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Y Chromosomal STR Locus DYS385 in Azoospermic and Fertile Men from the Aegean Region of Turkey: Is there any Forensic Relevance? Balkan J Med Genet 2008. [DOI: 10.2478/v10034-008-0027-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Nonaka I, Minaguchi K, Takezaki N. Y-chromosomal binary haplogroups in the Japanese population and their relationship to 16 Y-STR polymorphisms. Ann Hum Genet 2007; 71:480-95. [PMID: 17274803 DOI: 10.1111/j.1469-1809.2006.00343.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated Y chromosomal binary and STR polymorphisms in 263 unrelated male individuals from the Japanese population and further examined the relationships between the two separate types of data. Using 47 biallelic markers we distinguished 20 haplogroups, four of which (D2b1/-022457, O3/-002611*, O3/-LINE1 del, and O3/-021354*) were newly defined in this study. Most haplogroups in the Japanese population are found in one of the three major clades, C, D, or O. Among these, two major lineages, D2b and O2b, account for 66% of Japanese Y chromosomes. Haplotype diversity of binary markers was calculated at 86.3%. The addition of 16 Y-STR markers increased the number of haplotypes to 225, yielding a haplotype diversity of 99.40%. A comparison of binary haplogroups and Y-STR type revealed a close association between certain binary haplogroups and Y-STR allelic or conformational differences, such as those at the DXYS156Y, DYS390m, DYS392, DYS437, DYS438 and DYS388 loci. Based on our data on the relationships between binary and STR polymorphisms, we estimated the binary haplogroups of individuals from STR haplotypes and frequencies of binary haplogroups in other Japanese, Korean and Taiwanese Han populations. The present data will enable researchers to connect data from binary haplogrouping in anthropological studies and Y-STR typing in forensic studies in East Asian populations, especially those in and around Japan.
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Affiliation(s)
- I Nonaka
- Department of Forensic Odontology, Tokyo Dental College, 1-2-2 Masago, Mihama-ku, Chiba City, 261-0011, Japan
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Tang JSW, Wong HY, Syn CKC, Tan-Siew WF, Chow ST, Budowle B. Population study of 11 Y-chromosomal STR loci in Singapore Chinese. Forensic Sci Int 2006; 158:65-71. [PMID: 15919167 DOI: 10.1016/j.forsciint.2005.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2004] [Revised: 03/05/2005] [Accepted: 04/01/2005] [Indexed: 10/25/2022]
Abstract
In this study of 212 unrelated Singapore Chinese males, allelic frequencies and gene diversities of 11 Y-chromosome specific STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS438 and DYS439) were established. A total of 184 haplotypes were observed in the 212 individuals studied, of which 165 (89.67%) were unique. The most common haplotype was observed in five (2.35%) individuals. The overall haplotype diversity for the 11 Y-STR loci was 99.81%, and the discrimination capacity was 86.79%.
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Affiliation(s)
- June Sheau Wei Tang
- DNA Profiling Laboratory, Centre for Forensic Science, Health Sciences Authority, 11 Outram Road, 169078 Singapore, Singapore.
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Hwang JH, Lee H, Lee YA, Han MS, Kim W, Jin I, Cho NS. Haplotypes for 12 Y-chromosomal STR loci in a Korean population (the central region). Forensic Sci Int 2006; 168:73-84. [PMID: 16517109 DOI: 10.1016/j.forsciint.2006.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Revised: 01/23/2006] [Accepted: 01/24/2006] [Indexed: 10/24/2022]
Abstract
Haplotypes and allele frequencies of 12 STR loci included in the PowerPlex Y system (DYS391, DYS389I, DYS439, DYS389II, DYS438, DYS437, DYS19, DYS392, DYS393, DYS390, and DYS385a/b) were obtained from a sample of 569 unrelated individuals living in the central region of Korea. A total of 473 haplotypes were observed in the 569 individuals studied, of which 426 (90.06%) were unique. The overall haplotype diversity for the 12 Y-STR loci was 0.9985, and the discrimination capacity was 0.8313. In DYS439, we found a new intermediate-sized allele that added an A at base 3 upstream from the repeat region's first GATA motif. The allele was named 11 (U3Ains) according to its sequence structure.
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Affiliation(s)
- Jung Ho Hwang
- Department of Forensic Medicine, Central District Office, National Institute of Scientific Investigation, Daejeon 305-348, Republic of Korea
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Kwak KD, Suren G, Tundewrentsen S, Jin HJ, Hong SB, Han MS, Kim W. Y-chromosome STR haplotype profiling in the Mongolian population. Leg Med (Tokyo) 2006; 8:58-61. [PMID: 16221555 DOI: 10.1016/j.legalmed.2005.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Revised: 08/06/2005] [Accepted: 08/19/2005] [Indexed: 11/22/2022]
Abstract
Eleven Y-chromosome STR loci (DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, two DYS385 loci and DXYS156Y) were analyzed in 92 randomly chosen males from Mongolia. Allelic frequencies and gene diversity for each Y-STR locus and haplotype diversity were determined to evaluate their usefulness in forensic casework. A total of 84 different haplotypes were identified, among which 77 (83.7%) were individual-specific. The most frequent haplotype surveyed here was found in three individuals (3.6%), of which the 'minimal haplotype' (excluding DYS388 and DXYS156Y) was not found in the worldwide Y-STR haplotype reference database (YHRD) available at .
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Affiliation(s)
- Kyoung Don Kwak
- Department of Biological Sciences, Dankook University, Cheonan 330-714, South Korea
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Kwak KD, Jin HJ, Shin DJ, Kim JM, Roewer L, Krawczak M, Tyler-Smith C, Kim W. Y-chromosomal STR haplotypes and their applications to forensic and population studies in east Asia. Int J Legal Med 2005; 119:195-201. [PMID: 15856270 DOI: 10.1007/s00414-004-0518-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2004] [Accepted: 12/08/2004] [Indexed: 11/26/2022]
Abstract
We have analyzed 11 Y-STR loci (DYS19, the two DYS385 loci, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DXYS156Y) in 700 males from ten ethnic groups in east Asia in order to evaluate their usefulness for forensic and population genetic studies. A total of 644 different haplotypes were identified, among which 603 (86.14%) were individual-specific. The haplotype diversity averaged over all populations was 0.9997; using only the nine Y-STRs comprising the "minimal haplotype" (excluding DYS388 and DXYS156Y) it was 0.9996, a value similar to that found in 1924 samples from other Asian populations (0.9996; Lessig et al. Legal Medicine 5(2003) 160-163), and slightly higher than in European populations (0.9976; n=11,610; Roewer et al. For Sci International (2001) 118:103-111). All of the individual east Asian populations examined here had high haplotype diversity (> or =0.997), except for the Mongolians (0.992) and Manchurians (0.960). The most frequent haplotype identified by the nine markers was present at only 1% (7/700). Population comparisons based on Phi(ST) or rho genetic distance measures revealed clustering according to the traditional northeast-southeast distinction, but with exceptions. For example, the Yunnan population from southern China lay among the northern populations, possibly reflecting recent migration, while the Korean population, traditionally considered northern, lay at the boundary between northern and southern populations. An admixture estimate suggested 55(51-59)% northern, 45(41-49)% southern contribution to the Koreans, illustrating the complexity of the genetic history of this region.
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Affiliation(s)
- Kyoung Don Kwak
- Department of Biological Sciences, Dankook University, Cheonan, 330-714, South Korea
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Dobashi Y, Kido A, Fujitani N, Susukida R, Hara M, Oya M. Y-chromosome STR haplotypes in a Bangladeshi population. Leg Med (Tokyo) 2005; 7:122-6. [PMID: 15708337 DOI: 10.1016/j.legalmed.2004.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Revised: 08/11/2004] [Accepted: 08/11/2004] [Indexed: 10/26/2022]
Abstract
Allele frequencies and haplotypes for 10 Y-chromosome STR loci, DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS438 and DY439, were determined in 72 unrelated Bangladeshi males using Y-PLEX5 and Y-PLEX6 Amplification Kits. This population demonstrated 71 haplotypes, of which 70 were unique. The haplotype diversity calculated from the 10 Y-STR loci was 0.9996 and the discrimination capacity was 0.9861.
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Affiliation(s)
- Yuji Dobashi
- Scientific Crime Detection Laboratory, Yamanashi Prefectual Police Headquaters, Yamanashi 406-0036, Japan
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Butler JM, Schoske R. Duplication of DYS19 flanking regions in other parts of the Y chromosome. Int J Legal Med 2004; 118:178-83. [PMID: 15069570 DOI: 10.1007/s00414-004-0436-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2003] [Accepted: 03/02/2004] [Indexed: 10/26/2022]
Abstract
During the testing of alternative primers for the Y chromosome short tandem repeat marker DYS19, a duplicated region of the Y chromosome was discovered. The duplicated sequence is contained within GenBank accession AC006335 and has a high degree of homology with the DYS19 flanking region (GenBank accession AC017019) but without the polymorphic TAGA repeat. Bioinformatic approaches have been taken to try and understand the implications of this homolog to enable improved primer design for DYS19. Sequence alignments and careful placement of primers in order to obtain specific amplification of the DYS19 locus are discussed in the context of all previously published primer sets. Since the DYS19 locus is part of the widely used minimal haplotype, its robust amplification is highly desirable particularly in multiplex reactions. The discovery of this duplicated region of the Y chromosome shows the value of newly available human genome sequence information for assay design and the importance of using sequence queries and alignments in the primer design process.
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Affiliation(s)
- John M Butler
- Biotechnology Division, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 8311, Gaithersburg, MD 20899, USA.
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Tie J, Wang X, Suzuki Y, Tsukamoto S, Oshida S. Polymorphisms of six Y-chromosome STRs in a Chinese population. Leg Med (Tokyo) 2004; 6:41-6. [PMID: 15177072 DOI: 10.1016/j.legalmed.2003.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2003] [Revised: 07/08/2003] [Accepted: 09/24/2003] [Indexed: 11/19/2022]
Abstract
The polymorphic short tandem repeat (STR) loci of six Y-chromosome markers were investigated in 112 unrelated Chinese males using a multiplex polymerase chain reaction (PCR). Allele and haplotype frequencies for the Y-specific STR loci DYS19, DYS385, DYS389II, DYS390, DYS391 and DYS393 were analyzed by the Y-PLEX 6 Kit. The commonest allele for each locus was: DYS19, allele 15; DYS385, allele 12; DYS389II, allele 28; DYS390, allele 23; DYS391, 10; and DYS393, allele 12. Gene diversity value was calculated from the allelic frequency for each locus. The DYS385 locus proved to be highly polymorphic (0.890), DYS391 showed the lowest value (0.489), and the other loci showed values ranging from 0.646 to 0.897. A total of 99 haplotypes were observed in six Y-specific STR loci, the haplotype diversity was raised to 0.999. The results revealed that a set of six Y-specific STR loci were able to discriminate most of the male individuals in the Chinese population.
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Affiliation(s)
- Jian Tie
- Department of Legal Medicine, Nihon University School of Medicine, 30-1, Oyaguchi-Kamimachi, Itabashi-Ku, Tokyo 173-8610, Japan.
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Jin HJ, Kwak KD, Hammer MF, Nakahori Y, Shinka T, Lee JW, Jin F, Jia X, Tyler-Smith C, Kim W. Y-chromosomal DNA haplogroups and their implications for the dual origins of the Koreans. Hum Genet 2003; 114:27-35. [PMID: 14505036 DOI: 10.1007/s00439-003-1019-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2003] [Accepted: 07/31/2003] [Indexed: 10/26/2022]
Abstract
We have analyzed eight Y-chromosomal binary markers (YAP, RPS4Y(711), M9, M175, LINE1, SRY(+465), 47z, and M95) and three Y-STR markers (DYS390, DYS391, and DYS393) in 738 males from 11 ethnic groups in east Asia in order to study the male lineage history of Korea. Haplogroup DE-YAP was found at a high frequency only in Japan but was also present at low frequencies in northeast Asia, including 2.5% in Korea, suggesting a northern origin for these chromosomes. Haplogroup C-RPS4Y(711) was present in Korea and Manchuria at moderate frequencies: higher than in populations from southeast Asia, but lower than those in the northeast, which may imply a northern Asian expansion of these lineages, perhaps from Mongolia or Siberia. The major Y-chromosomal expansions in east Asia were those of haplogroup O-M175 (and its sublineages). This haplogroup is likely to have originated in southern east Asia and subsequently expanded to all of east Asia. The moderate frequency of one sublineage in the Koreans, haplogroup O-LINE1 (12.5%), could be a result of interaction with Chinese populations. The age of another sublineage, haplogroup O-SRY(+465), and Y-STR haplotype diversity provide evidence for relatively recent male migration, originally from China, through Korea into Japan. In conclusion, the distribution pattern of Y-chromosomal haplogroups reveals the complex origin of the Koreans, resulting from genetic contributions involving the northern Asian settlement and range expansions mostly from southern-to-northern China.
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Affiliation(s)
- Han-Jun Jin
- Department of Biological Sciences, Dankook University, 330-714 Cheonan, Korea
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