −
punch sampler for direct amplification. Multiplex PCR of 24 Y-STRs loci
(DYS426, DYS434, DYS531, DYS439, DYS19, DYS392, DYS643,
DYS391, DYS570, DYS635, DYS448, DYS593, DYS645, DYS393,
DYS389I, DYS390, DYS389II, DYS596, DYS576, DYS458, DYS481,
DYS385a/b, DYS443) was performed in a 10 μL mixture including
6.0 μL of deionized water, 2.0 μL of 5 × PCR reaction pre-mixed solution, 2.0 μL of 5 × 24Y primer mixture and blood sample of 1.2 mm
diameter. The loci were assigned into four different groups with primers
that labeled with 6-FAM, HEX, TAMRA and ROX, respectively. PCR was
performed on GeneAmp PCR 9700 thermal cyclers (Applied Biosystem,
Foster City, CA) using the MAX mode with an initial denaturation at
95 °C for 2 min, followed by 30 cycles of denaturation at 94 °C for 5s,
annealing at 60 °Cfor 1 min, extension at 60 °Cfor 10 min and finally
kept at 15 °C. Size of the PCR products were analyzed using electrophoresis: 1 μL of each amplified product was mixed with 9 μL of a 17:1
mixture of Hi–Di formamide (Applied Biosystem, Foster City, CA) and
ORG-500 Size Standard for electrophoresis. ORG-500 labeled with
fluorescence SIZ was used as the internal lane standard. The PCR products were detectd by capillary electrophoresis using an ABI 3130xl
⁎
Corresponding authors at: Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Higher Education District, Wenzhou, 325035, Zhejiang
Province, China.
E-mail addresses: bianyingnan@yeah.net (Y. Bian), lichengtaohla@163.com (C. Li).
1
These authors contributed equally to this work.
http://dx.doi.org/10.1016/j.fsigss.2017.09.047
Received 30 June 2017; Accepted 11 September 2017
1875-1768/ © 2017 Elsevier B.V. All rights reserved.
Please cite this article as: Li, M., Forensic Science International: Genetics Supplement Series (2017),
http://dx.doi.org/10.1016/j.fsigss.2017.09.047
Forensic Science International: Genetics Supplement Series xxx (xxxx) xxx–xxx
M. Li et al.
Table 1
The Allele frequencies of the 24 Y-STRs loci in Heze Han male population in China (n = 195).
DYS426
DYS392
DYS635
DYS390
DYS385
Allele
Frequency
Allele
Frequency
Allele
Frequency
Allele
Frequency
Allele
Frequency
10
11
12
DYS434
Allele
8
9
10
11
DYS531
Allele
9
10
11
11.11)
12
13
DYS439
Allele
8
10
11
12
13
14
DYS19
Allele
13
14
15
16
17
DYS443
Allele
11
12
13
14
15
16
DYS389I
Allele
11
12
13
14
15
0.0051
0.9538
0.0410
10
11
12
13
14
15
16
17
DYS643
Allele
8
9
10
11
12
13
DYS391
Allele
6
9
10
11
12
DYS570
Allele
14
15
16
17
18
19
20
21
23
24
DYS576
Allele
10
14
15
16
17
18
19
20
21
22
0.0154
0.1436
0.1436
0.2974
0.3744
0.0154
0.0051
0.0051
17
19
20
21
22
23
24
25
DYS448
Allele
16
16.11)
17
18
19
20
21
22
DYS593
Allele
15
16
17
18
DYS645
Allele
8
9
DYS393
Allele
11
12
13
14
15
DYS458
Allele
14
15
16
17
18
18.2a
19
20
21
22
0.0051
0.0821
0.3026
0.3846
0.1231
0.0718
0.0256
0.0051
21
22
23
24
25
26
DYS389II
Allele
24
26
27
28
29
30
31
32
33
DYS596
Allele
13
14
15
16
17
18
DYS481
Allele
20
21
22
23
24
25
26
27
28
29
0.0051
0.0410
0.4359
0.3487
0.1538
0.0154
10,19
11
11,12
11,13
11,14
11,15
11,16
11,17
11,18
11,19
11,20
12
12,13
12,14
12,15
12,16
12,17
12,18
12,19
12,20
12,22
13
13,14
13,16
13,17
13,18
13,19
13,20
13,21
13,22
13,23
14
14,17
14,18
14,19
14,20
14,21
15,16
15,17
15,21
16
16,17
16,20
16,22
17
18
0.0051
0.0154
0.0410
0.0205
0.0154
0.0051
0.0103
0.0256
0.0205
0.0308
0.0051
0.0256
0.0205
0.0103
0.0205
0.0564
0.0667
0.0769
0.0359
0.0205
0.0051
0.0256
0.0051
0.0103
0.0462
0.0462
0.0923
0.0205
0.0154
0.0103
0.0051
0.0051
0.0256
0.0359
0.0410
0.0103
0.0103
0.0103
0.0103
0.0051
0.0103
0.0051
0.0051
0.0051
0.0051
0.0051
a
Frequency
0.1026
0.7744
0.0410
0.0821
Frequency
0.0205
0.1282
0.6615
0.0103
0.1744
0.0051
Frequency
0.0051
0.0718
0.4154
0.4256
0.0718
0.0103
Frequency
0.0256
0.3128
0.4256
0.1641
0.0718
Frequency
0.0051
0.0359
0.3026
0.3077
0.3128
0.0359
Frequency
0.0154
0.5692
0.2308
0.1744
0.0103
Frequency
0.0410
0.0923
0.1692
0.5077
0.1795
0.0103
Frequency
0.0103
0.0154
0.7795
0.1897
0.0051
Frequency
0.0205
0.0410
0.1949
0.2103
0.2256
0.2205
0.0615
0.0154
0.0051
0.0051
Frequency
0.0051
0.0051
0.0154
0.0718
0.1692
0.4051
0.1897
0.0974
0.0308
0.0103
Frequency
0.0051
0.0051
0.0154
0.1179
0.3590
0.3897
0.0872
0.0205
Frequency
0.2821
0.5436
0.1538
0.0205
Frequency
0.9538
0.0462
Frequency
0.0154
0.5641
0.2359
0.1231
0.0615
Frequency
0.0154
0.1385
0.1795
0.2615
0.2154
0.0051
0.1333
0.0256
0.0205
0.0051
Frequency
0.0051
0.0103
0.0769
0.3538
0.2718
0.1795
0.0821
0.0154
0.0051
Frequency
0.0103
0.4462
0.3949
0.1179
0.0256
0.0051
Frequency
0.0154
0.0462
0.1897
0.2923
0.2256
0.1026
0.0821
0.0308
0.0051
0.0103
Represent alleles out of ladder.
Genetic Analyzer (Applied Biosystem, Foster City, CA) and analyzed
with GeneMapper ID v3.2 software (Applied Biosystem, Foster City,
CA). Control DNA of 9948 (Promega, WI, USA) human cell line was
used as positive control. The nomenclature of Y-STR alleles was according to the latest recommendations of the DNA commission of the
International Society of Forensic Genetics [6]. Allele or haplytope frequencies were computed using direct counting. Haplotype diversity
(HD) was computed using Nei’s formula: HD = n(1 − ∑Pi2)/(n − 1),
where Pi is the frequency of the ith haplotype and n indicates the total
number of samples. Haplotype discrimination capacity (DC) was given
by DC = h/n, where h is the total number of unique haplotypes. Gene
diversity (GD) was calculated as GD = n(1 − ∑pi2)/(n − 1), where pi is
the frequency of the ith Allele [7].
copy-allele frequencies (DYS385a/b) ranging from 0.0051 to 0.0923
(Table 1). Microvariants were observed at three different loci: 11.1 at
DYS531(n = 2), 16.1 at DYS448(n = 1) and 18.2 at DYS458(n = 1)
(Table 1).
GD of each locus ranged from 0.0085 (DYS645) to 0.9646
(DYS385a/b) (Table 2). All loci have GD values greater than 0.5, except
DYS645, DYS426, DYS434 and DYS391, suggesting high polymorphism
at the selected loci within the Heze Han population.
A total of 195 different haplotypes were observed from the 195 Heze
Han males. The haplotype diversity (HD) and discrimination capacity
(DC) of the 24 Y-STR loci was 1 – The system was able to differentiate
all subjects recruited in the study. The ultra-high power in discrimination of the 24-plex Y-STR typing system suggested for its usefulness in forensic casework and paternity testing at least in Chinese
Han populations. The 11 additionally selected loci were an important
supplement to the currently available Y-STR genotyping.
3. Results and discussions
A total of 188 alleles were observed across the 24 Y-STR loci, with
single-copy-allele frequencies ranging from 0.0051 to 0.9538 and multi2
Forensic Science International: Genetics Supplement Series xxx (xxxx) xxx–xxx
M. Li et al.
China (No. 81601651 and 81625013), the Ministry of Finance of China
(GY2016D1), the Shanghai science and Technology Innovation Fund
(16dz1205500, 16DZ2290900, 17DZ2273200) and the Shanghai science and Technology Innovation Fund (16dz1205500). The funders did
not participate in study design, data analysis, decision for publication,
or the preparation of the manuscript.
Table 2
The gene diversity of the 24 Y-STRs loci in Heze Han male population in China (n = 195).
Locus
DYS426
DYS434
DYS531
DYS439
DYS19
DYS392
DYS643
DYS391
Gene
diversity
Locus
Gene
diversity
Locus
Gene
diversity
0.0889
0.3834
0.5176
0.6391
0.6918
0.7334
0.6745
0.3579
DYS570
DYS635
DYS448
DYS593
DYS645
DYS393
DYS389I
DYS390
0.8163
0.7366
0.7006
0.6040
0.0885
0.6101
0.5950
0.6662
DYS389II
DYS596
DYS576
DYS458
DYS481
DYS385
DYS443
0.7596
0.6336
0.7591
0.8189
0.8111
0.9646
0.7170
References
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Genome Res. 12 (2) (2002) 339–348.
[2] M.A. Jobling, A. Pandya, C. Tyler-Smith, The Y chromosome in forensic analysis and
paternity testing, Int. J. Legal Med. 110 (3) (1997) 118–124.
[3] M. Kayser, et al., A comprehensive survey of human Y-chromosomal microsatellites,
Am. J. Hum. Genet. 74 (6) (2004) 1183–1197.
[4] M. Vermeulen, et al., Improving global and regional resolution of male lineage differentiation by simple single-copy Y-chromosomal short tandem repeat polymorphisms, Forensic Sci. Int. Genet. 3 (4) (2009) 205–213.
[5] A.E. Decker, et al., The impact of additional Y-STR loci on resolving common haplotypes and closely related individuals, Forensic Sci. Int. Genet. 1 (2) (2007)
215–217.
[6] L. Gusmao, et al., DNA Commission of the International Society of Forensic Genetics
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[7] M. Nei, Molecular Evolutionary Genetics, Columbia University Press, New York, NY,
1987, pp. pp. 176–179.
Conflict of interest statement
All authors declare no conflicts of interest.
Acknowledgements
We are very grateful to the volunteers in our study. This study was
supported by the National Key Research and Development Program of
China (2016YFC0800703), the National Natural Science Foundation of
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