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Haplotype diversity of 13 RM Y-STRs in Chinese Han population and an update on the allele designation of DYF403S1
Accepted Manuscript Title: Haplotype diversity of 13 RM Y-STRs in Chinese Han population and an update on the allele designation of DYF403S1 Author: Wenqiong Zhang Chao Xiao Tian Wei Chao Pan Shaohua Yi Daixin Huang PII: DOI: Reference:
S1872-4973(16)30069-2 http://dx.doi.org/doi:10.1016/j.fsigen.2016.04.013 FSIGEN 1510
To appear in:
Forensic Science International: Genetics
Received date: Revised date: Accepted date:
16-10-2015 27-4-2016 29-4-2016
Please cite this article as: Wenqiong Zhang, Chao Xiao, Tian Wei, Chao Pan, Shaohua Yi, Daixin Huang, Haplotype diversity of 13 RM Y-STRs in Chinese Han population and an update on the allele designation of DYF403S1, Forensic Science International: Genetics http://dx.doi.org/10.1016/j.fsigen.2016.04.013 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Forensic Population Genetics – Short Communications
Haplotype diversity of 13 RM Y-STRs in Chinese Han population and an update on the allele designation of DYF403S1
Wenqiong Zhang, Chao Xiao, Tian Wei, Chao Pan, Shaohua Yi, Daixin Huang*
Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, No. 13, Hangkong Road, Wuhan 430030, China
* Corresponding author. Tel.: ＋86-27-8369-2645; fax: ＋86-27-8363-1216. E-mail address: [email protected] (D. Huang).
Highlights:
Haplotype diversity of 13 RM Y-STRs in Chinese Han population was investigated.
The RM Y-STR set showed great discrimination power in Chinese Han population.
An update on the allele designation of DYF403S1 was proposed.
Distinctive multi-allelic patterns were observed at 4 multi-copy Y-STR markers.
Abstract Rapidly mutating Y-STRs (RM Y-STRs) have been paid much attention in recent years. The 13 RM Y-STRs have been proved to have substantially higher haplotype diversity and discrimination capacity than conventionally used Y-STRs, indicating the considerable power in paternal lineage differentiation. To investigate the haplotype diversity in Chinese Han population, we collected 252 unrelated male samples and tested the genotype of the 13 RM Y-STRs. Among 252 male individuals, a total of 250 haplotypes were observed in which only 2 haplotypes were shared by 2 males respectively. The haplotype diversity reached 0.999937 and the discrimination capacity was 99.21%, showing a great discrimination power in Chinese Han population. In addition, an update on the allele designation of DYF403S1 was proposed. Keywords: Y chromosome; Rapidly mutating Y-STR; Haplotype diversity; Lineage differentiation; Nomenclature
1. Introduction Due to their paternal inheritance characteristic, the analysis of Y-chromosomal genetic markers, especially Y-chromosomal short tandem repeats (Y-STRs) is becoming a useful tool for tracing human evolution through male lineages [1] as well as application in a variety of forensic situations [2] including personal identification in sexual assault cases [3–6] and paternity testing with male children [7–9]. However, there are some limitations on the application of Y-STRs in forensic investigations. First, in populations which have encountered bottleneck effect or founder effect, the current Y-STR panels show limited resolution due to the overall reduced diversity [10–12]. Second, conventional Y-STRs are only suitable to distinguish between paternal lineages but not between individuals. Recently, the mutation rates of 186 Y-STR markers were systematically studied by Ballantyne et al. [1], and a set of 13 Y-STR markers (DYF387S1, DYF399S1, DYF403S1, DYF404S1, DYS449, DYS518, DYS526, DYS547, DYS570, DYS576, DYS612, DYS626 and DYS627) with exceptionally high mutation rates (>10-2 per locus per generation) was identified as “rapidly mutating” (RM) Y-STRs [1, 2]. These RM Y-STRs had been proved not only able to improve the resolution of male lineage differentiation, but also to allow close male relative separation with a power unsurpassed by standard Y-STRs [2–5]. To verify the haplotype diversity and the applicability of the 13 novel RM Y-STRs in Chinese Han population, we performed a population genetics survey on Chinese Han group as well as an update on the allele designation of the multi-copy Y-STR locus DYF403S1 on the basis of Ballantyne et al. [3]. 2. Materials and methods 2.1. DNA samples Blood samples were collected from 252 male unrelated healthy blood donors of Chinese Han population in Hubei province. Genomic DNA was isolated from whole blood using the Chelex-100 method [6]. The AmpFlSTR control DNA 007 was used as
control DNA source. 2.2. PCR amplification and genotyping Primers used for amplifying these RM Y-STRs in our study were the same as those reported by Ballantyne et al. [2] except for DYF403S1 and DYS526. The primers for typing DYF403S1 were redesigned by using the Primer 3 software (http://bioinfo.ut.ee/primer3/)
to
5′-CCTCCCTTCTCCCTGTCTTT-3′,
shorten
the
amplicons
(Primer
Primer
A: B:
5′-ACAGAGCAGGATTCCATCTA-3′). Primers for DYS526 used in this study were in accordance with that of Rogalla et al. [5], which only can amplify the allele of DYS526b but not the allele of DYS526a. One of each primer pairs was labelled with 6-FAM dye for detection using ABI 3130 Genetic Analyser (Thermo Fisher Scientific, MA, USA). Amplification for the 13 markers was conducted separately. PCR was performed in a total reaction volume of 20 L containing 5～10 ng genomic DNA, 10 mM Tris–HCl buffer (pH 8.3), 50 mM KCl, 1.5 mM MgCl2, 200 M each dNTP, 0.1 M of each primer, and 1 U AmpliTaq Gold® DNA polymerase (Thermo Fisher Scientific, MA, USA). The cycling conditions were: 95°C for 11 min soak, 30 cycles of 30 s at 94°C, 30 s at 60°C (DYF399S1, DYS518, DYS526b, DYS547, DYS576, DYS612, DYS626 and DYS627) or 62°C (DYF387S1, DYF403S1, DYF404S1, DYS449 and DYS570) and 45 s at 72°C followed by a 30 min extension period at 72°C. For fragment length analysis, 1 μL aliquot of PCR products was added to 8.7 μL Hi-Di formamide (Thermo Fisher Scientific, MA, USA) and 0.3 μL of LIZ-500 (Thermo Fisher Scientific, MA, USA). The amplified products were resolved and detected on a 3130 Genetic Analyzer (Thermo Fisher Scientific, MA, USA) according to vendor instructions, using a 36 cm array, POP-4 polymer and dye set G5. The sample run data were analyzed using GeneMapper ID v3.2 software (Thermo Fisher Scientific, MA, USA). 2.3. Sequence analysis
A total of 128 fragments (107 different alleles) were selected for sequence analysis. PCR products of single-copy markers amplified by unlabelled primers were directly sequenced after purification. The amplification products of multi-copy markers were separated by the polyacrylamide gel electrophoresis, and the selected alleles were recovered independently from the gel, then a re-amplification was performed. All of the PCR products were purified using TaKaRa MiniBEST DNA Fragment Purification Kit Ver.4.0 (Takara), and then were sent to the Sangon Biotech （Shanghai）Co., Ltd. for bidirectional sequencing. 2.4. Allele designation Nomenclature for the 13 RM Y-STR markers was based on our sequencing results, the allele designation way used by Ballantyne et al. [3] and the recommendations of the International Society of Forensic Genetics (ISFG) on the use of Y-STRs [7, 8]. 2.5. Statistical analysis Allele and haplotype frequencies were determined using the counting method. The gene diversity (GD) or haplotype diversity (HD) was calculated using the formula
h n 1 pi2 / n 1 where n is the number of individuals and pi represents the frequency of the ith allele or haplotype [9]. The discrimination capacity (DC) was determined by the formula #H/N where #H represents the number of observed haplotypes and N is the number of samples [10]. 3. Results and discussion 3.1. Allele designation As shown in Table 1, the allele nomenclature for these markers was consistent with that of Ballantyne et al. [3] except for the loci DYF399S1, DYF403S1, DYS526b and DYS626. In our previous study [11], not only a different allele designation for the DYF399S1 was proposed, but also a T deletion occurring inside a homopolymeric T tract located between nucleotide positions 13 and 16 downstream of the repeat was
reported in the Chinese Han population (0.8% incidence rate). DYF403S1 is a duplicated STR system with four positions on the Y-chromosome (DYF403S1a contains three copies, and one in DYF403S1b). Our sequencing results showed that there were three different repeat structures in the DYF403S1 system, and two structures (TTCT)nATC(TTCT)o and (TTCT)nTT(TTCT)3 existed in the DYF403S1a
(Fig.
S1)
and
another
structure
(TTCT)nCT(TTCT)o(TTCC)p(TTCT)qTT(TTCT)3 in the DYF403S1b, which is in accordance with the sequences listed in GenBank entry NC_000024.10 (Fig. S2). In order to comply with the guidelines of the ISFG, we suggest designating the alleles of DYF403S1a with the general structure (TTCT)nN2-3(TTCT)p as (n+p) instead of the (n+o+p) way of Ballantyne et al. [3] based on the structure (TTCT)nNo(TTCT)p, because the number of nucleotide that interrupting the two repeat regions is less than the base number of repeat motif. In addition, we also suggest to designate the alleles of DYF403S1b as (n+o+p+q+3) instead of (n+o+p+q) used by Ballantyne et al. [3] which did not involve the last three non-variant (TTCT) repeat motifs since they are only two bases from the former repeats and should be considered as a part of the repeat region (Fig. S2). The reference structure, sequencing results and proposed nomenclature for the DYF403S1 are shown in Table 2. In a series of our samples, we found four different intermediate alleles in the DYF403S1a due to an incomplete repeat within the variant repeat block, and all of them are in the positions with the structure (TTCT)nATC(TTCT)p. In these variant alleles, the tetramer TTCT repeat block before the interrupting nucleotides “ATC” is interrupted by a CT or TTT motif, and the repeat block after the “ATC” is interrupted by a TT motif. According to their sequence structure these alleles were designated as 30.2, 30.3, 31.2 and 33.2. As listed in Table 2, we also found two sequence subtypes (A and B) of alleles 26, 27, 28, 29, 30 and 32, differing in the number of the TTCT motif both before and after the interrupting nucleotides “ATC”. In addition, all of the four alleles detected from the control DNA 007 were also sequenced and their repeat structures are (TTCT)17TT(TTCT)3,
(TTCT)11ATC(TTCT)15,
(TTCT)12CT(TTCT)8(TTCC)12(TTCT)15TT(TTCT)3
(TTCT)13ATC(TTCT)15 respectively,
and
and the
corresponding fragment lengths are 215 bp, 210 bp, 218 bp and 327 bp respectively. Thus, its genotype is 20-26-28-50 in our way, which is distinctly different from that of Ballantyne et al. [3]. For the DYF403S1b alleles of the DNA 007, even if not to take the last three non-variant repeats (TTCT)3 into consideration, the allele designation would be 47 according to our sequencing results rather than 51 reported by Ballantyne et al. [3]. It is worth noting that different types of repeat structures existing in the DYF403S1a result in the complexity in allele nomenclature. For the same STR marker, it is generally acknowledged that with the fragment length increases, the repeat number of repetitive motifs increases at the same time. As shown in Table 2 and Fig. S2, however, the sum of the 5′ and 3′ flanking region of the repeat structure (TTCT)nTT(TTCT)3
is
significantly
longer
than
that
of
the
structure
(TTCT)nATC(TTCT)p, which result in a mismatch of the fragment length and the repeat number, namely the larger amplification fragments may have smaller repeat number. For example, the total number of repeats of 202 bp allele with the structure (TTCT)nATC(TTCT)p is 24, whereas the total number of repeats of 223 bp allele with the structure (TTCT)nTT(TTCT)3 is only 22 (Table 2). In addition, as shown in Table 2, there only is 1 bp difference in length among many alleles came from different copies of DYF403S1a, and this will result in the difficulty in fragment separation and the construction of allelic ladder. The use of POP-6/POP-7 or next-generation sequencing (NGS) techniques would appear to provide a solution to the DYF403S1 problem in the future. If samples already genotyped with the Ballantyne et al. method [3] need to be converted to the new proposed nomenclature, both the length as well as the sequencing results should be taken into consideration. Direct conversion might not work because of the complexity of the structure. Removing the number "o" from the DYF403S1a repeat (TTCT)nNo(TTCT)p (n+o+p) is technically feasible, but the allele call in DNA 007 as reported by Ballantyne et al. (alleles 11-13-18) [3] still does not correspond with our allele designation (alleles 20-26-28). For DYF403S1b adding the 3 repeats to the Ballantyne nomenclature will make both nomenclatures concordant.
However, even after adding the 3 repeats the allele call in DNA 007 as reported by Ballantyne et al. (allele 51) [3] still does not correspond with our allele sequence and designation (allele 50). Although the same nomenclature was used, there still are some inconsistencies at the DYS526b, DYS547 and DYS626 between our results and the reports of Ballantyne et al. [3]. For the DYS547, our sequencing results showed there are 54 nucleotides between (CCTT)nT(CTTC)o and (TTTC)pN10(CCTT)4(TCTC)1(TTTC)q rather than 56 nucleotides, which is in accordance with the sequences listed in GenBank entry NC_000024.10. For the DYS526b and DYS626, the inconsistencies of the allele designation in the control DNA 007 compared with that of Ballantyne et al. [3] had already been reported in our previous study [11]. 3.2. Haplotype and gene diversity The allele or haplotype (for multi-copy locus) frequencies and gene diversity values for all 13 RM Y-STRs in a Chinese Han population were shown in Table S1. A total of 197 alleles for all these loci were found, and 7 (DYF404S1) to 44 (DYF403S1) alleles for each locus were observed. The gene diversity (GD) ranged from 0.7862 (DYS576) to 0.9953 (DYF403S1). For the whole set of 13 RM Y-STRs, a total of 250 haplotypes were observed in 252 male individuals in which only 2 haplotypes were shared by 2 males respectively (Table 3). The haplotype diversity was estimated to be 0.999937 and the discrimination capacity was 99.21%, showing a great discrimination power in Chinese Han population. It is worth noting that distinctive multi-allelic patterns with extra alleles were observed in some samples for multi-copy loci DYF387S1 (n=5), DYF399S1 (n=15), DYF403S1 (n=1) and DYF404S1 (n=4) (Table 3), which is consistent with the reports of Brito et al. [12] and Oh et al. [13]. For the locus DYF387S1, five individuals were observed to have three different alleles while the other samples usually showed double-allele patterns. Four to six different alleles were observed in fifteen individuals at DYF399S1, which usually exists as three copies. A total of 25 extra-allelic patterns were observed in 20 individuals, four of them have extra alleles in more than one
locus. All samples with extra alleles were tested repeatedly to exclude the possibility of sample pollution. Extra stripes have been confirmed to be alleles of the locus by sequencing. In addition, we also collected blood samples of sons of these individuals with extra-allelic patterns, all showed the same genotype with their fathers (Fig. 1). 4. Conclusion Rapidly mutating Y-STRs have been proven to have strong ability in differentiating male individuals in many regions all of the world, our study also support its applicability in Chinese Han population. Discrepancy on the nomenclature of a few loci has been observed in our study, and further verification by different labs is expected. In our future study, it will be conducted to validate its ability in differentiating patrilineal relatives in Chinese Han population.
References [1] M.A. Jobling, C. Tyler-Smith, Fathers and sons: the Y chromosome and human evolution, Trends Genet. 11 (1995) 449–456. [2] M. Kayser, A. Caglià, D. Corach, N. Fretwell, C. Gehrig, G. Graziosi, et al., Evaluation of Y-chromosomal STRs: a multicenter study, Int. J. Legal Med. 110 (1997) 125–133. [3] M. Prinz, K. Boll, H. Baum, B. Shaler, Multiplexing of Y chromosome specific STRs and performance for mixed samples, Forensic Sci. Int. 85 (1997) 209–218. [4] M. Prinz, A. Ishii, A. Coleman, H.J. Baum, R.C. Shaler, Validation and casework application of a Y chromosome specific STR multiplex, Forensic Sci. Int. 120 (2001) 177–188. [5] W. Parson, H. Niederstätter, A. Brandstätter, B. Berger, Improved 217 specificity of Y-STR typing in DNA mixture samples, Int. J. Legal Med. 117 (2003) 109–114. [6] Roewer L, Y chromosome STR typing in crime casework, Forensic Sci. Med. Pathol. 5 (2009) 77–84. [7] B. Rolf, W. Keil, B. Brinkmann, L. Roewer, R. Fimmers, Paternity testing using Y-STR haplotypes: assigning a probability for paternity in cases of mutations, Int. J. Legal Med. 115 (2001) 12–15. [8] I. Ayadi, N. Mahfoudh-Lahiani, H. Makni, L. Ammar-Keskes, A. Rebaï, Combining autosomal and Y-chromosomal short tandem repeat data in paternity testing with male child: methods and application, J. Forensic Sci. 52 (2007) 1068–1072. [9] Z.H. Deng, Q. Li, S. Wu, D.C. Li, B.C. Yang, Application of 17 Y-chromosome specific STR loci in paternity testing, Zhongguo Shi Yan Xue Ye Xue Za Zhi 16 (2008) 699–703. [10] M. Hedman, V. Pimenoff, M. Lukka, P. Sistonen, A. Sajantila, Analysis of 16 Y STR loci in
the Finnish population reveals a local reduction in the diversity of
male lineages, Forensic Sci.
Int. 142 (2004) 37–43.
[11] M. Woz’niak, M. Derenko, B.A. Malyarchuk, I. Dambueva, T. Grzybowski, D. Mis’cicka-S’liwka, Allelic and haplotypic frequencies at 11 Y-STR loci in Buryats from South-East Siberia, Forensic Sci. Int. 164 (2006) 271–275. [12] M. Hedman, A.M. Neuvonen, A. Sajantila, J.U. Palo, Dissecting the Finnish male uniformity: the value of additional Y-STR loci, Forensic Sci. Int. Genet. 5 (2011) 199–201. [1] K.N. Ballantyne, M. Goedbloed, R. Fang, O. Schaap, O. Lao, A. Wollstein, et al., Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic Am. J. Hum. Genet. 87 (2010) 341–353. [2] K.N. Ballantyne, V. Keerl, A. Wollstein, Y. Choi, S.B. Zuniga, A. Ralf, et al., A new future of forensic Y-chromosome analysis: rapidly mutating Y-STRs for differentiating male relatives and paternal lineages, Forensic Sci. Int. Genet. 6 (2012) 208–218. [3] K.N. Ballantyne, A. Ralf, R. Aboukhalid, N.M. Achakzai, M.J. Anjos, Q. Ayub, et al., Toward male individualization with rapidly mutating Y-chromosomal short tandem repeats, Hum. Mutat. 35 (2014) 1021–1032. [4] C. Robino, A. Ralf, S. Pasino, M.R. De Marchi, K.N. Ballantyne, A. Barbaro, et al., Development of an Italian RM Y-STR haplotype database: Results of the 2013 GEFI collaborative exercise, Forensic Sci. Int. Genet. 15 (2015) 56–63. [5] U. Rogalla, M. Woźniak, J. Swobodziński, M. Derenko, B.A. Malyarchuk, I. Dambueva, et al., A novel multiplex assay amplifying 13 Y-STRs characterized by rapid and moderate mutation rate, Forensic Sci. Int. Genet. 15 (2015) 49–55. [6] P.S. Walsh, D.A. Metzger, R. Higuchi, Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material, Biotechniques 10 (1991) 506–513. [7] P. Gill, C. Brenner, B. Brinkmann, B. Budowle, A. Carracedo, M.A. Jobling, et al., DNA Commission of the International Society of Forensic Genetics: recommendations on forensic analysis using Y-chromosome STRs, Forensic Sci. Int. 124 (2001) 5–10. [8] L. Gusmão, J.M. Butler, A. Carracedo, P. Gill, M. Kayser, W.R. Mayr, et al.,
DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis, Forensic Sci. Int. 157 (2006) 187–197. [9] M. Nei, Molecular Evolutionary Genetics, Columbia University Press, New York, 1987, pp. 176–181. [10] M.D. Coble, C.R. Hill, J.M. Butler, Haplotype data for 23 Y-chromosome markers in four U.S. population groups, Forensic Sci. Int. Genet. 7 (2013) e66–e68. [11] W.Q. Zhang, C. Xiao, J. Yu, T. Wei, C. Pan, D.X. Huang, Allele repeat structure and designation update for the Y-STR loci DYF399S1, DYS526b and DYS626, Forensic Sci. Int. Genet. 20 (2016) 147–148. [12] P. Brito, M. Carvalho, V. Bogas, A.M. Bento, A. Serra, et al., Study of rapidly mutating Y-STRs in a Portuguese population, Forensic Sci. Int. Genet. 4 (2013) e83–e84. [13] Y.N. Oh, H.Y. Lee, E.Y. Lee, E.H. Kim, W.I. Yang, K.J. Shin, Haplotype and mutation analysis for newly suggested Y-STRs in Korean father-son pairs, Forensic Sci. Int. Genet. 15 (2015) 64–68.
Fig. 1. Distinctive multi-allelic patterns for DYF387S1 (a), DYF399S1 (b) and DYF404S1 (c) observed in two father–son pairs.
Table 1: The repeat structures, allelic designations, and control DNA 007 and 2800M genotypes of 13 RM Y-STRs. RM Y-STR
Repeat structure
Allele
Control DNA 007
Control DNA 2800M
Allele
designation
genotype
genotype
observed
DYF387S1
(AAAG)3(GTAG)1(GAAG)4(AAAG)2(GAAG)1(AAAG)2(GAAG)n(AAAG)o
13+n+o
35, 37
37, 38
33–42
DYF399S1
(GAAA)3N7-8(GAAA)n
5+n or 4.3+n
23.3, 26
23.3, 25, 26
16.3–30
DYF403S1a
(TTCT)nN2-3(TTCT)p
n+p
20, 26, 28
19, 26, 29
13–37
DYF403S1b
(TTCT)nN2(TTCT)o(TTCC)p(TTCT)qN2(TTCT)3
n+o+p+q+3
50
45
42–57
DYF404S1
(TTTC)n
n
14, 16
13,16
11–17
DYS449
(TTTC)nN50(TTTC)o
n+o
30
34
24–37
DYS518
(AAAG)3(GAAG)1(AAAG)n(GGAG)1(AAAG)4N6(AAAG)o
9+n+o
37
36
32–43
DYS526b
(CTTT)n(CCTT)oN113(CCTT)p
n+o+p
35
35
32–42
DYS547
(CCTT)nT(CTTC)oN54(TTTC)pN10(CCTT)4(TCTC)1(TTTC)q
n+o+p+5+q
49
45
42–55
DYS570
(TTTC)n
n
17
17
13–23
DYS576
(AAAG)n
n
19
18
15–22
DYS612
(CCT)5(CTT)1(TCT)4(CCT)1(TCT)n
11+n
37
35
29–41
DYS626
(GAAA)nN24(GAAA)3N6(GAAA)5(AAA)1(GAAA)o(GAAG)1(GAAA)3
n+10+o
29
28
25–34
DYS627
(AGAG)3(AAAG)n
3+n
21
22
17–25
Segments in bold are not counted in the allele designation.
range
Table 2: The reference structure and proposed nomenclature for the multi-copy locus DYF403S1 according to the sequencing results. Consensus structure
PrimerA.ctttcttccctccttcccttctccctgtctgtctttctttcgttctctttctttttcttt(ttct)ntt(ttct)3ttcctctaactctgtatctctgtttaatatttt.PrimerB
(a position of DYF403S1a) Allele
Sequence
13 (187 bp)
PrA(20bp) 60bp(ttct)102bp(ttct)333bp PrB(20bp)
14 (191 bp)
PrA(20bp) 60bp(ttct)112bp(ttct)333bp PrB(20bp)
15 (195 bp)
PrA(20bp) 60bp(ttct)122bp(ttct)333bp PrB(20bp)
16 (199 bp)
PrA(20bp) 60bp(ttct)132bp(ttct)333bp PrB(20bp)
17 (203 bp)
PrA(20bp) 60bp(ttct)142bp(ttct)333bp PrB(20bp)
18 (207 bp)
PrA(20bp) 60bp(ttct)152bp(ttct)333bp PrB(20bp)
19 (211 bp)
PrA(20bp) 60bp(ttct)162bp(ttct)333bp PrB(20bp)
20 (215 bp)
PrA(20bp) 60bp(ttct)172bp(ttct)333bp PrB(20bp)
21 (219 bp)
PrA(20bp) 60bp(ttct)182bp(ttct)333bp PrB(20bp)
22 (223 bp)
PrA(20bp) 60bp(ttct)192bp(ttct)333bp PrB(20bp)
Consensus structure
PrimerA.ctttccttctttccttctttctttcc(ttct)natc(ttct)ptcctttcctctatctctgtatctctgtttaatatttt.PrimerB
(other two positions of DYF403S1a) Allele
Sequence
24 (202 bp)
PrA(20bp) 26bp(ttct)113bp(ttct)1337bp PrB(20bp)
25 (206 bp)
PrA(20bp) 26bp(ttct)123bp(ttct)1337bp PrB(20bp)
26A (210 bp)
PrA(20bp) 26bp(ttct)133bp(ttct)1337bp PrB(20bp)
26B (210 bp)
PrA(20bp) 26bp(ttct)113bp(ttct)1537bp PrB(20bp)
27A (214 bp)
PrA(20bp) 26bp(ttct)143bp(ttct)1337bp PrB(20bp)
27B (214 bp)
PrA(20bp) 26bp(ttct)123bp(ttct)1537bp PrB(20bp)
28A (218 bp)
PrA(20bp) 26bp(ttct)153bp(ttct)1337bp PrB(20bp)
28B (218 bp)
PrA(20bp) 26bp(ttct)133bp(ttct)1537bp PrB(20bp)
29A (222 bp)
PrA(20bp) 26bp(ttct)133bp(ttct)1637bp PrB(20bp)
29B (222 bp)
PrA(20bp) 26bp(ttct)153bp(ttct)1437bp PrB(20bp)
30A (226 bp)
PrA(20bp) 26bp(ttct)163bp(ttct)1437bp PrB(20bp)
30B (226 bp)
PrA(20bp) 26bp(ttct)133bp(ttct)1737bp PrB(20bp)
30.2 (228 bp)
PrA(20bp) 26bp(ttct)3ct(ttct)93bp(ttct)1837bp PrB(20bp)
30.3 (229 bp)
PrA(20bp) 26bp(ttct)2ttt(ttct)123bp(ttct)1637bp PrB(20bp)
31 (230 bp)
PrA(20bp) 26bp(ttct)133bp(ttct)1837bp PrB(20bp)
31.2 (232 bp)
PrA(20bp) 26bp(ttct)3ct(ttct)113bp(ttct)1737bp PrB(20bp)
32A (234 bp)
PrA(20bp) 26bp(ttct)153bp(ttct)1737bp PrB(20bp)
32B (234 bp)
PrA(20bp) 26bp(ttct)133bp(ttct)1937bp PrB(20bp)
33 (238 bp)
PrA(20bp) 26bp(ttct)163bp(ttct)1737bp PrB(20bp)
33.2 (240 bp)
PrA(20bp) 26bp(ttct)113bp(ttct)20tt(ttct)237bp PrB(20bp)
34 (242 bp)
PrA(20bp) 26bp(ttct)143bp(ttct)2037bp PrB(20bp)
35 (246 bp)
PrA(20bp) 26bp(ttct)163bp(ttct)1937bp PrB(20bp)
36 (250 bp)
PrA(20bp) 26bp(ttct)173bp(ttct)1937bp PrB(20bp)
37 (254 bp)
PrA(20bp) 26bp(ttct)193bp(ttct)1837bp PrB(20bp)
Consensus structure
PrimerA.ctttcttccctccttcccttctccctgtctttctttcgttctctttcttt(ttct)nct(ttct)o(ttcc)p(ttct)qtt(ttct)3ttcctctaactctgtatctctgtttaatatttt.PrimerB
(DYF403S1b) Allele
Sequence
43 (299 bp)
PrA(20bp) 50bp(ttct)112bp(ttct)7(ttcc)11(ttct)112bp(ttct)333bp PrB(20bp)
45 (307 bp)
PrA(20bp) 50bp(ttct)102bp(ttct)10(ttcc)10(ttct)122bp(ttct)333bp PrB(20bp)
50 (327 bp)
PrA(20bp) 50bp(ttct)122bp(ttct)8(ttcc)12(ttct)152bp(ttct)333bp PrB(20bp)
55 (347 bp)
PrA(20bp) 50bp(ttct)142bp(ttct)12(ttcc)13(ttct)132bp(ttct)333bp PrB(20bp)
Table 3: Haplotypes of 13 RM Y-STRs from 252 samples in Chinese Han population. Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
1
37,39
21.3,24
15,27,29
53
13,14
32
39
35
51
18
19
37
30
24
2
36,40
19.3,25.3,27
20,30,31
54
13,14
36
38
37
50
16
18
32
29
21
3
35,38
19.3,25
17,25,27
50
12,14
31
40
36
50
19
20
38
29
21
4
36,38
20.3,23.3,25
16,29,30
52
13,14
32
36
36
48
18
17
39
27
19
5
35,38
19.3,22.3,24
18,29
52
12,13
35
36
36
49
19
19
38
28
18
6
35,38
20.3,24
16,28,29
52
13,14
32
35
37
51
18
15
38
27
18
7
36,37
20.3,22,22.3
16,25,28
50
14,15
31
40
36
51
19
21
38
28
20
8
36,38
19.3,22,22.3
16,29,30
51
14,16
30
42
34
48
17
18
35
29
20
9
37,38
20.3,21.3,22
14,33,35
46
15,16
32
38
34
44
13
18
33
29
17
10
36,38
20.3,21
15,28
53
14,17
35
39
36
49
19
17
38
30
20
11
37
29
17,27,28
49
13
28
36
36
46
18
19
35
31
25
12
37,42
21.3,22.3,23
17,27,30
50
14,15
30
36
36
48
20
18
38
28
21
13
35
23.3,24,25
16,27,29
49
13
25
42
35
49
20
17
41
27
20
14
35,41
18.3,24.3,26
18,30
54
14,16
34
36
37
49
16
18
34
28
23
15
36,40
19.3,23.3,25.3
16,28
50
14,16
32
34
34
49
18
20
35
30
22
16
34
24,24.3
14,31,34
48
14
28
38
33
47
16
20
36
34
22
17
38,39
19.3,21.3
16,28
51
14,15
33
40
36
46
18
18
36
29
20
18
36,37
21.3,23.3,27
13,27
52
13,15
31
37
36
46
20
18
36
28
22
19
36
17.3,22.3,24
15,27,30
49
13,16
26
41
34
47
18
19
36
28
21
20
38,39
19.3,21,22.3
15,30
56
14,15
32
39
38
51
17
16
37
29
20
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
21
38,39
21.3,22.3,23
16,29
54
14,15
30
34
36
48
15
19
36
32
20
22
37,39
20.3,22,22.3
15,28,29
49
14,15
31
39
37
52
18
20
39
27
21
23
35,38
18.3,21.3,22.3,24,25,26
17,28,31
52
13,14
33
34
37
50
20
19
38
27
19
24
37,38
20.3,22.3,26
19,28
52
13
32
34
36
49
17
19
37
28
18
25
35
24
14,27,28
50
13
30
37
36
44
19
19
30
29
21
26
36,38
20.3,24.3,26
17,29
53
13,15
30
33
38
48
18
20
39
26
17
27
36
22
14,24,30
46
15
28
38
34
47
21
18
34
29
25
28
38,40
19.3,25.3,28
18,28,30
53
12,17
33
38
37
49
17
19
37
30
22
29
37,39
21.3,24.3,26
20,28
53
12,14
31
38
38
48
16
20
37
29
21
30
35,37
19.3,21.3,22
15,26
53
14
32
39
37
51
18
20
37
30
20
31
37,38
23,24.3,27
18,27,29
50
15
29
37
36
51
17
18
36
29
23
32
35,38
21.3,22,22.3
16,29
52
13
32
35
37
47
18
19
33
27
18
33
36
24
16,27,28
51
14
29
38
34
43
20
18
36
30
22
34
35,36
20.3,21.3,23
14,30,35
45
15,17
29
39
35
46
16
18
33
31
23
35
39
19.3,20.3,28.1
15,26,33
49
12,17
30
39
33
51
18
18
39
29
21
36
37
23,23.3
14,27,29
52
13
31
39
38
51
18
17
33
29
21
37
38
21.3,23.3
14,32,33
45
17
30
38
33
44
16
20
36
31
22
38
36,40
18.3,23.3,27
18,28,30
55
12,15
34
39
36
50
20
18
38
28
24
39
35,37
21.3,25
16,27,29
54
13,14,15
31
38
38
50
18
18
35
27
20
40
35,40
21.3,24.3,25
19,28,29
56
13
35
35
36
47
17
19
38
28
22
41
35,36
20.3,22,22.3
16,25,26
55
13,15
33
39
36
49
17
20
35
31
20
42
35,37
21.3,24,24.3
17,30
52
14
32
32
35
48
16
19
36
26
18
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
43
37,40
22.3,25,25.3
16,27
49
12,15
27
41
36
49
17
19
35
29
20
44
35,40
19.3,20.3,24
18,26
50
13,16
32
37
37
49
20
16
38
30
20
45
38,40
20.3,22.3,23
18,27,32
48
13,14
29
37
36
47
19
18
39
29
22
46
35
19.3,21.3,23
18,24,33
46
14,15
30
39
34
49
16
18
40
27
19
47
40
20.3,25
20,27,31
50
14,16
31
39
35
47
20
18
38
28
22
48
35,38
20.3,23.3,25
18,30,31
53
14,15
33
36
35
50
17
19
37
31
20
49
34,37
20.3,21,21.3,24
14,31,33
45
12,16
30
39
34
44
17
19
37
30
22
50
35
24
14,27,30.3
49
14
29
38
35
44
19
18
29
29
20
51
38
20.3,21
15,28,29
55
15
36
39
35
53
21
16
38
29
22
52
35,38
19.3,23.3,25
17,28,31
52
12,14
35
36
36
48
19
20
38
27
18
53
34,37
24,27
15,25,28
51
15,16
29
39
34
45
19
15
32
27
17
54
35,39
20.3,23.3,28
16,28,30
54
13,14
33
37
38
49
17
18
37
26
20
55
36,39
20.3,23.3,27
19,29
57
13,15
35
37
37
48
18
19
35
29
19
56
36,37
20.3,22.3,23
15,25,27
56
14,15
32
39
36
52
17
21
39
30
19
57a
36,40
20.3,21.3,25
20,27,29
50
14
31
37
37
50
17
16
40
27
22
58
36,38
20.3,24,25.3
17,28
51
13,14
35
41
34
45
18
16
36
33
22
59
35,38
21.3,22.3,27
16,28,31
55
13,14
32
38
36
49
17
19
37
28
17
60
35
24
16,27,29
48
14
29
35
35
42
20
17
31
29
20
61
36
19.3,24,26.3
15,28
49
13,14
26
43
35
49
19
19
37
27
20
62
36,39
22.3,23.3,24
15,27,37
48
14,15
30
38
35
47
19
16
39
29
21
63
36,37
18.3,24,25.3
15,26,29
53
14,17
27
38
36
48
18
20
38
27
22
64
36,38
20.3,23.3,24
17,26,30
49
12,15
33
40
37
47
20
17
36
33
17
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
65
34,35,38
19.3,20.3,22,24
14,30.2,31
45
15,17
31
41
34
46
16
16
36
28
19
66
35
21.3,24.3,25
17,28,30
53
13,14
35
33
38
51
18
19
37
27
18
67
34,38
20.3,23,24.3
17,28,30
53
13
35
37
36
50
20
18
38
28
18
68
36,38
21.3,22.3,25
18,28,32
51
14,15
31
37
36
48
18
19
39
28
21
69
36,37
20.3,22.3,27
15,25,29
54
15
32
38
36
48
18
19
35
30
19
70
36,39
19.3,22.3,24.3
20,28,29
43
14,15
25
40
37
52
19
18
36
30
19
71
37,39
19.3,22,22.3
16,25,26
52
14,15
33
38
38
51
17
21
35
29
22
72
35,40
20.3,23,24.3
18,28,31
55
14,16
33
36
37
50
19
17
36
32
20
73
37,39
21.3,22.3,23
20,25,27
49
14,15
32
40
38
49
19
18
37
30
18
74
35,38
22.3,25.3,26
16,28,30
53
13,14
32
38
38
49
17
18
37
26
20
75
36
20.3,21.3,25
14,32,33
45
14,16
28
40
35
47
16
18
36
32
23
76
38,39
21.3,22,23.3,24
19,30,31
54
15
30
36.2
35
48
20
18
36
30
21
77
36,37
19.3,20,20.3,21.3,23
15,32,33
47
12,13
30
37
35
48
16
16
34
30
22
78
39,41
20.3,23.3,24
20,25,30
53
13,15
32
38
38
48
14
17
39
27
21
79
40
20.3,28
20,27,32
48
14,15
32
41
36
47
20
18
39
28
24
80
37
20.3,22.3,24
16,26,27
53
15,16
26
39
41
46
20
18
37
27
24
81
36,38
20.3,26
21,30
54
11,13
32
37
36
48
17
19
33
29
21
82
36,38
21.3,23,24.3
15,30,34
47
14,16
30
37
33
48
17
17
32
31
23
83
37,39
18.3,26,28
21,32
53
13,15
34
39
37
51
16
20
37
29
22
84
37,39
17.3,23.3,28
19,30,32
54
14
32
39
37
50
16
19
36
28
22
85
38,41
20.3,21.3,24,24.3
22,28,33
51
14,15
33
37
34
45
16
18
38
29
23
86
35
20.3,22
15,25,26
54
15
32
40
35
50
17
18
36
30
22
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
87
36,37
20.3,21.3,23
15,33.2,35
45
15
29
42
34
46
15
17
35
31
22
88
39,40
18.3,22.3,23
13,26
53
12,14
34
36
35
49
17
20
36
30
22
89
38,40
21.3,23.3,24
19,27,34
50
14,16
31
38
32
48
18
17
39
29
23
90
37
20.3,21,22.3
14,28,32
49
13,14
30
36
36
48
17
17
31
31
20
91
36
25
13,26,32
49
13,14
29
34
35
44
17
19
33
30
23
92
36,38
22.3,23.3,25
15,29
53
13,14
33
35
37
49
17
22
37
28
19
93
35,38
20.3,24.3,25
16,27,30,32
53
13,14
33
36
35
46
19
19
39
27
18
94
37,41
18.3,22,22.3
15,28
50
14,15
35
38
36
48
19
19
39
30
20
95
37,38
19.3,24.3,25,27
19,26,29
51
14,15
31
32
35
48
20
17
38
31
20
96
37
19.3,24.3,25
19,28,31
53
12,13
30
37
36
52
18
17
34
30
21
97
37,38
23.3,24,27
17,27,31
50
14,15
29
36
36
50
17
16
36
29
22
98
35,37
20.3,21.3,22
15,26,27
55
14,16
31
39
36
49
18
20
36
30
21
99
38,41
22.3,23,23.3
17,27,28
51
14,15
30
37
36
45
17
18
39
27
17
100
36,39
20.3,21.3,28
15,26
51
13,15
30
38
35
48
16
19
36
27
19
101
35,37
20.3,23,23.3
14,32,33
45
14,17
29
38
37
50
17
20
36
32
23
102
37,38
21.3,22.3,25
16,28,33
47
14
29
37
34
49
21
17
38
29
21
103
35,38
20.3,21.3,23,23.3
17,24,28
52
13
30
37
36
52
19
18
35
27
21
104
35,40
20.3,23,23.3
15,25,28
47
15,16
29
40
34
46
18
19
37
29
21
105
38,39
17.3,23.3,30
18,30,31
53
14,15
33
39
37
51
17
19
36
29
21
106
36,37,38
21.3,23,24
17,28
55
12,14,16
27
34
36
49
16
19
38
31
20
107
36,39
17.3,21.3,26
14,29,32
45
14,16
29
40
36
45
18
19
32
30
23
108
37,40
20.3,22.3,24
20,27,34
50
14,16
31
38
35
46
17
17
39
29
22
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
109
36,39
17.3,24.3,25
18,30
54
13,14
36
37
42
48
17
20
35
31
19
110
36,38
20.3,21.3,22.3,23,24
16,25,26
52
13,14
30
38
38
49
18
18
37
28
21
111
37,39
20.3,21.3,22.3
16,27,28
52
12,13,16
29
36
36
48
17
20
36
32
20
112
36,39
18.3,22.3,24.3
19,29,30
43
15,16
24
37
36
50
18
18
35
31
18
113
34
22
14,25,28
49
14
31
39
37
44
20
17
29
29
20
114
37
26
17,26,27
50
15
27
38
33
42
17
18
37
30
20
115
37,40
22.3,24.3,25
20,28,31
57
13,14
36
35
37
47
17
17
36
30
23
116
34,40
16.3,21.3,27
19,29
54
13,14
32
36
35
49
16
21
36
30
23
117
35,39
22.3,23,24.3
16,27,28
51
13
32
35
37
48
18
17
36
28
18
118
35,38,40
19.3,21.3,26,27
16,29,30
53
12,13,14
31
34
37
48
19
18
37
27
19
119
38,40
20.3,26.3,27,27.3
16,27,31
50
14,15
30
32
36
49
19
17
35
30
21
120
36,39
21.3,22.3,25
15,25,29
50
15,16
31
39
38
46
18
19
33
30
21
121a
36,40
20.3,21.3,25
20,27,29
50
14
31
37
37
50
17
16
40
27
22
122
35,38
22.3,24.3,25
20,27,29
54
14
34
37
36
45
15
19
40
30
19
123
36
18.3,23.3,26
15,27,30
49
15
26
41
36
49
19
18
38
27
20
124
36,39
21.3,22.3,26
17,28,30
50
13
32
35
35
47
17
19
38
28
17
125
35,38
18.3,23.3,26
17,28
54
13
33
36
36
48
18
17
37
25
22
126
36,38
21.3,22.3,26
15,30,31
47
14,16
29
39
37
48
16
16
33
31
23
127
37,39
21.3,23.3,26
19,27,30
51
14,15
32
32
36
48
18
16
38
30
22
128
37,39
18,19.3,24.3
16,26,28
51
12,16
25
42
38
49
16
17
37
28
19
129
38,40
21.3,26
18,27,33
48
14,15
32
38
34
48
21
18
37
28
22
130
37,39
20.3,24,25.3
17,29,36
56
13,15
32
36
37
50
15
18
39
28
22
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
131
36,37,39
19.3,20.3,22.3,26
15,25,28
52
14,15
31
37
36
46
18
16
38
29
22
132
37
21.3,24
14,32,36
45
14
30
40
35
46
19
19
36
29
22
133
36,38
20.3,21.3,24
16,26
54
14,15
27
42
38
48
21
16
35
26
21
134
37
21.3,24
15,32,33
46
16
31
37
33
45
16
18
32
28
23
135
38
23.3,24
19,31
53
14
30
39.2
36
47
19
17
37
29
22
136
38,40
20.3,23.3,25
21,27,33
50
14,15
33
38
34
48
17
19
40
29
23
137
35,39
22.3,23
19,27,28
51
13,14
30
35
35
52
19
16
38
26
21
138
37,40
21.3,22.3,27
19,28,33
51
13,15
31
38
36
47
17
18
39
27
23
139
38,40
20.3,22.3,27
20,27,34
50
14,15
29
37
35
46
18
18
39
29
21
140
37,41
22.3,24,26.3
16,27,31
51
12,14
26
39
36
48
17
20
35
30
21
141
36,40
21,21.3,23.3
15,30
52
13,15
33
39
37
49
20
18
36
30
21
142
37,39
21.3,23
17,27,29
48
13,14
33
41
35
46
17
19
33
32
20.2
143
36
21.3,22
14,30,34
47
15,16
29
37
36
46
16
16
36
30
24
144
38,39
20.3,23,23.3
19,27,36
48
14,15
31
37
34
46
20
19
36
30
21
145
36,39
18.3,24.3,27
19,30,32
54
13,14
34
40
38
48
16
20
37
29
21
146
36,41
19.3,23.3,27
19,31,32
54
13,14
33
39
37
51
16
20
36
28
21
147
36,41
19.3,21.3,26
17,28,32
49
15,16
32
34
34
49
20
19
37
32
22
148
35,37
20.3,21.3,22
15,25,28
53
14,15
31
39
36
50
17
19
36
28
20
149
36,37
19.3,21.3,26
13,27
52
13,16
31
36
36
45
18
18
37
26
22
150
39
23.3,24
20,30,31
55
15
31
36.2
36
47
19
19
36
31
23
151
33,38
22,22.3,23.3
15,26,27
53
14,15
33
42
40
46
19
18
39
29
22
152
38
23,24.3
17,31
54
15
30
37.2
38
46
20
19
33
30
20
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
153
36,37
19.3,23,25.3
15,26,27
53
13,17
27
38
37
49
18
18
37
27
22
154
38,39
19.3,20.3,23
15,27,28
52
13,15
37
40
36
49
21
18
37
33
21
155
37,40
20.3,22.3
15,27,28
51
13,15
27
40
35
48
16
19
35
31
21
156
35,39
19.3,23,25.3
21,29,32
56
12,13
28
37
37
50
15
19
36
29
21
157
37
20.3,22.3,24
13,27,29
52
14,17
32
37
36
45
20
20
36
29
22
158
36,38
19.3,23
16,28,29
53
13,14
28
35
38
48
16
19
38
28
21
159
36,39
18.3,21.3,24
14,30,32
44
14,16
28
38
34
49
17
18
34
32
21
160
37,41
21.3
15,27,31
50
13,14
33
39
35
47
19
18
37
28
22
161
36,38
19.3,22.3,28
17,27,29
53
14,15
32
36
37
48
17
19
38
29
19
162
35,36
20.3,23.3,26
16,26,30
50
13,14
27
42
35
49
18
20
40
28
20
163
38,40
20.3,22.3,26
20,27,34
50
14,15
34
38
33
48
18
17
39
29
24
164
36,39
19.3,21.3,25
18,28,31
56
13,15
36
36
38
51
16
19
34
29
22
165
38
19.3,22,24.3
15,25,26
53
14
32
38
40
49
17
20
36
29
21
166
38
20.3,23.3,27
15,25,30
51
14,15
31
39
38
46
20
17
30
27
19.1
167
36,40
20.3,21.3,22.3,23.3
16,27,29
49
13,16
33
37
33
47
15
18
37
29
23
168
35,40
20.3,21.3,24
19,26,27
49
13,15
33
36
37
49
18
18
40
28
21
169
36
20.3,21.3,27
20,27
49
13,14
30
37
35
49
20
16
36
26
22
170
36,37
20.3,23.3,26
15,26,28
51
14,15
31
41
35
51
19
20
38
31
20
171
35,39
22.3,23.3,25
16,27,31
53
13,15
30
37
38
49
18
19
36
27
19
172
36,38
19.3,21,23.3
15,25,26
51
14,16
31
39
38
50
17
19
36
29
21
173
39,40
18.3,24.3,27
18,27,31
50
13,15
28
35
35
49
18
18
37
30
23
174
37
21.3,22.3,24
16,31,33
45
14,15
28
36
35
48
17
17
33
29
23
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
175
36,39
19.3,25.3,26
20,27
54
13,14
37
35
37
48
16
18
36
31
23
176
36,37
18.3,22.3,25
19,28,29
56
12,13
32
37
37
52
17
17
36
29
20
177
36,38
20.3,21.3,27
16,31,34
45
14,15
29
34
33
47
16
18
37
30
23
178
36,39
20.3,22.3,25
15,26,27
52
13,14
30
37
36
48
17
18
38
27
21
179
38
21.3,25
19,30
53
16
30
35.2
34
47
20
20
34
29
23
180
37,38
21.3,24.3,26
20,30,31
56
13
36
38
39
49
18
19
35
29
22
181
36
21.3,22.3,26
15,25,29
50
14,15
33
39
34
50
22
20
38
30
20
182
38,39
21.3,23,23.3
17,27,33
49
15
29
39
34
50
19
16
36
29
21
183
36
20.3,26
14,31,34
43
16
28
40
35
45
15
19
36
31
22
184
37,39
19.3,20,29.1
16,24,31
51
13,17
30
41
37
53
19
20
37
31
22
185
37,42
20.3,22.3,24
18,27,34
48
15
30
38
36
46
19
17
36
29
21
186
36,37
20.3,22.3,24
16,28,32
52
13,14
35
34
36
48
18
18
38
28
18
187
34,40
20.3,22.3,23
15,26,31
52
13,14
30
39
35
49
17
18
34
32
20
188
35,38
19.3,25.3,26
17,29,31
51
13
35
37
37
51
19
17
39
29
18
189
36
20.3,21.3,24
14,32,33
45
15
27
39
36
46
15
17
29
31
22
190
36,37
21.3,26
15,25,28
51
15
32
37
36
48
17
18
37
29
19
191
36
21.3,22,22.3
14,31,33
45
15
29
39
36
46
16
18
35
32
23
192
34,37
20.3,22.3,26
18,28
54
15
34
37
36
55
18
19
35
29
23
193
36,38
20.3,23,25.3
16,28,29
52
13
31
35
36
48
19
19
37
26
18
194
38
23,24
22,26,37
43
11
33
37
33
44
16
16
37
29
23
195
36,39
20,22,24.3
19,25,29
42
14,15
29
43
38
46
19
17
39
33
21
196
37,38
22,23.3,26
15,27,33
50
13,15
28
38
34
49
20
19
37
29
22
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
197
35,38
21.3,22,24.3
14,25,34
51
13,14
32
36
34
48
17
19
37
27
18
198
38,40
19.3,26
19,26,33
49
14,15
31
40
37
49
18
18
37
28
24
199
36
25,28.3
15,27,28
49
14
25
42
34
49
17
19
38
28
21
200
37,39
18.3,22.3,27
15,26,27
51
14
32
36
35
49
18
17
38
29
21
201
37,38
18.3,22.3,24
18,28
50
14,15
28
39
34
50
19
15
36
29
18
202
35,40
18.3,22.3,29
19,29
53
14,16
36
38
39
50
18
21
39
31
23
203
34
21.3,27
15,27,30
52
14
30
41
38
50
20
19
36
32
23
204b
35,37
20.3,23.3,25
17,29,30
53
13,14
33
33
37
49
19
18
37
26
18
205b
35,37
20.3,23.3,25
17,29,30
53
13,14
33
33
37
49
19
18
37
26
18
206
36,40
20.3,24.3,25
18,30,31
53
13,14
33
36
37
49
16
18
35
29
20
207
36,37
21.3,22,22.3,23
16,24,28
51
13
30
37
37
52
20
17
36
27
22
208
36,40
20.3,24.3,26
18,29,30
55
13,15
34
36
36
52
17
19
36
27
20
209
34
22
14,26,30
49
15
30
38
37
44
20
19
31
30
21
210
36
24
15,28,29
52
14
28
37
34
46
18
16
34
32
22
211
35,41
20.3,21,22.3
15,29,31
50
13,16
33
43
39
52
20
19
37
32
21
212
35,37
18.3,22,22.3
15,25,26
53
14,15
31
39
36
49
17
19
38
30
20
213
37,38
23,23.3,27
17,27,29
50
15
28
38
36
50
17
18
36
29
23
214
37,39
20.3,22.3,23
16,26,29
50
13,17
27
41
39
49
16
21
36
28
21
215
37,39
20.3,23.3,24
19,24,29
49
14
32
40
35
45
20
19
35
31
17
216
35,38
20.3,22.3,25
17,30
54
13,15
33
37
36
48
19
18
38
27
18
217
36,37
21.3,22.3,24
15,33,34
45
13,14
30
38
34
46
16
16
31
30
21
218
36,38
19.3,24.3,25
20,29
55
13,14
32
35
34
54
20
19
36
31
18
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
219
37,39
21.3,22,24.3
19,26,27
50
14
31
36
34
54
20
16
35
29
21
220
37,38
21.3,22.3,23
14,31,33
46
17
30
38
34
44
17
18
33
30
17
221
35,38
20.3,22.3,26
21,30
54
13,15
35
39
37
48
17
17
36
27
23
222
34,36,37
21.3,22.3,23
14,30
47
14
28
37
33
46
17
19
35
33
20
223
41
22,23.3
18,30,32
55
13
33
41
37
47
16
18
40
29
19
224
38,39
20.3,23.3,28
19,28,29
54
14,15
33
36
37
50
16
18
34
29
22
225
35,37
20.3,21.3,22
15,24,26
54
14,16
31
39
38
50
17
18
38
31
20
226
33,39
20.3,24.3,26
19,26,31
54
13
34
35
36
53
17
17
37
26
21
227
35,39
19.3,24
17,29,30
51
13
35
36
36
50
21
18
38
28
18
228
38,40
21.3,22.3,26
21,27,34
50
14
33
39
36
47
18
19
39
30
22
229
36,39
19.3,22.3,25
15,26,29
51
14,16
32
37
35
47
18
17
39
29
22
230
37
21.3,23.3,25
13,27
52
13,15
31
37
36
45
20
18
37
28
22
231
36,38
20.3,22.3,23
14,31.2,32
44
13,15
31
40
36
46
16
16
33
29
20
232
37,40
19.3,24.3,25
15,26,29
47
12,16
27
42
37
51
16
17
36
29
22
233
36,37
20.3,24.3,25
13,27,29
51
13,16
32
37
36
46
18
18
37
28
22
234
34
23.3,27
15,25
52
15
31
38
39
48
18
20
36
30
19
235
37,38
18.3,24.3,25
18,29,31
49
13,15
27
39
35
48
19
15
37
29
18
236
37,38
21,23.3
14,27,29
53
13
33
39
36
49
16
19
38
30
21
237
36,37
22.3,25
16,28,29
54
13,14
34
35
36
45
19
19
39
28
18
238
36,38
19.3,22.3,26
15,26,27
53
14,15
31
39
37
46
15
20
35
29
21
239
38,40
20,21,22.3
17,27,32
42
13
31
35
34
51
20
17
36
28
22
240
35,37
20.3,21,23.3
15,29
54
15
35
41
36
52
18
17
33
30
21
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
241
36,38
20.3,24
22,27,34
50
14,16
32
38
36
47
18
19
39
28
22
242
36,39
19.3,23,24.3
19,31
53
14,15
33
37
37
48
16
20
36
29
22
243
37,38
19.3,22.3,24
18,28,33
46
14,15
28
42
36
49
19
17
39
28
23
244
37,38
22.3,23.3,24,25
20,27,28
53
15
30
37.2
36
47
23
18
34
29
23
245
36,37
19.3,20.3,24
18,25,26
52
14,16
29
41
36
48
18
17
39
30
20
246
36,38
20.3,21.3,25
14,26
51
13,16
30
38
38
50
17
19
35
29
22
247
38,40
21.3,22.3,25
19,27,33
50
13,15
31
39
34
48
18
19
39
29
21
248
35,37
20.3,23.3,25
17,28,31
52
14,15
33
32
38
49
17
16
38
26
17.2
249
36,38
17.3,22.3,24
17,30,31
54
15
31
36
37
51
19
18
37
28
21
250
36,38
22.3,23
16,25,29
50
14,16
29
42
39
50
19
18
36
32
21
251
35,39
21.3,23.3,24
18,31
52
14,16
32
36
37
50
17
16
36
30
20
252
35,38
19.3,22.3,25
16,29,30
51
13
32
37
36
50
18
19
39
28
18
a,b
Samples labeled with the same letter have the same haplotype.
S1872-4973(16)30069-2 http://dx.doi.org/doi:10.1016/j.fsigen.2016.04.013 FSIGEN 1510
To appear in:
Forensic Science International: Genetics
Received date: Revised date: Accepted date:
16-10-2015 27-4-2016 29-4-2016
Please cite this article as: Wenqiong Zhang, Chao Xiao, Tian Wei, Chao Pan, Shaohua Yi, Daixin Huang, Haplotype diversity of 13 RM Y-STRs in Chinese Han population and an update on the allele designation of DYF403S1, Forensic Science International: Genetics http://dx.doi.org/10.1016/j.fsigen.2016.04.013 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Forensic Population Genetics – Short Communications
Haplotype diversity of 13 RM Y-STRs in Chinese Han population and an update on the allele designation of DYF403S1
Wenqiong Zhang, Chao Xiao, Tian Wei, Chao Pan, Shaohua Yi, Daixin Huang*
Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, No. 13, Hangkong Road, Wuhan 430030, China
* Corresponding author. Tel.: ＋86-27-8369-2645; fax: ＋86-27-8363-1216. E-mail address: [email protected] (D. Huang).
Highlights:
Haplotype diversity of 13 RM Y-STRs in Chinese Han population was investigated.
The RM Y-STR set showed great discrimination power in Chinese Han population.
An update on the allele designation of DYF403S1 was proposed.
Distinctive multi-allelic patterns were observed at 4 multi-copy Y-STR markers.
Abstract Rapidly mutating Y-STRs (RM Y-STRs) have been paid much attention in recent years. The 13 RM Y-STRs have been proved to have substantially higher haplotype diversity and discrimination capacity than conventionally used Y-STRs, indicating the considerable power in paternal lineage differentiation. To investigate the haplotype diversity in Chinese Han population, we collected 252 unrelated male samples and tested the genotype of the 13 RM Y-STRs. Among 252 male individuals, a total of 250 haplotypes were observed in which only 2 haplotypes were shared by 2 males respectively. The haplotype diversity reached 0.999937 and the discrimination capacity was 99.21%, showing a great discrimination power in Chinese Han population. In addition, an update on the allele designation of DYF403S1 was proposed. Keywords: Y chromosome; Rapidly mutating Y-STR; Haplotype diversity; Lineage differentiation; Nomenclature
1. Introduction Due to their paternal inheritance characteristic, the analysis of Y-chromosomal genetic markers, especially Y-chromosomal short tandem repeats (Y-STRs) is becoming a useful tool for tracing human evolution through male lineages [1] as well as application in a variety of forensic situations [2] including personal identification in sexual assault cases [3–6] and paternity testing with male children [7–9]. However, there are some limitations on the application of Y-STRs in forensic investigations. First, in populations which have encountered bottleneck effect or founder effect, the current Y-STR panels show limited resolution due to the overall reduced diversity [10–12]. Second, conventional Y-STRs are only suitable to distinguish between paternal lineages but not between individuals. Recently, the mutation rates of 186 Y-STR markers were systematically studied by Ballantyne et al. [1], and a set of 13 Y-STR markers (DYF387S1, DYF399S1, DYF403S1, DYF404S1, DYS449, DYS518, DYS526, DYS547, DYS570, DYS576, DYS612, DYS626 and DYS627) with exceptionally high mutation rates (>10-2 per locus per generation) was identified as “rapidly mutating” (RM) Y-STRs [1, 2]. These RM Y-STRs had been proved not only able to improve the resolution of male lineage differentiation, but also to allow close male relative separation with a power unsurpassed by standard Y-STRs [2–5]. To verify the haplotype diversity and the applicability of the 13 novel RM Y-STRs in Chinese Han population, we performed a population genetics survey on Chinese Han group as well as an update on the allele designation of the multi-copy Y-STR locus DYF403S1 on the basis of Ballantyne et al. [3]. 2. Materials and methods 2.1. DNA samples Blood samples were collected from 252 male unrelated healthy blood donors of Chinese Han population in Hubei province. Genomic DNA was isolated from whole blood using the Chelex-100 method [6]. The AmpFlSTR control DNA 007 was used as
control DNA source. 2.2. PCR amplification and genotyping Primers used for amplifying these RM Y-STRs in our study were the same as those reported by Ballantyne et al. [2] except for DYF403S1 and DYS526. The primers for typing DYF403S1 were redesigned by using the Primer 3 software (http://bioinfo.ut.ee/primer3/)
to
5′-CCTCCCTTCTCCCTGTCTTT-3′,
shorten
the
amplicons
(Primer
Primer
A: B:
5′-ACAGAGCAGGATTCCATCTA-3′). Primers for DYS526 used in this study were in accordance with that of Rogalla et al. [5], which only can amplify the allele of DYS526b but not the allele of DYS526a. One of each primer pairs was labelled with 6-FAM dye for detection using ABI 3130 Genetic Analyser (Thermo Fisher Scientific, MA, USA). Amplification for the 13 markers was conducted separately. PCR was performed in a total reaction volume of 20 L containing 5～10 ng genomic DNA, 10 mM Tris–HCl buffer (pH 8.3), 50 mM KCl, 1.5 mM MgCl2, 200 M each dNTP, 0.1 M of each primer, and 1 U AmpliTaq Gold® DNA polymerase (Thermo Fisher Scientific, MA, USA). The cycling conditions were: 95°C for 11 min soak, 30 cycles of 30 s at 94°C, 30 s at 60°C (DYF399S1, DYS518, DYS526b, DYS547, DYS576, DYS612, DYS626 and DYS627) or 62°C (DYF387S1, DYF403S1, DYF404S1, DYS449 and DYS570) and 45 s at 72°C followed by a 30 min extension period at 72°C. For fragment length analysis, 1 μL aliquot of PCR products was added to 8.7 μL Hi-Di formamide (Thermo Fisher Scientific, MA, USA) and 0.3 μL of LIZ-500 (Thermo Fisher Scientific, MA, USA). The amplified products were resolved and detected on a 3130 Genetic Analyzer (Thermo Fisher Scientific, MA, USA) according to vendor instructions, using a 36 cm array, POP-4 polymer and dye set G5. The sample run data were analyzed using GeneMapper ID v3.2 software (Thermo Fisher Scientific, MA, USA). 2.3. Sequence analysis
A total of 128 fragments (107 different alleles) were selected for sequence analysis. PCR products of single-copy markers amplified by unlabelled primers were directly sequenced after purification. The amplification products of multi-copy markers were separated by the polyacrylamide gel electrophoresis, and the selected alleles were recovered independently from the gel, then a re-amplification was performed. All of the PCR products were purified using TaKaRa MiniBEST DNA Fragment Purification Kit Ver.4.0 (Takara), and then were sent to the Sangon Biotech （Shanghai）Co., Ltd. for bidirectional sequencing. 2.4. Allele designation Nomenclature for the 13 RM Y-STR markers was based on our sequencing results, the allele designation way used by Ballantyne et al. [3] and the recommendations of the International Society of Forensic Genetics (ISFG) on the use of Y-STRs [7, 8]. 2.5. Statistical analysis Allele and haplotype frequencies were determined using the counting method. The gene diversity (GD) or haplotype diversity (HD) was calculated using the formula
h n 1 pi2 / n 1 where n is the number of individuals and pi represents the frequency of the ith allele or haplotype [9]. The discrimination capacity (DC) was determined by the formula #H/N where #H represents the number of observed haplotypes and N is the number of samples [10]. 3. Results and discussion 3.1. Allele designation As shown in Table 1, the allele nomenclature for these markers was consistent with that of Ballantyne et al. [3] except for the loci DYF399S1, DYF403S1, DYS526b and DYS626. In our previous study [11], not only a different allele designation for the DYF399S1 was proposed, but also a T deletion occurring inside a homopolymeric T tract located between nucleotide positions 13 and 16 downstream of the repeat was
reported in the Chinese Han population (0.8% incidence rate). DYF403S1 is a duplicated STR system with four positions on the Y-chromosome (DYF403S1a contains three copies, and one in DYF403S1b). Our sequencing results showed that there were three different repeat structures in the DYF403S1 system, and two structures (TTCT)nATC(TTCT)o and (TTCT)nTT(TTCT)3 existed in the DYF403S1a
(Fig.
S1)
and
another
structure
(TTCT)nCT(TTCT)o(TTCC)p(TTCT)qTT(TTCT)3 in the DYF403S1b, which is in accordance with the sequences listed in GenBank entry NC_000024.10 (Fig. S2). In order to comply with the guidelines of the ISFG, we suggest designating the alleles of DYF403S1a with the general structure (TTCT)nN2-3(TTCT)p as (n+p) instead of the (n+o+p) way of Ballantyne et al. [3] based on the structure (TTCT)nNo(TTCT)p, because the number of nucleotide that interrupting the two repeat regions is less than the base number of repeat motif. In addition, we also suggest to designate the alleles of DYF403S1b as (n+o+p+q+3) instead of (n+o+p+q) used by Ballantyne et al. [3] which did not involve the last three non-variant (TTCT) repeat motifs since they are only two bases from the former repeats and should be considered as a part of the repeat region (Fig. S2). The reference structure, sequencing results and proposed nomenclature for the DYF403S1 are shown in Table 2. In a series of our samples, we found four different intermediate alleles in the DYF403S1a due to an incomplete repeat within the variant repeat block, and all of them are in the positions with the structure (TTCT)nATC(TTCT)p. In these variant alleles, the tetramer TTCT repeat block before the interrupting nucleotides “ATC” is interrupted by a CT or TTT motif, and the repeat block after the “ATC” is interrupted by a TT motif. According to their sequence structure these alleles were designated as 30.2, 30.3, 31.2 and 33.2. As listed in Table 2, we also found two sequence subtypes (A and B) of alleles 26, 27, 28, 29, 30 and 32, differing in the number of the TTCT motif both before and after the interrupting nucleotides “ATC”. In addition, all of the four alleles detected from the control DNA 007 were also sequenced and their repeat structures are (TTCT)17TT(TTCT)3,
(TTCT)11ATC(TTCT)15,
(TTCT)12CT(TTCT)8(TTCC)12(TTCT)15TT(TTCT)3
(TTCT)13ATC(TTCT)15 respectively,
and
and the
corresponding fragment lengths are 215 bp, 210 bp, 218 bp and 327 bp respectively. Thus, its genotype is 20-26-28-50 in our way, which is distinctly different from that of Ballantyne et al. [3]. For the DYF403S1b alleles of the DNA 007, even if not to take the last three non-variant repeats (TTCT)3 into consideration, the allele designation would be 47 according to our sequencing results rather than 51 reported by Ballantyne et al. [3]. It is worth noting that different types of repeat structures existing in the DYF403S1a result in the complexity in allele nomenclature. For the same STR marker, it is generally acknowledged that with the fragment length increases, the repeat number of repetitive motifs increases at the same time. As shown in Table 2 and Fig. S2, however, the sum of the 5′ and 3′ flanking region of the repeat structure (TTCT)nTT(TTCT)3
is
significantly
longer
than
that
of
the
structure
(TTCT)nATC(TTCT)p, which result in a mismatch of the fragment length and the repeat number, namely the larger amplification fragments may have smaller repeat number. For example, the total number of repeats of 202 bp allele with the structure (TTCT)nATC(TTCT)p is 24, whereas the total number of repeats of 223 bp allele with the structure (TTCT)nTT(TTCT)3 is only 22 (Table 2). In addition, as shown in Table 2, there only is 1 bp difference in length among many alleles came from different copies of DYF403S1a, and this will result in the difficulty in fragment separation and the construction of allelic ladder. The use of POP-6/POP-7 or next-generation sequencing (NGS) techniques would appear to provide a solution to the DYF403S1 problem in the future. If samples already genotyped with the Ballantyne et al. method [3] need to be converted to the new proposed nomenclature, both the length as well as the sequencing results should be taken into consideration. Direct conversion might not work because of the complexity of the structure. Removing the number "o" from the DYF403S1a repeat (TTCT)nNo(TTCT)p (n+o+p) is technically feasible, but the allele call in DNA 007 as reported by Ballantyne et al. (alleles 11-13-18) [3] still does not correspond with our allele designation (alleles 20-26-28). For DYF403S1b adding the 3 repeats to the Ballantyne nomenclature will make both nomenclatures concordant.
However, even after adding the 3 repeats the allele call in DNA 007 as reported by Ballantyne et al. (allele 51) [3] still does not correspond with our allele sequence and designation (allele 50). Although the same nomenclature was used, there still are some inconsistencies at the DYS526b, DYS547 and DYS626 between our results and the reports of Ballantyne et al. [3]. For the DYS547, our sequencing results showed there are 54 nucleotides between (CCTT)nT(CTTC)o and (TTTC)pN10(CCTT)4(TCTC)1(TTTC)q rather than 56 nucleotides, which is in accordance with the sequences listed in GenBank entry NC_000024.10. For the DYS526b and DYS626, the inconsistencies of the allele designation in the control DNA 007 compared with that of Ballantyne et al. [3] had already been reported in our previous study [11]. 3.2. Haplotype and gene diversity The allele or haplotype (for multi-copy locus) frequencies and gene diversity values for all 13 RM Y-STRs in a Chinese Han population were shown in Table S1. A total of 197 alleles for all these loci were found, and 7 (DYF404S1) to 44 (DYF403S1) alleles for each locus were observed. The gene diversity (GD) ranged from 0.7862 (DYS576) to 0.9953 (DYF403S1). For the whole set of 13 RM Y-STRs, a total of 250 haplotypes were observed in 252 male individuals in which only 2 haplotypes were shared by 2 males respectively (Table 3). The haplotype diversity was estimated to be 0.999937 and the discrimination capacity was 99.21%, showing a great discrimination power in Chinese Han population. It is worth noting that distinctive multi-allelic patterns with extra alleles were observed in some samples for multi-copy loci DYF387S1 (n=5), DYF399S1 (n=15), DYF403S1 (n=1) and DYF404S1 (n=4) (Table 3), which is consistent with the reports of Brito et al. [12] and Oh et al. [13]. For the locus DYF387S1, five individuals were observed to have three different alleles while the other samples usually showed double-allele patterns. Four to six different alleles were observed in fifteen individuals at DYF399S1, which usually exists as three copies. A total of 25 extra-allelic patterns were observed in 20 individuals, four of them have extra alleles in more than one
locus. All samples with extra alleles were tested repeatedly to exclude the possibility of sample pollution. Extra stripes have been confirmed to be alleles of the locus by sequencing. In addition, we also collected blood samples of sons of these individuals with extra-allelic patterns, all showed the same genotype with their fathers (Fig. 1). 4. Conclusion Rapidly mutating Y-STRs have been proven to have strong ability in differentiating male individuals in many regions all of the world, our study also support its applicability in Chinese Han population. Discrepancy on the nomenclature of a few loci has been observed in our study, and further verification by different labs is expected. In our future study, it will be conducted to validate its ability in differentiating patrilineal relatives in Chinese Han population.
References [1] M.A. Jobling, C. Tyler-Smith, Fathers and sons: the Y chromosome and human evolution, Trends Genet. 11 (1995) 449–456. [2] M. Kayser, A. Caglià, D. Corach, N. Fretwell, C. Gehrig, G. Graziosi, et al., Evaluation of Y-chromosomal STRs: a multicenter study, Int. J. Legal Med. 110 (1997) 125–133. [3] M. Prinz, K. Boll, H. Baum, B. Shaler, Multiplexing of Y chromosome specific STRs and performance for mixed samples, Forensic Sci. Int. 85 (1997) 209–218. [4] M. Prinz, A. Ishii, A. Coleman, H.J. Baum, R.C. Shaler, Validation and casework application of a Y chromosome specific STR multiplex, Forensic Sci. Int. 120 (2001) 177–188. [5] W. Parson, H. Niederstätter, A. Brandstätter, B. Berger, Improved 217 specificity of Y-STR typing in DNA mixture samples, Int. J. Legal Med. 117 (2003) 109–114. [6] Roewer L, Y chromosome STR typing in crime casework, Forensic Sci. Med. Pathol. 5 (2009) 77–84. [7] B. Rolf, W. Keil, B. Brinkmann, L. Roewer, R. Fimmers, Paternity testing using Y-STR haplotypes: assigning a probability for paternity in cases of mutations, Int. J. Legal Med. 115 (2001) 12–15. [8] I. Ayadi, N. Mahfoudh-Lahiani, H. Makni, L. Ammar-Keskes, A. Rebaï, Combining autosomal and Y-chromosomal short tandem repeat data in paternity testing with male child: methods and application, J. Forensic Sci. 52 (2007) 1068–1072. [9] Z.H. Deng, Q. Li, S. Wu, D.C. Li, B.C. Yang, Application of 17 Y-chromosome specific STR loci in paternity testing, Zhongguo Shi Yan Xue Ye Xue Za Zhi 16 (2008) 699–703. [10] M. Hedman, V. Pimenoff, M. Lukka, P. Sistonen, A. Sajantila, Analysis of 16 Y STR loci in
the Finnish population reveals a local reduction in the diversity of
male lineages, Forensic Sci.
Int. 142 (2004) 37–43.
[11] M. Woz’niak, M. Derenko, B.A. Malyarchuk, I. Dambueva, T. Grzybowski, D. Mis’cicka-S’liwka, Allelic and haplotypic frequencies at 11 Y-STR loci in Buryats from South-East Siberia, Forensic Sci. Int. 164 (2006) 271–275. [12] M. Hedman, A.M. Neuvonen, A. Sajantila, J.U. Palo, Dissecting the Finnish male uniformity: the value of additional Y-STR loci, Forensic Sci. Int. Genet. 5 (2011) 199–201. [1] K.N. Ballantyne, M. Goedbloed, R. Fang, O. Schaap, O. Lao, A. Wollstein, et al., Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic Am. J. Hum. Genet. 87 (2010) 341–353. [2] K.N. Ballantyne, V. Keerl, A. Wollstein, Y. Choi, S.B. Zuniga, A. Ralf, et al., A new future of forensic Y-chromosome analysis: rapidly mutating Y-STRs for differentiating male relatives and paternal lineages, Forensic Sci. Int. Genet. 6 (2012) 208–218. [3] K.N. Ballantyne, A. Ralf, R. Aboukhalid, N.M. Achakzai, M.J. Anjos, Q. Ayub, et al., Toward male individualization with rapidly mutating Y-chromosomal short tandem repeats, Hum. Mutat. 35 (2014) 1021–1032. [4] C. Robino, A. Ralf, S. Pasino, M.R. De Marchi, K.N. Ballantyne, A. Barbaro, et al., Development of an Italian RM Y-STR haplotype database: Results of the 2013 GEFI collaborative exercise, Forensic Sci. Int. Genet. 15 (2015) 56–63. [5] U. Rogalla, M. Woźniak, J. Swobodziński, M. Derenko, B.A. Malyarchuk, I. Dambueva, et al., A novel multiplex assay amplifying 13 Y-STRs characterized by rapid and moderate mutation rate, Forensic Sci. Int. Genet. 15 (2015) 49–55. [6] P.S. Walsh, D.A. Metzger, R. Higuchi, Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material, Biotechniques 10 (1991) 506–513. [7] P. Gill, C. Brenner, B. Brinkmann, B. Budowle, A. Carracedo, M.A. Jobling, et al., DNA Commission of the International Society of Forensic Genetics: recommendations on forensic analysis using Y-chromosome STRs, Forensic Sci. Int. 124 (2001) 5–10. [8] L. Gusmão, J.M. Butler, A. Carracedo, P. Gill, M. Kayser, W.R. Mayr, et al.,
DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis, Forensic Sci. Int. 157 (2006) 187–197. [9] M. Nei, Molecular Evolutionary Genetics, Columbia University Press, New York, 1987, pp. 176–181. [10] M.D. Coble, C.R. Hill, J.M. Butler, Haplotype data for 23 Y-chromosome markers in four U.S. population groups, Forensic Sci. Int. Genet. 7 (2013) e66–e68. [11] W.Q. Zhang, C. Xiao, J. Yu, T. Wei, C. Pan, D.X. Huang, Allele repeat structure and designation update for the Y-STR loci DYF399S1, DYS526b and DYS626, Forensic Sci. Int. Genet. 20 (2016) 147–148. [12] P. Brito, M. Carvalho, V. Bogas, A.M. Bento, A. Serra, et al., Study of rapidly mutating Y-STRs in a Portuguese population, Forensic Sci. Int. Genet. 4 (2013) e83–e84. [13] Y.N. Oh, H.Y. Lee, E.Y. Lee, E.H. Kim, W.I. Yang, K.J. Shin, Haplotype and mutation analysis for newly suggested Y-STRs in Korean father-son pairs, Forensic Sci. Int. Genet. 15 (2015) 64–68.
Fig. 1. Distinctive multi-allelic patterns for DYF387S1 (a), DYF399S1 (b) and DYF404S1 (c) observed in two father–son pairs.
Table 1: The repeat structures, allelic designations, and control DNA 007 and 2800M genotypes of 13 RM Y-STRs. RM Y-STR
Repeat structure
Allele
Control DNA 007
Control DNA 2800M
Allele
designation
genotype
genotype
observed
DYF387S1
(AAAG)3(GTAG)1(GAAG)4(AAAG)2(GAAG)1(AAAG)2(GAAG)n(AAAG)o
13+n+o
35, 37
37, 38
33–42
DYF399S1
(GAAA)3N7-8(GAAA)n
5+n or 4.3+n
23.3, 26
23.3, 25, 26
16.3–30
DYF403S1a
(TTCT)nN2-3(TTCT)p
n+p
20, 26, 28
19, 26, 29
13–37
DYF403S1b
(TTCT)nN2(TTCT)o(TTCC)p(TTCT)qN2(TTCT)3
n+o+p+q+3
50
45
42–57
DYF404S1
(TTTC)n
n
14, 16
13,16
11–17
DYS449
(TTTC)nN50(TTTC)o
n+o
30
34
24–37
DYS518
(AAAG)3(GAAG)1(AAAG)n(GGAG)1(AAAG)4N6(AAAG)o
9+n+o
37
36
32–43
DYS526b
(CTTT)n(CCTT)oN113(CCTT)p
n+o+p
35
35
32–42
DYS547
(CCTT)nT(CTTC)oN54(TTTC)pN10(CCTT)4(TCTC)1(TTTC)q
n+o+p+5+q
49
45
42–55
DYS570
(TTTC)n
n
17
17
13–23
DYS576
(AAAG)n
n
19
18
15–22
DYS612
(CCT)5(CTT)1(TCT)4(CCT)1(TCT)n
11+n
37
35
29–41
DYS626
(GAAA)nN24(GAAA)3N6(GAAA)5(AAA)1(GAAA)o(GAAG)1(GAAA)3
n+10+o
29
28
25–34
DYS627
(AGAG)3(AAAG)n
3+n
21
22
17–25
Segments in bold are not counted in the allele designation.
range
Table 2: The reference structure and proposed nomenclature for the multi-copy locus DYF403S1 according to the sequencing results. Consensus structure
PrimerA.ctttcttccctccttcccttctccctgtctgtctttctttcgttctctttctttttcttt(ttct)ntt(ttct)3ttcctctaactctgtatctctgtttaatatttt.PrimerB
(a position of DYF403S1a) Allele
Sequence
13 (187 bp)
PrA(20bp) 60bp(ttct)102bp(ttct)333bp PrB(20bp)
14 (191 bp)
PrA(20bp) 60bp(ttct)112bp(ttct)333bp PrB(20bp)
15 (195 bp)
PrA(20bp) 60bp(ttct)122bp(ttct)333bp PrB(20bp)
16 (199 bp)
PrA(20bp) 60bp(ttct)132bp(ttct)333bp PrB(20bp)
17 (203 bp)
PrA(20bp) 60bp(ttct)142bp(ttct)333bp PrB(20bp)
18 (207 bp)
PrA(20bp) 60bp(ttct)152bp(ttct)333bp PrB(20bp)
19 (211 bp)
PrA(20bp) 60bp(ttct)162bp(ttct)333bp PrB(20bp)
20 (215 bp)
PrA(20bp) 60bp(ttct)172bp(ttct)333bp PrB(20bp)
21 (219 bp)
PrA(20bp) 60bp(ttct)182bp(ttct)333bp PrB(20bp)
22 (223 bp)
PrA(20bp) 60bp(ttct)192bp(ttct)333bp PrB(20bp)
Consensus structure
PrimerA.ctttccttctttccttctttctttcc(ttct)natc(ttct)ptcctttcctctatctctgtatctctgtttaatatttt.PrimerB
(other two positions of DYF403S1a) Allele
Sequence
24 (202 bp)
PrA(20bp) 26bp(ttct)113bp(ttct)1337bp PrB(20bp)
25 (206 bp)
PrA(20bp) 26bp(ttct)123bp(ttct)1337bp PrB(20bp)
26A (210 bp)
PrA(20bp) 26bp(ttct)133bp(ttct)1337bp PrB(20bp)
26B (210 bp)
PrA(20bp) 26bp(ttct)113bp(ttct)1537bp PrB(20bp)
27A (214 bp)
PrA(20bp) 26bp(ttct)143bp(ttct)1337bp PrB(20bp)
27B (214 bp)
PrA(20bp) 26bp(ttct)123bp(ttct)1537bp PrB(20bp)
28A (218 bp)
PrA(20bp) 26bp(ttct)153bp(ttct)1337bp PrB(20bp)
28B (218 bp)
PrA(20bp) 26bp(ttct)133bp(ttct)1537bp PrB(20bp)
29A (222 bp)
PrA(20bp) 26bp(ttct)133bp(ttct)1637bp PrB(20bp)
29B (222 bp)
PrA(20bp) 26bp(ttct)153bp(ttct)1437bp PrB(20bp)
30A (226 bp)
PrA(20bp) 26bp(ttct)163bp(ttct)1437bp PrB(20bp)
30B (226 bp)
PrA(20bp) 26bp(ttct)133bp(ttct)1737bp PrB(20bp)
30.2 (228 bp)
PrA(20bp) 26bp(ttct)3ct(ttct)93bp(ttct)1837bp PrB(20bp)
30.3 (229 bp)
PrA(20bp) 26bp(ttct)2ttt(ttct)123bp(ttct)1637bp PrB(20bp)
31 (230 bp)
PrA(20bp) 26bp(ttct)133bp(ttct)1837bp PrB(20bp)
31.2 (232 bp)
PrA(20bp) 26bp(ttct)3ct(ttct)113bp(ttct)1737bp PrB(20bp)
32A (234 bp)
PrA(20bp) 26bp(ttct)153bp(ttct)1737bp PrB(20bp)
32B (234 bp)
PrA(20bp) 26bp(ttct)133bp(ttct)1937bp PrB(20bp)
33 (238 bp)
PrA(20bp) 26bp(ttct)163bp(ttct)1737bp PrB(20bp)
33.2 (240 bp)
PrA(20bp) 26bp(ttct)113bp(ttct)20tt(ttct)237bp PrB(20bp)
34 (242 bp)
PrA(20bp) 26bp(ttct)143bp(ttct)2037bp PrB(20bp)
35 (246 bp)
PrA(20bp) 26bp(ttct)163bp(ttct)1937bp PrB(20bp)
36 (250 bp)
PrA(20bp) 26bp(ttct)173bp(ttct)1937bp PrB(20bp)
37 (254 bp)
PrA(20bp) 26bp(ttct)193bp(ttct)1837bp PrB(20bp)
Consensus structure
PrimerA.ctttcttccctccttcccttctccctgtctttctttcgttctctttcttt(ttct)nct(ttct)o(ttcc)p(ttct)qtt(ttct)3ttcctctaactctgtatctctgtttaatatttt.PrimerB
(DYF403S1b) Allele
Sequence
43 (299 bp)
PrA(20bp) 50bp(ttct)112bp(ttct)7(ttcc)11(ttct)112bp(ttct)333bp PrB(20bp)
45 (307 bp)
PrA(20bp) 50bp(ttct)102bp(ttct)10(ttcc)10(ttct)122bp(ttct)333bp PrB(20bp)
50 (327 bp)
PrA(20bp) 50bp(ttct)122bp(ttct)8(ttcc)12(ttct)152bp(ttct)333bp PrB(20bp)
55 (347 bp)
PrA(20bp) 50bp(ttct)142bp(ttct)12(ttcc)13(ttct)132bp(ttct)333bp PrB(20bp)
Table 3: Haplotypes of 13 RM Y-STRs from 252 samples in Chinese Han population. Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
1
37,39
21.3,24
15,27,29
53
13,14
32
39
35
51
18
19
37
30
24
2
36,40
19.3,25.3,27
20,30,31
54
13,14
36
38
37
50
16
18
32
29
21
3
35,38
19.3,25
17,25,27
50
12,14
31
40
36
50
19
20
38
29
21
4
36,38
20.3,23.3,25
16,29,30
52
13,14
32
36
36
48
18
17
39
27
19
5
35,38
19.3,22.3,24
18,29
52
12,13
35
36
36
49
19
19
38
28
18
6
35,38
20.3,24
16,28,29
52
13,14
32
35
37
51
18
15
38
27
18
7
36,37
20.3,22,22.3
16,25,28
50
14,15
31
40
36
51
19
21
38
28
20
8
36,38
19.3,22,22.3
16,29,30
51
14,16
30
42
34
48
17
18
35
29
20
9
37,38
20.3,21.3,22
14,33,35
46
15,16
32
38
34
44
13
18
33
29
17
10
36,38
20.3,21
15,28
53
14,17
35
39
36
49
19
17
38
30
20
11
37
29
17,27,28
49
13
28
36
36
46
18
19
35
31
25
12
37,42
21.3,22.3,23
17,27,30
50
14,15
30
36
36
48
20
18
38
28
21
13
35
23.3,24,25
16,27,29
49
13
25
42
35
49
20
17
41
27
20
14
35,41
18.3,24.3,26
18,30
54
14,16
34
36
37
49
16
18
34
28
23
15
36,40
19.3,23.3,25.3
16,28
50
14,16
32
34
34
49
18
20
35
30
22
16
34
24,24.3
14,31,34
48
14
28
38
33
47
16
20
36
34
22
17
38,39
19.3,21.3
16,28
51
14,15
33
40
36
46
18
18
36
29
20
18
36,37
21.3,23.3,27
13,27
52
13,15
31
37
36
46
20
18
36
28
22
19
36
17.3,22.3,24
15,27,30
49
13,16
26
41
34
47
18
19
36
28
21
20
38,39
19.3,21,22.3
15,30
56
14,15
32
39
38
51
17
16
37
29
20
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
21
38,39
21.3,22.3,23
16,29
54
14,15
30
34
36
48
15
19
36
32
20
22
37,39
20.3,22,22.3
15,28,29
49
14,15
31
39
37
52
18
20
39
27
21
23
35,38
18.3,21.3,22.3,24,25,26
17,28,31
52
13,14
33
34
37
50
20
19
38
27
19
24
37,38
20.3,22.3,26
19,28
52
13
32
34
36
49
17
19
37
28
18
25
35
24
14,27,28
50
13
30
37
36
44
19
19
30
29
21
26
36,38
20.3,24.3,26
17,29
53
13,15
30
33
38
48
18
20
39
26
17
27
36
22
14,24,30
46
15
28
38
34
47
21
18
34
29
25
28
38,40
19.3,25.3,28
18,28,30
53
12,17
33
38
37
49
17
19
37
30
22
29
37,39
21.3,24.3,26
20,28
53
12,14
31
38
38
48
16
20
37
29
21
30
35,37
19.3,21.3,22
15,26
53
14
32
39
37
51
18
20
37
30
20
31
37,38
23,24.3,27
18,27,29
50
15
29
37
36
51
17
18
36
29
23
32
35,38
21.3,22,22.3
16,29
52
13
32
35
37
47
18
19
33
27
18
33
36
24
16,27,28
51
14
29
38
34
43
20
18
36
30
22
34
35,36
20.3,21.3,23
14,30,35
45
15,17
29
39
35
46
16
18
33
31
23
35
39
19.3,20.3,28.1
15,26,33
49
12,17
30
39
33
51
18
18
39
29
21
36
37
23,23.3
14,27,29
52
13
31
39
38
51
18
17
33
29
21
37
38
21.3,23.3
14,32,33
45
17
30
38
33
44
16
20
36
31
22
38
36,40
18.3,23.3,27
18,28,30
55
12,15
34
39
36
50
20
18
38
28
24
39
35,37
21.3,25
16,27,29
54
13,14,15
31
38
38
50
18
18
35
27
20
40
35,40
21.3,24.3,25
19,28,29
56
13
35
35
36
47
17
19
38
28
22
41
35,36
20.3,22,22.3
16,25,26
55
13,15
33
39
36
49
17
20
35
31
20
42
35,37
21.3,24,24.3
17,30
52
14
32
32
35
48
16
19
36
26
18
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
43
37,40
22.3,25,25.3
16,27
49
12,15
27
41
36
49
17
19
35
29
20
44
35,40
19.3,20.3,24
18,26
50
13,16
32
37
37
49
20
16
38
30
20
45
38,40
20.3,22.3,23
18,27,32
48
13,14
29
37
36
47
19
18
39
29
22
46
35
19.3,21.3,23
18,24,33
46
14,15
30
39
34
49
16
18
40
27
19
47
40
20.3,25
20,27,31
50
14,16
31
39
35
47
20
18
38
28
22
48
35,38
20.3,23.3,25
18,30,31
53
14,15
33
36
35
50
17
19
37
31
20
49
34,37
20.3,21,21.3,24
14,31,33
45
12,16
30
39
34
44
17
19
37
30
22
50
35
24
14,27,30.3
49
14
29
38
35
44
19
18
29
29
20
51
38
20.3,21
15,28,29
55
15
36
39
35
53
21
16
38
29
22
52
35,38
19.3,23.3,25
17,28,31
52
12,14
35
36
36
48
19
20
38
27
18
53
34,37
24,27
15,25,28
51
15,16
29
39
34
45
19
15
32
27
17
54
35,39
20.3,23.3,28
16,28,30
54
13,14
33
37
38
49
17
18
37
26
20
55
36,39
20.3,23.3,27
19,29
57
13,15
35
37
37
48
18
19
35
29
19
56
36,37
20.3,22.3,23
15,25,27
56
14,15
32
39
36
52
17
21
39
30
19
57a
36,40
20.3,21.3,25
20,27,29
50
14
31
37
37
50
17
16
40
27
22
58
36,38
20.3,24,25.3
17,28
51
13,14
35
41
34
45
18
16
36
33
22
59
35,38
21.3,22.3,27
16,28,31
55
13,14
32
38
36
49
17
19
37
28
17
60
35
24
16,27,29
48
14
29
35
35
42
20
17
31
29
20
61
36
19.3,24,26.3
15,28
49
13,14
26
43
35
49
19
19
37
27
20
62
36,39
22.3,23.3,24
15,27,37
48
14,15
30
38
35
47
19
16
39
29
21
63
36,37
18.3,24,25.3
15,26,29
53
14,17
27
38
36
48
18
20
38
27
22
64
36,38
20.3,23.3,24
17,26,30
49
12,15
33
40
37
47
20
17
36
33
17
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
65
34,35,38
19.3,20.3,22,24
14,30.2,31
45
15,17
31
41
34
46
16
16
36
28
19
66
35
21.3,24.3,25
17,28,30
53
13,14
35
33
38
51
18
19
37
27
18
67
34,38
20.3,23,24.3
17,28,30
53
13
35
37
36
50
20
18
38
28
18
68
36,38
21.3,22.3,25
18,28,32
51
14,15
31
37
36
48
18
19
39
28
21
69
36,37
20.3,22.3,27
15,25,29
54
15
32
38
36
48
18
19
35
30
19
70
36,39
19.3,22.3,24.3
20,28,29
43
14,15
25
40
37
52
19
18
36
30
19
71
37,39
19.3,22,22.3
16,25,26
52
14,15
33
38
38
51
17
21
35
29
22
72
35,40
20.3,23,24.3
18,28,31
55
14,16
33
36
37
50
19
17
36
32
20
73
37,39
21.3,22.3,23
20,25,27
49
14,15
32
40
38
49
19
18
37
30
18
74
35,38
22.3,25.3,26
16,28,30
53
13,14
32
38
38
49
17
18
37
26
20
75
36
20.3,21.3,25
14,32,33
45
14,16
28
40
35
47
16
18
36
32
23
76
38,39
21.3,22,23.3,24
19,30,31
54
15
30
36.2
35
48
20
18
36
30
21
77
36,37
19.3,20,20.3,21.3,23
15,32,33
47
12,13
30
37
35
48
16
16
34
30
22
78
39,41
20.3,23.3,24
20,25,30
53
13,15
32
38
38
48
14
17
39
27
21
79
40
20.3,28
20,27,32
48
14,15
32
41
36
47
20
18
39
28
24
80
37
20.3,22.3,24
16,26,27
53
15,16
26
39
41
46
20
18
37
27
24
81
36,38
20.3,26
21,30
54
11,13
32
37
36
48
17
19
33
29
21
82
36,38
21.3,23,24.3
15,30,34
47
14,16
30
37
33
48
17
17
32
31
23
83
37,39
18.3,26,28
21,32
53
13,15
34
39
37
51
16
20
37
29
22
84
37,39
17.3,23.3,28
19,30,32
54
14
32
39
37
50
16
19
36
28
22
85
38,41
20.3,21.3,24,24.3
22,28,33
51
14,15
33
37
34
45
16
18
38
29
23
86
35
20.3,22
15,25,26
54
15
32
40
35
50
17
18
36
30
22
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
87
36,37
20.3,21.3,23
15,33.2,35
45
15
29
42
34
46
15
17
35
31
22
88
39,40
18.3,22.3,23
13,26
53
12,14
34
36
35
49
17
20
36
30
22
89
38,40
21.3,23.3,24
19,27,34
50
14,16
31
38
32
48
18
17
39
29
23
90
37
20.3,21,22.3
14,28,32
49
13,14
30
36
36
48
17
17
31
31
20
91
36
25
13,26,32
49
13,14
29
34
35
44
17
19
33
30
23
92
36,38
22.3,23.3,25
15,29
53
13,14
33
35
37
49
17
22
37
28
19
93
35,38
20.3,24.3,25
16,27,30,32
53
13,14
33
36
35
46
19
19
39
27
18
94
37,41
18.3,22,22.3
15,28
50
14,15
35
38
36
48
19
19
39
30
20
95
37,38
19.3,24.3,25,27
19,26,29
51
14,15
31
32
35
48
20
17
38
31
20
96
37
19.3,24.3,25
19,28,31
53
12,13
30
37
36
52
18
17
34
30
21
97
37,38
23.3,24,27
17,27,31
50
14,15
29
36
36
50
17
16
36
29
22
98
35,37
20.3,21.3,22
15,26,27
55
14,16
31
39
36
49
18
20
36
30
21
99
38,41
22.3,23,23.3
17,27,28
51
14,15
30
37
36
45
17
18
39
27
17
100
36,39
20.3,21.3,28
15,26
51
13,15
30
38
35
48
16
19
36
27
19
101
35,37
20.3,23,23.3
14,32,33
45
14,17
29
38
37
50
17
20
36
32
23
102
37,38
21.3,22.3,25
16,28,33
47
14
29
37
34
49
21
17
38
29
21
103
35,38
20.3,21.3,23,23.3
17,24,28
52
13
30
37
36
52
19
18
35
27
21
104
35,40
20.3,23,23.3
15,25,28
47
15,16
29
40
34
46
18
19
37
29
21
105
38,39
17.3,23.3,30
18,30,31
53
14,15
33
39
37
51
17
19
36
29
21
106
36,37,38
21.3,23,24
17,28
55
12,14,16
27
34
36
49
16
19
38
31
20
107
36,39
17.3,21.3,26
14,29,32
45
14,16
29
40
36
45
18
19
32
30
23
108
37,40
20.3,22.3,24
20,27,34
50
14,16
31
38
35
46
17
17
39
29
22
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
109
36,39
17.3,24.3,25
18,30
54
13,14
36
37
42
48
17
20
35
31
19
110
36,38
20.3,21.3,22.3,23,24
16,25,26
52
13,14
30
38
38
49
18
18
37
28
21
111
37,39
20.3,21.3,22.3
16,27,28
52
12,13,16
29
36
36
48
17
20
36
32
20
112
36,39
18.3,22.3,24.3
19,29,30
43
15,16
24
37
36
50
18
18
35
31
18
113
34
22
14,25,28
49
14
31
39
37
44
20
17
29
29
20
114
37
26
17,26,27
50
15
27
38
33
42
17
18
37
30
20
115
37,40
22.3,24.3,25
20,28,31
57
13,14
36
35
37
47
17
17
36
30
23
116
34,40
16.3,21.3,27
19,29
54
13,14
32
36
35
49
16
21
36
30
23
117
35,39
22.3,23,24.3
16,27,28
51
13
32
35
37
48
18
17
36
28
18
118
35,38,40
19.3,21.3,26,27
16,29,30
53
12,13,14
31
34
37
48
19
18
37
27
19
119
38,40
20.3,26.3,27,27.3
16,27,31
50
14,15
30
32
36
49
19
17
35
30
21
120
36,39
21.3,22.3,25
15,25,29
50
15,16
31
39
38
46
18
19
33
30
21
121a
36,40
20.3,21.3,25
20,27,29
50
14
31
37
37
50
17
16
40
27
22
122
35,38
22.3,24.3,25
20,27,29
54
14
34
37
36
45
15
19
40
30
19
123
36
18.3,23.3,26
15,27,30
49
15
26
41
36
49
19
18
38
27
20
124
36,39
21.3,22.3,26
17,28,30
50
13
32
35
35
47
17
19
38
28
17
125
35,38
18.3,23.3,26
17,28
54
13
33
36
36
48
18
17
37
25
22
126
36,38
21.3,22.3,26
15,30,31
47
14,16
29
39
37
48
16
16
33
31
23
127
37,39
21.3,23.3,26
19,27,30
51
14,15
32
32
36
48
18
16
38
30
22
128
37,39
18,19.3,24.3
16,26,28
51
12,16
25
42
38
49
16
17
37
28
19
129
38,40
21.3,26
18,27,33
48
14,15
32
38
34
48
21
18
37
28
22
130
37,39
20.3,24,25.3
17,29,36
56
13,15
32
36
37
50
15
18
39
28
22
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
131
36,37,39
19.3,20.3,22.3,26
15,25,28
52
14,15
31
37
36
46
18
16
38
29
22
132
37
21.3,24
14,32,36
45
14
30
40
35
46
19
19
36
29
22
133
36,38
20.3,21.3,24
16,26
54
14,15
27
42
38
48
21
16
35
26
21
134
37
21.3,24
15,32,33
46
16
31
37
33
45
16
18
32
28
23
135
38
23.3,24
19,31
53
14
30
39.2
36
47
19
17
37
29
22
136
38,40
20.3,23.3,25
21,27,33
50
14,15
33
38
34
48
17
19
40
29
23
137
35,39
22.3,23
19,27,28
51
13,14
30
35
35
52
19
16
38
26
21
138
37,40
21.3,22.3,27
19,28,33
51
13,15
31
38
36
47
17
18
39
27
23
139
38,40
20.3,22.3,27
20,27,34
50
14,15
29
37
35
46
18
18
39
29
21
140
37,41
22.3,24,26.3
16,27,31
51
12,14
26
39
36
48
17
20
35
30
21
141
36,40
21,21.3,23.3
15,30
52
13,15
33
39
37
49
20
18
36
30
21
142
37,39
21.3,23
17,27,29
48
13,14
33
41
35
46
17
19
33
32
20.2
143
36
21.3,22
14,30,34
47
15,16
29
37
36
46
16
16
36
30
24
144
38,39
20.3,23,23.3
19,27,36
48
14,15
31
37
34
46
20
19
36
30
21
145
36,39
18.3,24.3,27
19,30,32
54
13,14
34
40
38
48
16
20
37
29
21
146
36,41
19.3,23.3,27
19,31,32
54
13,14
33
39
37
51
16
20
36
28
21
147
36,41
19.3,21.3,26
17,28,32
49
15,16
32
34
34
49
20
19
37
32
22
148
35,37
20.3,21.3,22
15,25,28
53
14,15
31
39
36
50
17
19
36
28
20
149
36,37
19.3,21.3,26
13,27
52
13,16
31
36
36
45
18
18
37
26
22
150
39
23.3,24
20,30,31
55
15
31
36.2
36
47
19
19
36
31
23
151
33,38
22,22.3,23.3
15,26,27
53
14,15
33
42
40
46
19
18
39
29
22
152
38
23,24.3
17,31
54
15
30
37.2
38
46
20
19
33
30
20
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
153
36,37
19.3,23,25.3
15,26,27
53
13,17
27
38
37
49
18
18
37
27
22
154
38,39
19.3,20.3,23
15,27,28
52
13,15
37
40
36
49
21
18
37
33
21
155
37,40
20.3,22.3
15,27,28
51
13,15
27
40
35
48
16
19
35
31
21
156
35,39
19.3,23,25.3
21,29,32
56
12,13
28
37
37
50
15
19
36
29
21
157
37
20.3,22.3,24
13,27,29
52
14,17
32
37
36
45
20
20
36
29
22
158
36,38
19.3,23
16,28,29
53
13,14
28
35
38
48
16
19
38
28
21
159
36,39
18.3,21.3,24
14,30,32
44
14,16
28
38
34
49
17
18
34
32
21
160
37,41
21.3
15,27,31
50
13,14
33
39
35
47
19
18
37
28
22
161
36,38
19.3,22.3,28
17,27,29
53
14,15
32
36
37
48
17
19
38
29
19
162
35,36
20.3,23.3,26
16,26,30
50
13,14
27
42
35
49
18
20
40
28
20
163
38,40
20.3,22.3,26
20,27,34
50
14,15
34
38
33
48
18
17
39
29
24
164
36,39
19.3,21.3,25
18,28,31
56
13,15
36
36
38
51
16
19
34
29
22
165
38
19.3,22,24.3
15,25,26
53
14
32
38
40
49
17
20
36
29
21
166
38
20.3,23.3,27
15,25,30
51
14,15
31
39
38
46
20
17
30
27
19.1
167
36,40
20.3,21.3,22.3,23.3
16,27,29
49
13,16
33
37
33
47
15
18
37
29
23
168
35,40
20.3,21.3,24
19,26,27
49
13,15
33
36
37
49
18
18
40
28
21
169
36
20.3,21.3,27
20,27
49
13,14
30
37
35
49
20
16
36
26
22
170
36,37
20.3,23.3,26
15,26,28
51
14,15
31
41
35
51
19
20
38
31
20
171
35,39
22.3,23.3,25
16,27,31
53
13,15
30
37
38
49
18
19
36
27
19
172
36,38
19.3,21,23.3
15,25,26
51
14,16
31
39
38
50
17
19
36
29
21
173
39,40
18.3,24.3,27
18,27,31
50
13,15
28
35
35
49
18
18
37
30
23
174
37
21.3,22.3,24
16,31,33
45
14,15
28
36
35
48
17
17
33
29
23
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
175
36,39
19.3,25.3,26
20,27
54
13,14
37
35
37
48
16
18
36
31
23
176
36,37
18.3,22.3,25
19,28,29
56
12,13
32
37
37
52
17
17
36
29
20
177
36,38
20.3,21.3,27
16,31,34
45
14,15
29
34
33
47
16
18
37
30
23
178
36,39
20.3,22.3,25
15,26,27
52
13,14
30
37
36
48
17
18
38
27
21
179
38
21.3,25
19,30
53
16
30
35.2
34
47
20
20
34
29
23
180
37,38
21.3,24.3,26
20,30,31
56
13
36
38
39
49
18
19
35
29
22
181
36
21.3,22.3,26
15,25,29
50
14,15
33
39
34
50
22
20
38
30
20
182
38,39
21.3,23,23.3
17,27,33
49
15
29
39
34
50
19
16
36
29
21
183
36
20.3,26
14,31,34
43
16
28
40
35
45
15
19
36
31
22
184
37,39
19.3,20,29.1
16,24,31
51
13,17
30
41
37
53
19
20
37
31
22
185
37,42
20.3,22.3,24
18,27,34
48
15
30
38
36
46
19
17
36
29
21
186
36,37
20.3,22.3,24
16,28,32
52
13,14
35
34
36
48
18
18
38
28
18
187
34,40
20.3,22.3,23
15,26,31
52
13,14
30
39
35
49
17
18
34
32
20
188
35,38
19.3,25.3,26
17,29,31
51
13
35
37
37
51
19
17
39
29
18
189
36
20.3,21.3,24
14,32,33
45
15
27
39
36
46
15
17
29
31
22
190
36,37
21.3,26
15,25,28
51
15
32
37
36
48
17
18
37
29
19
191
36
21.3,22,22.3
14,31,33
45
15
29
39
36
46
16
18
35
32
23
192
34,37
20.3,22.3,26
18,28
54
15
34
37
36
55
18
19
35
29
23
193
36,38
20.3,23,25.3
16,28,29
52
13
31
35
36
48
19
19
37
26
18
194
38
23,24
22,26,37
43
11
33
37
33
44
16
16
37
29
23
195
36,39
20,22,24.3
19,25,29
42
14,15
29
43
38
46
19
17
39
33
21
196
37,38
22,23.3,26
15,27,33
50
13,15
28
38
34
49
20
19
37
29
22
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
197
35,38
21.3,22,24.3
14,25,34
51
13,14
32
36
34
48
17
19
37
27
18
198
38,40
19.3,26
19,26,33
49
14,15
31
40
37
49
18
18
37
28
24
199
36
25,28.3
15,27,28
49
14
25
42
34
49
17
19
38
28
21
200
37,39
18.3,22.3,27
15,26,27
51
14
32
36
35
49
18
17
38
29
21
201
37,38
18.3,22.3,24
18,28
50
14,15
28
39
34
50
19
15
36
29
18
202
35,40
18.3,22.3,29
19,29
53
14,16
36
38
39
50
18
21
39
31
23
203
34
21.3,27
15,27,30
52
14
30
41
38
50
20
19
36
32
23
204b
35,37
20.3,23.3,25
17,29,30
53
13,14
33
33
37
49
19
18
37
26
18
205b
35,37
20.3,23.3,25
17,29,30
53
13,14
33
33
37
49
19
18
37
26
18
206
36,40
20.3,24.3,25
18,30,31
53
13,14
33
36
37
49
16
18
35
29
20
207
36,37
21.3,22,22.3,23
16,24,28
51
13
30
37
37
52
20
17
36
27
22
208
36,40
20.3,24.3,26
18,29,30
55
13,15
34
36
36
52
17
19
36
27
20
209
34
22
14,26,30
49
15
30
38
37
44
20
19
31
30
21
210
36
24
15,28,29
52
14
28
37
34
46
18
16
34
32
22
211
35,41
20.3,21,22.3
15,29,31
50
13,16
33
43
39
52
20
19
37
32
21
212
35,37
18.3,22,22.3
15,25,26
53
14,15
31
39
36
49
17
19
38
30
20
213
37,38
23,23.3,27
17,27,29
50
15
28
38
36
50
17
18
36
29
23
214
37,39
20.3,22.3,23
16,26,29
50
13,17
27
41
39
49
16
21
36
28
21
215
37,39
20.3,23.3,24
19,24,29
49
14
32
40
35
45
20
19
35
31
17
216
35,38
20.3,22.3,25
17,30
54
13,15
33
37
36
48
19
18
38
27
18
217
36,37
21.3,22.3,24
15,33,34
45
13,14
30
38
34
46
16
16
31
30
21
218
36,38
19.3,24.3,25
20,29
55
13,14
32
35
34
54
20
19
36
31
18
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
219
37,39
21.3,22,24.3
19,26,27
50
14
31
36
34
54
20
16
35
29
21
220
37,38
21.3,22.3,23
14,31,33
46
17
30
38
34
44
17
18
33
30
17
221
35,38
20.3,22.3,26
21,30
54
13,15
35
39
37
48
17
17
36
27
23
222
34,36,37
21.3,22.3,23
14,30
47
14
28
37
33
46
17
19
35
33
20
223
41
22,23.3
18,30,32
55
13
33
41
37
47
16
18
40
29
19
224
38,39
20.3,23.3,28
19,28,29
54
14,15
33
36
37
50
16
18
34
29
22
225
35,37
20.3,21.3,22
15,24,26
54
14,16
31
39
38
50
17
18
38
31
20
226
33,39
20.3,24.3,26
19,26,31
54
13
34
35
36
53
17
17
37
26
21
227
35,39
19.3,24
17,29,30
51
13
35
36
36
50
21
18
38
28
18
228
38,40
21.3,22.3,26
21,27,34
50
14
33
39
36
47
18
19
39
30
22
229
36,39
19.3,22.3,25
15,26,29
51
14,16
32
37
35
47
18
17
39
29
22
230
37
21.3,23.3,25
13,27
52
13,15
31
37
36
45
20
18
37
28
22
231
36,38
20.3,22.3,23
14,31.2,32
44
13,15
31
40
36
46
16
16
33
29
20
232
37,40
19.3,24.3,25
15,26,29
47
12,16
27
42
37
51
16
17
36
29
22
233
36,37
20.3,24.3,25
13,27,29
51
13,16
32
37
36
46
18
18
37
28
22
234
34
23.3,27
15,25
52
15
31
38
39
48
18
20
36
30
19
235
37,38
18.3,24.3,25
18,29,31
49
13,15
27
39
35
48
19
15
37
29
18
236
37,38
21,23.3
14,27,29
53
13
33
39
36
49
16
19
38
30
21
237
36,37
22.3,25
16,28,29
54
13,14
34
35
36
45
19
19
39
28
18
238
36,38
19.3,22.3,26
15,26,27
53
14,15
31
39
37
46
15
20
35
29
21
239
38,40
20,21,22.3
17,27,32
42
13
31
35
34
51
20
17
36
28
22
240
35,37
20.3,21,23.3
15,29
54
15
35
41
36
52
18
17
33
30
21
Sample
DYF387S1
DYF399S1
DYF403S1a
DYF403S1b
DYF404S1
DYS449
DYS518
DYS526b
DYS547
DYS570
DYS576
DYS612
DYS626
DYS627
241
36,38
20.3,24
22,27,34
50
14,16
32
38
36
47
18
19
39
28
22
242
36,39
19.3,23,24.3
19,31
53
14,15
33
37
37
48
16
20
36
29
22
243
37,38
19.3,22.3,24
18,28,33
46
14,15
28
42
36
49
19
17
39
28
23
244
37,38
22.3,23.3,24,25
20,27,28
53
15
30
37.2
36
47
23
18
34
29
23
245
36,37
19.3,20.3,24
18,25,26
52
14,16
29
41
36
48
18
17
39
30
20
246
36,38
20.3,21.3,25
14,26
51
13,16
30
38
38
50
17
19
35
29
22
247
38,40
21.3,22.3,25
19,27,33
50
13,15
31
39
34
48
18
19
39
29
21
248
35,37
20.3,23.3,25
17,28,31
52
14,15
33
32
38
49
17
16
38
26
17.2
249
36,38
17.3,22.3,24
17,30,31
54
15
31
36
37
51
19
18
37
28
21
250
36,38
22.3,23
16,25,29
50
14,16
29
42
39
50
19
18
36
32
21
251
35,39
21.3,23.3,24
18,31
52
14,16
32
36
37
50
17
16
36
30
20
252
35,38
19.3,22.3,25
16,29,30
51
13
32
37
36
50
18
19
39
28
18
a,b
Samples labeled with the same letter have the same haplotype.