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Ge J, Crysup B, Peters D, Franco R, Liu M, Wang X, Huang M, Budowle B. MPKin-YSTR: Interpretation of Y chromosome STR haplotypes for missing persons cases. Electrophoresis 2023; 44:1080-1087. [PMID: 37016479 DOI: 10.1002/elps.202200225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 03/22/2023] [Accepted: 03/30/2023] [Indexed: 04/06/2023]
Abstract
Y chromosome Short Tandem Repeat (STR) haplotypes have been used in assisting forensic investigations primarily for identification and male lineage determination. The current SWGDAM interpretation guidelines for Y-STR typing provide helpful guidance on those purposes but do not address the issue of kinship analysis with Y-STR haplotypes. Because of the high mutation rate of Y-STRs, there are complex missing person cases in which inconsistent Y-STR haplotypes between true paternal lineage relatives will arise and cases with two or more male references in the same lineage and yet differ in their haplotypes. Therefore, more useful methods are needed for interpreting the Y-STR haplotype data. Computational methods and interpretation guidelines have been developed specifically addressing this issue, either using a mismatch-based counting method or a pedigree likelihood ratio method. In this study, a software program, MPKin-YSTR, was developed by implementing those more sophisticated methods. This software should be able to improve the interpretation of complex cases with Y-STR haplotype evidence. Thus, more biological evidence will be interpreted, which in turn will result in more investigation leads to help solve crimes.
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Affiliation(s)
- Jianye Ge
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Benjamin Crysup
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Dixie Peters
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Romy Franco
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Muyi Liu
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Xuewen Wang
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Meng Huang
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
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2
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Woerner AE, Hewitt FC, Gardner MW, Freitas MA, Schulte KQ, LeSassier DS, Baniasad M, Reed AJ, Powals ME, Smith AR, Albright NC, Ludolph BC, Zhang L, Allen LW, Weber K, Budowle B. An algorithm for random match probability calculation from peptide sequences. Forensic Sci Int Genet 2020; 47:102295. [DOI: 10.1016/j.fsigen.2020.102295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/23/2020] [Accepted: 03/25/2020] [Indexed: 02/01/2023]
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3
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Song F, Xie M, Xie B, Wang S, Liao M, Luo H. Genetic diversity and phylogenetic analysis of 29 Y-STR loci in the Tibetan population from Sichuan Province, Southwest China. Int J Legal Med 2019; 134:513-516. [DOI: 10.1007/s00414-019-02043-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/08/2019] [Indexed: 11/28/2022]
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4
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Fan H, Wang X, Chen H, Long R, Liang A, Li W, Chen J, Wang W, Qu Y, Song T, Zhang P, Deng J. The evaluation of forensic characteristics and the phylogenetic analysis of the Ong Be language-speaking population based on Y-STR. Forensic Sci Int Genet 2018; 37:e6-e11. [DOI: 10.1016/j.fsigen.2018.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/24/2018] [Accepted: 09/24/2018] [Indexed: 11/25/2022]
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5
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Liu C, Yang X, Chen L, Liu H, Liu C. Haplotype analysis of the polymorphic 24 Y-STR markers in six ethnic populations from China. AUST J FORENSIC SCI 2018. [DOI: 10.1080/00450618.2017.1281347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Changhui Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University , Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute , Guangzhou, People’s Republic of China
| | - Xingyi Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University , Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute , Guangzhou, People’s Republic of China
| | - Ling Chen
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University , Guangzhou, People’s Republic of China
| | - Hong Liu
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute , Guangzhou, People’s Republic of China
| | - Chao Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University , Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute , Guangzhou, People’s Republic of China
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Zhou Y, Shao C, Li L, Zhang Y, Liu B, Yang Q, Tang Q, Li S, Xie J. Genetic analysis of 29 Y-STR loci in the Chinese Han population from Shanghai. Forensic Sci Int Genet 2018; 32:e1-e4. [DOI: 10.1016/j.fsigen.2017.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 09/27/2017] [Accepted: 11/09/2017] [Indexed: 10/18/2022]
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7
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Wang Z, Du W, He G, Liu J, Hou Y. Forensic characteristics and phylogenetic analysis of Hubei Han population in central China using 17 Y-STR loci. Forensic Sci Int Genet 2017; 29:e4-e8. [DOI: 10.1016/j.fsigen.2017.04.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 03/12/2017] [Accepted: 04/17/2017] [Indexed: 11/25/2022]
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8
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Haplotype analysis of the polymorphic 40 Y-STR markers in Chinese populations. Forensic Sci Int Genet 2015; 19:255-262. [DOI: 10.1016/j.fsigen.2015.08.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/19/2015] [Accepted: 08/22/2015] [Indexed: 10/23/2022]
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9
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Wang Y, Liu C, Zhang CC, Li R, LI Y, Ou XL, Sun HY. Analysis of 17 Y-STR loci haplotype and Y-chromosome haplogroup distribution in five Chinese ethnic groups. Electrophoresis 2015; 36:2546-52. [DOI: 10.1002/elps.201500089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 06/12/2015] [Accepted: 06/12/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Ying Wang
- Department of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
| | - Chao Liu
- Guangdong Provincial Key Laboratory of Forensic Genetics; Guangzhou P. R. China
- Guangzhou Institute of Criminal Science and Technology; Guangzhou P. R. China
| | - Chu-chu Zhang
- Department of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
| | - Ran Li
- Department of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
| | - Yue LI
- Guangdong Provincial Key Laboratory of Forensic Genetics; Guangzhou P. R. China
- Guangzhou Institute of Criminal Science and Technology; Guangzhou P. R. China
| | - Xue-ling Ou
- Department of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
| | - Hong-yu Sun
- Department of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
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Forensic typing of short tandem repeat markers on the X and Y chromosomes. Forensic Sci Int Genet 2015; 18:140-51. [DOI: 10.1016/j.fsigen.2015.03.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/22/2015] [Accepted: 03/24/2015] [Indexed: 11/17/2022]
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Zhang GQ, Yang SY, Niu LL, Guo DW. Structure and polymorphism of 16 novel Y-STRs in Chinese Han population. GENETICS AND MOLECULAR RESEARCH 2012; 11:4487-500. [PMID: 23096913 DOI: 10.4238/2012.october.11.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Y-chromosome short tandem repeats (Y-STRs) are useful tools for identifying paternity origin and male-female mixed samples because of their male-specificity, haploid inheritance and relatively simplicity. We focused on novel Y-STRs deposited in the human Genome database from DYS708 to DYS726. We typed 16 male-specific Y-STRs from males of a Chinese Han population residing in Shanxi Province (north China), including DYS708-719, DYS721-723, and DYS726, but failed in typing DYS720, DYS724 and DYS725. The 16 Y-STRs, with mean gene diversity (GD) of 0.79, included three trinucleotide Y-STRs (711, 718, 719), nine tetranucleotide STRs (708, 709, 710, 712, 713, 715, 722, 723, 726) and four pentanucleotide repeat STRs (714, 716, 717, 721). DYS712, consisting of eight alleles, was the most informative STR in our population, with a GD of 0.843. The STRs were classified as simple STRs and complex STRs, according to their structures based on sequencing. Genetic indexes, including allele frequencies, haplotype distribution and male-specificity were determined. The Y-STRs, especially those male-specific, tetra- and penta-nucleotide, with only one copy on Y-chromosome, and relative simple structures, such as DYS709, DYS714, DYS715, DYS716, DYS718, DYS719, and DYS726, were suggested for the future forensic DNA analysis, while DYS724 and DYS725 were not recommended for their multi-copy distribution. The population data provided putative Y-STRs for future genetic and forensic applications.
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Affiliation(s)
- G Q Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi, P.R. China.
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Cockerton S, McManus K, Buckleton J. Interpreting lineage markers in view of subpopulation effects. Forensic Sci Int Genet 2012; 6:393-7. [DOI: 10.1016/j.fsigen.2011.04.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 04/05/2011] [Accepted: 04/30/2011] [Indexed: 11/16/2022]
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Ballantyne KN, Keerl V, Wollstein A, Choi Y, Zuniga SB, Ralf A, Vermeulen M, de Knijff P, Kayser M. A new future of forensic Y-chromosome analysis: Rapidly mutating Y-STRs for differentiating male relatives and paternal lineages. Forensic Sci Int Genet 2012; 6:208-18. [DOI: 10.1016/j.fsigen.2011.04.017] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2011] [Revised: 04/08/2011] [Accepted: 04/27/2011] [Indexed: 10/18/2022]
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Martínez-González LJ, Saiz M, Álvarez-Cubero MJ, Gómez-Martín A, Álvarez JC, Martínez-Labarga C, Lorente JA. Distribution of Y chromosomal STRs loci in Mayan and Mestizo populations from Guatemala. Forensic Sci Int Genet 2012; 6:136-42. [DOI: 10.1016/j.fsigen.2011.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 02/18/2011] [Accepted: 04/02/2011] [Indexed: 11/28/2022]
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15
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Buckleton JS, Krawczak M, Weir BS. The interpretation of lineage markers in forensic DNA testing. Forensic Sci Int Genet 2011; 5:78-83. [PMID: 21397888 DOI: 10.1016/j.fsigen.2011.01.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Mitochondrial DNA (mtDNA) and the non-recombining portion of the Y-chromosome are inherited matrilinealy and patrilinealy, respectively, and without recombination. Collectively they are termed 'lineage markers'. Lineage markers may be used in forensic testing of an item, such as a hair from a crime scene, against a hypothesised source, or in relationship testing. An estimate of the evidential weight of a match is usually provided by a count of the occurrence in some database of the mtDNA or Y-STR haplotype under consideration. When the factual statement of a count in the database is applied to a case, issues of relevance of the database and sampling uncertainty may arise. In this paper, we re-examine the issues of sampling uncertainty, the relevance of the database, and the combination of autosomal and lineage marker evidence. We also review the recent developments by C.H. Brenner.
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Y-STR loci diversity in native Alaskan populations. Int J Legal Med 2011; 125:559-63. [DOI: 10.1007/s00414-011-0568-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 02/14/2011] [Indexed: 10/18/2022]
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17
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Ge J, Budowle B, Planz JV, Eisenberg AJ, Ballantyne J, Chakraborty R. US forensic Y-chromosome short tandem repeats database. Leg Med (Tokyo) 2010; 12:289-95. [DOI: 10.1016/j.legalmed.2010.07.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 07/26/2010] [Accepted: 07/29/2010] [Indexed: 10/19/2022]
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18
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Gayden T, Chennakrishnaiah S, La Salvia J, Jimenez S, Regueiro M, Maloney T, Persad PJ, Bukhari A, Perez A, Stojkovic O, Herrera RJ. Y-STR diversity in the Himalayas. Int J Legal Med 2010; 125:367-75. [PMID: 20652582 DOI: 10.1007/s00414-010-0485-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 06/28/2010] [Indexed: 11/24/2022]
Abstract
Linguistic and ethnic diversity throughout the Himalayas suggests that this mountain range played an important role in shaping the genetic landscapes of the region. Previous Y-chromosome work revealed that the Himalayas acted as a biased bidirectional barrier to gene flow across the cordillera. In the present study, 17 Y-chromosomal short tandem repeat (Y-STR) loci included in the AmpFlSTR® Yfiler kit were analyzed in 344 unrelated males from three Nepalese populations (Tamang, Newar, and Kathmandu) and a general collection from Tibet. The latter displays the highest haplotype diversity (0.9990) followed by Kathmandu (0.9977), Newar (0.9570), and Tamang (0.9545). The overall haplotype diversity for the Himalayan populations at 17 Y-STR loci was 0.9973, and the corresponding values for the extended (11 loci) and minimal (nine loci) haplotypes were 0.9955 and 0.9942, respectively. No Y-STR profiles are shared across the four Himalayan collections at the 17-, 11-, and nine-locus resolutions considered, indicating a lack of recent gene flow among them. Phylogenetic analyses support our previous findings that Kathmandu, and to some extent Newar, received significant genetic influence from India while Tamang and Tibet exhibit limited or no gene flow from the subcontinent. A median-joining network of haplogroup O3a3c-M134 based on 15 Y-STR loci from our four Himalayan populations suggests either a male founder effect in Tamang, possibly from Tibet, or a recent bottleneck following their arrival south of the Himalayas from Tibet leading to their highly reduced Y single-nucleotide polymorphism and Y-STR diversity. The genetic uniqueness of the four Himalayan populations examined in this study merits the creation of separate databases for individual identification, parentage analysis, and population genetic studies.
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Affiliation(s)
- Tenzin Gayden
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
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Ge J, Budowle B, Chakraborty R. Interpreting Y chromosome STR haplotype mixture. Leg Med (Tokyo) 2010; 12:137-43. [DOI: 10.1016/j.legalmed.2010.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 11/09/2009] [Accepted: 02/03/2010] [Indexed: 10/19/2022]
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20
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Palha TJBF, Rodrigues EMR, dos Santos SEB. Y-STR haplotypes of Native American populations from the Brazilian Amazon region. Forensic Sci Int Genet 2010; 4:e121-3. [PMID: 20457062 DOI: 10.1016/j.fsigen.2009.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 10/22/2009] [Accepted: 12/13/2009] [Indexed: 10/19/2022]
Abstract
The allele and haplotype frequencies of nine Y-STRs (DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393, DYS385 I/II) were determined in a sample of six native tribes from the Brazilian Amazon (Tiriyó, Awa-Guajá, Waiãpi, Urubu-Kaapor, Zoé and Parakanã). Forty-eight different haplotypes were identified, 28 of which unique. Five haplotypes are very frequent and were shared by over 10 individuals. The estimated haplotype diversity (0.9114) was very low compared to other geographic groups, including Africans, Europeans and Asians.
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