1
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Chiao A, Ge J. Determining lineages between individuals with high-density mitochondrial and Y-chromosomal single-nucleotide polymorphisms. Electrophoresis 2024; 45:843-851. [PMID: 38010138 DOI: 10.1002/elps.202300142] [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: 06/29/2023] [Revised: 10/19/2023] [Accepted: 11/12/2023] [Indexed: 11/29/2023]
Abstract
Genetic genealogy has been more frequently used in forensic investigations in identifying criminals. However, the current genetic genealogy applications usually do not consider lineage markers (including both Y and mitochondrial deoxyribonucleic acid (DNA)), which is probably because not all distant relatives share the same lineage markers. In addition, there is no study to show how to use lineage markers and what methods or thresholds should be applied in genetic genealogy. In this study, we developed a method to quickly determine if two single-nucleotide polymorphism (SNP) profiles are from the same paternal or material lineages by using a mismatch frequency of the SNPs in Y-chromosomal or mitochondrial DNA. For both Y and mitochondrial SNPs, profile pairs from the same or different lineages can be decided with high accuracies (i.e., 0.380% or 0.157% error rates with Y and mitochondrial DNA, respectively). With kinship coefficient filtering based on autosomal SNPs, the accuracies of determining maternal and paternal lineage can be further improved (i.e., 0.120% or 0.057% error rates with Y and mitochondrial DNA, respectively, using a threshold of kinship coefficient >0). This study shows that lineage markers can be very powerful tools with high accuracies to determine lineages, which could help solve cases and reduce costs for genetic genealogy investigations.
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Affiliation(s)
- Austin Chiao
- 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
| | - 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
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Eskandarion MR, Tabrizi AA, Shirkoohi R, Raoofian R, Naji M, Pazhoomand R, Salari H, Samadirad B, Sabouri A, Zohour MM, Namazi H, Farhadi P, Baratieh Z, Sayyari M, Dadgarmoghaddam M, Safdarian E, Nikbakht A, Golshan F, Baybordi F, Madhaji E, ShohodiFar S, Tabasi M, Mohebbi R. Haplotype diversity of 17 Y-STR in the Iranian population. BMC Genomics 2024; 25:332. [PMID: 38566001 PMCID: PMC10986111 DOI: 10.1186/s12864-024-10217-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
The current study aimed to evaluate Y chromosome haplotypes obtained from 1353 unrelated Iranian males using the AmpFlSTRTM YfilerTM kit; 1353 out of the 1353 identified haplotypes were unique. The haplotype diversity (HD) and discriminating capacity (DC) values were 1.00000 and 0.997, respectively. Analysis of genetic distance was performed using molecular variance (AMOVA) and multidimensional scaling plots (MDS), revealing a statistically significant difference between the study population and previous data reported for other Iranian populations and other neighboring countries. The present findings are likely to be useful for forensic casework analyses and kinship investigations.
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Affiliation(s)
- Mohammad Reza Eskandarion
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
- Cancer Research Institute, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Reza Shirkoohi
- Cancer Research Institute, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Raoofian
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Masume Naji
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Reza Pazhoomand
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Hooman Salari
- Plant Genetics and Production, Razi University, Kermanshah, Iran
| | - Bahram Samadirad
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Alireza Sabouri
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | | | - Hadi Namazi
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Pegah Farhadi
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Zohre Baratieh
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Minoo Sayyari
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Maliheh Dadgarmoghaddam
- Department of Community Medicine, School of Medicine, Mashhad University of Medical Science, Mashhad, Iran
| | - Esmat Safdarian
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Afrooz Nikbakht
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Farnaz Golshan
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Fatemeh Baybordi
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Elham Madhaji
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Shadi ShohodiFar
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Mohsen Tabasi
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
- Department of Molecular Biology, Pasteur Institute of Iran, Pasteur Ave, Tehran, Iran
| | - Ramezan Mohebbi
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
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Puch-Solis R, Pope S, Tully G. Considerations on the application of a mutation model for Y-STR interpretation. Sci Justice 2024; 64:180-192. [PMID: 38431375 DOI: 10.1016/j.scijus.2024.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/08/2024] [Accepted: 01/14/2024] [Indexed: 03/05/2024]
Abstract
If Y-STR profiling is to be more effective in criminal casework, the methods used to evaluate evidential weight require improvement. Many forensic scientists assign an evidential weight by estimating the number of times a Y-STR profile obtained from a questioned sample has been observed in YHRD datasets. More sophisticated models have been suggested but not yet implemented into routine casework, e.g. Andersen & Balding [1]. Mutation is inherent to STR meiosis (or inheritance) and is encountered in practice. We evaluated a mutation model that can be incorporated into a method for assigning evidential weight to Y-STR profiles, an essential part of bringing any method into practice. Since an important part of implementation to casework is communication, the article is written in an accessible format for practitioners as well as statisticians. The mutation component within the MUTEA model by Willems et al. [2] incorporates the potential for multistep mutations and a tendency for alleles to revert towards a central length, reflecting observed mutation data, e.g. [3]. We have estimated the parameters in this model and in a simplified symmetric version of this model, using sequence data from father/son pairs [4] and deep-rooted pedigrees [5]. Both datasets contain multistep mutations, which may have an effect on models based on simulations [1]. We introduce Beta-Binomial and Beta-Geometric conjugate analyses for estimating rate and step parameters for the mutation models presented here, which require only summations and multiplications. We proved mathematically that the parameters can be estimated independently. We show the importance of reporting the variability of the parameters and not only a point estimate. The parameters can be easily incorporated into statistical models, and updated sequentially as more data becomes available. We recommend fuller publication of data to enable the development and evaluation of a wider range of mutation models.
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Affiliation(s)
- Roberto Puch-Solis
- Leverhulme Research Centre for Forensic Science, University of Dundee, Dundee DD1 4HN, United Kingdom.
| | - Susan Pope
- Principal Forensic Services, 34 Southborough Road, Bromley, Kent BR1 2EB, United Kingdom
| | - Gillian Tully
- King's Forensics, King's College London, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom
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Mut P, Bertoni B, Sapiro R, Hidalgo PC, Torres A, Azambuja C, Sans M. Insights into the Y chromosome human diversity in Uruguay. Am J Hum Biol 2023; 35:e23963. [PMID: 37493343 DOI: 10.1002/ajhb.23963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/26/2023] [Accepted: 07/04/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND With regard to the origin of its population and microevolutionary processes, Uruguay exhibits distinctive features that distinguish it from other countries in Latin America, while at the same time sharing several similarities. In this article, we will focus on the variability of paternal genetic lineages in two geographical regions with different histories that can be considered as examples of distinct populations for the continent. In general terms, the genetic diversity is a result of different demographic processes related to the American conquest and colonisation. These resulted in distinct ancestral components which vary geographical and depend on the distribution by sex within these components. In Uruguay, native maternal haplogroups are significantly more frequent in the North. Although there are several studies about the geneticvariability of Uruguay, little is known about male genetic lineages. AIMS The aim of this work is to present an updated study of the male genetic variability of the Uruguayan population. METHODS We analyzed 13 biallelic markers and 27 STRs located in the male-specific region of the Y chromosome for 157 males: 98 from the capital, Montevideo, and 59 from Tacuarembó. RESULTS Almost all haplogroups found in both locations are European (99% and 93.2% respectively). One Sub-Saharan African haplogroup was found in Montevideo (1%) and 2 in Tacuarembó (3%), while Native haplogroups were found only in Tacuarembó, evidencing a strong sex-biased admixture. By crossing genetic and genealogical information we could relate European haplogroups with different waves and times of migrations. DISCUSSION Network analysis indicated a very diverse male population, suggesting that European migrants came from heterogeneous geographic locations and in different waves. Tacuarembó has closer population affinities with Iberian populations while Montevideo is more diverse. Male population expansion expansion, can be explained by the large number of migrants that arrived during the XIX century and the first half of the XX century. CONCLUSIONS The Uruguayan male gene pool is the result of several migration waves with diverse origins, with strong sex-biased admixture that can be explained by the European migration, the violence against the indigenous males, and the segregation of the Africansadmixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation of hte Africans.
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Affiliation(s)
- Patricia Mut
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, UdelaR, Montevideo, Uruguay
| | - Bernardo Bertoni
- Departamento de Genética, Facultad de Medicina, UdelaR, Montevideo, Uruguay
| | - Rossana Sapiro
- Departamento de Histología y Embriología, Facultad de Medicina, UdelaR, Montevideo, Uruguay
| | - Pedro C Hidalgo
- Polo de Desarrollo Universitario Diversidad Genética Humana, Centro Universitario Noreste, Tacuarembó, Uruguay
| | | | | | - Mónica Sans
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, UdelaR, Montevideo, Uruguay
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Fu D, Adnan A, Yao J, Aldayan NH, Wang CC, Hongyi C. Unraveling the paternal genetic structure and forensic traits of the Hui population in Liaoning Province, China using Y-chromosome analysis. BMC Genomics 2023; 24:691. [PMID: 37978341 PMCID: PMC10655310 DOI: 10.1186/s12864-023-09774-8] [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: 04/01/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
The Hui people are the second-largest ethnic minority in China, and they are distributed throughout the country. A previous study explored the paternal genetic structure of the Hui population in nine different regions of China, but it overlooked the Liaoning province. In this study, we examined the paternal genetic makeup and forensic traits of the Hui population in Liaoning province by analyzing 157 Y-chromosome single nucleotide polymorphisms (Y-SNPs) and 26 short tandem repeats (Y-STRs). We successfully genotyped 282 unrelated male individuals from the Hui population of Liaoning province using the SNaPshot® single base extension assay and Goldeneye™ Y26 system kit (PEOPLESPOT R&D, Beijing, China). The results revealed high haplotypic diversity (0.9998) and identified 46 terminal haplogroups for the Hui population. Additional analyses, such as heat maps, principal component analysis (PCA), genetic distance (FST), Multidimensional scaling (MDS) analysis, and median-joining network (MJ) analysis, showed that the Hui population could be classified into three groups: Northwest Hui populations (NWH), including Liaoning, Xinjiang, Qinghai, Gansu, Ningxia, Shaanxi, and Henan; Hui populations from Sichuan and Shandong (SSH); and Yunnan Hui populations (YNH). Pairwise genetic distance (Rst) comparisons with other Chinese populations revealed that the Hui population displayed genetic affinity with the Han population. The comprehensive understanding of the Hui population in Liaoning province, explored by Y-SNPs and Y-STRs, can be utilized to interpret their genetic structure and enhance the accuracy of forensic databases.
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Affiliation(s)
- Dazhi Fu
- First Affiliated Hospital of China Medical University, 155 Heping District, Shenyang, 110001, China
| | - Atif Adnan
- Department of Forensic Sciences, Collage of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Saudi Arabia.
| | - Jun Yao
- Department of Forensic Biology and Genetics, School of Forensic Medicine, China Medical University, Shenyang, 110001, China
| | - Noura H Aldayan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Ibn Abdulaziz University, Al-Kharj, 16273, Saudi Arabia
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, Fujian, People's Republic of China.
| | - Cao Hongyi
- First Affiliated Hospital of China Medical University, 155 Heping District, Shenyang, 110001, China.
- Department of Pathology, School of Basic Medical Sciences, China Medical University, Shenyang, 110001, China.
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6
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Liu Z, Long G, Lang Y, Liu D, Zhang B, Yu S, Guo F. Sequence-based mutation patterns at 41 Y chromosomal STRs in 2 548 father-son pairs. Forensic Sci Res 2023; 8:152-162. [PMID: 37621447 PMCID: PMC10445670 DOI: 10.1093/fsr/owad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/16/2023] [Indexed: 08/26/2023] Open
Abstract
A total of 2 548 unrelated healthy father-son pairs from a Northern Han Chinese population were genotyped at 41 Y chromosomal short tandem repeat (Y-STRs) including DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS444, DYS447, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS522, DYS549, DYS533, DYS557, DYS570, DYS576, DYS593, DYS596, DYS627, DYS635, DYS643, DYS645, Y-GATA-H4, DYF387S1a/b, DYF404S1a/b, DYS385a/b, and DYS527a/b. In 2 548 father samples, 2 387 unique haplotypes were detected with the haplotype diversity and discrimination capacity values of 0.999 956 608 and 0.96 741 007. The average gene diversity (GD) value was 0.6934 with a range from 0.1051 at DYS645 to 0.9657 at DYS385a/b. When comparing alleles at 24 overlapped Y-STRs between the ForenSeq™ deoxyribonucleic acid (DNA) Signature Prep Kit on the MiSeq FGx® Forensic Genomics System and the Goldeneye® DNA ID Y Plus Kit on the Applied Biosystems™ 3730 DNA Analyzer from 308 father samples in mutational pairs, 258 alleles were detected by massively parallel sequencing (MPS) typing including 156 length-based alleles that could be obtained by capillary electrophoresis (CE) typing, 95 repeat region (RR) variant alleles and seven flanking region variant alleles. Hereof, we found 16 novel RR variant alleles and firstly identified two SNPs (rs2016239814 at DYS19 and rs2089968964 at DYS448) and one 4-bp deletion (rs2053269960 at DYS439) that had been validated by the Database of Short Genetic Variation. Sanger sequencing or MPS was employed to confirm 356 mutations from 104 468 allele transfers generated from CE, where 96.63% resulted in one-step mutations, 2.25% in two-step, and 1.12% in multi-step, and the overall ratio of repeat gains versus losses was balanced (173 gains vs. 183 losses). In 308 father-son pairs, 268 pairs occurred mutations at a single locus, 33 pairs at two loci, six pairs at three loci, and one pair at four loci. The average Y-STR mutation rate at 41 Y-STRs was ⁓3.4 × 10-3 (95% confidence intervals: 3.1 × 10-3-3.8 × 10-3). The mutation rates at DYS576 and DYS627 were higher than 1 × 10-2 in Northern Han Chinese, whilst the mutation rates at DYF387S1a/b, DYF404S1a/b, DYS449, DYS518, and DYS570 were lower than initially defined. In this study, the classical molecular factors (the longer STR region, the more complex motif and the order father) were confirmed to drive Y-STR mutation rates increased, but the length of repeat unit did not conform to the convention. Lastly, the interactive graphical and installable StatsY was developed to facilitate forensic scientists to automatically calculate allele and haplotype frequencies, forensic parameters, and mutation rates at Y-STRs. Key points 308 of 2 548 father-son pairs from Northern Han Chinese occurred at least one mutation(s) across 41 Y-STRs.Sanger sequencing or MPS was employed to confirm those mutations generated from CE.The longer STR region, the more complex motif and the order father drove Y-STR mutation rates increased.StatsY was developed to calculate allele and haplotype frequencies, forensic parameters and mutation rates at Y-STRs.
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Affiliation(s)
- Ze Liu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, China
| | - Guannan Long
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, China
| | - Yubo Lang
- School of Public Security Information Technology and Intelligence, Criminal Investigation Police University of China, Shenyang, China
| | - Dahua Liu
- Department of Forensic Medicine, Jinzhou Medical University, Jinzhou, China
| | - Biao Zhang
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, China
| | - Shaobo Yu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, China
| | - Fei Guo
- School of Forensic Science and Technology, Criminal Investigation Police University of China, Shenyang, China
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Stephens KM, Barta R, Fleming K, Perez JC, Wu SF, Snedecor J, Holt CL, LaRue B, Budowle B. Developmental validation of the ForenSeq MainstAY kit, MiSeq FGx sequencing system and ForenSeq Universal Analysis Software. Forensic Sci Int Genet 2023; 64:102851. [PMID: 36907074 DOI: 10.1016/j.fsigen.2023.102851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
For human identification purposes, forensic genetics has primarily relied upon a core set of autosomal (and to a lesser extent Y chromosome) short tandem repeat (STR) markers that are enriched by amplification using the polymerase chain reaction (PCR) that are subsequently separated and detected using capillary electrophoresis (CE). While STR typing conducted in this manner is well-developed and robust, advances in molecular biology that have occurred over the last 15 years, in particular massively parallel sequencing (MPS) [1-7], offer certain advantages as compared to CE-based typing. First and foremost is the high throughput capacity of MPS. Current bench top high throughput sequencers enable larger batteries of markers to be multiplexed and multiple samples to be sequenced simultaneously (e.g., millions to billions of nucleotides can be sequenced in one run). Second, compared to the length-based CE approach, sequencing STRs increases discrimination power, enhances sensitivity of detection, reduces noise due to instrumentation, and improves mixture interpretation [4,8-23]. Third, since detection of STRs is based on sequence and not fluorescence, amplicons can be designed that are shorter in length and of similar lengths among loci, where possible, which can improve amplification efficiency and analysis of degraded samples. Lastly, MPS offers a single format approach that can be applied to analysis of a wide variety of genetic markers of forensic interest (e.g., STRs, mitochondrial DNA, single nucleotide polymorphisms, insertion/deletions). These features make MPS a desirable technology for casework [14,15,24,25-48]. The developmental validation of the ForenSeq MainstAY library preparation kit with the MiSeq FGx Sequencing System and ForenSeq Universal Software is reported here to assist with validation of this MPS system for casework [49]. The results show that the system is sensitive, accurate and precise, specific, and performs well with mixtures and mock case-type samples.
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Affiliation(s)
| | - Richelle Barta
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Keenan Fleming
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | | | - Shan-Fu Wu
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - June Snedecor
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Cydne L Holt
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Bobby LaRue
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Bruce Budowle
- University of Helsinki, Department of Forensic Medicine, Haartmaninkatu 8, P.O. Box 63, Helsinki 00014, Finland
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Large-scale pedigree analysis highlights rapidly mutating Y-chromosomal short tandem repeats for differentiating patrilineal relatives and predicting their degrees of consanguinity. Hum Genet 2023; 142:145-160. [PMID: 36190543 PMCID: PMC9839801 DOI: 10.1007/s00439-022-02493-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/26/2022] [Indexed: 01/18/2023]
Abstract
Rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) were suggested for differentiating patrilineally related men as relevant in forensic genetics, anthropological genetics, and genetic genealogy. Empirical data are available for closely related males, while differentiation rates for more distant relatives are scarce. Available RM Y-STR mutation rate estimates are typically based on father-son pair data, while pedigree-based studies for efficient analysis requiring less samples are rare. Here, we present a large-scale pedigree analysis in 9379 pairs of men separated by 1-34 meioses on 30 Y-STRs with increased mutation rates including all known RM Y-STRs (RMplex). For comparison, part of the samples were genotyped at 25 standard Y-STRs mostly with moderate mutation rates (Yfiler Plus). For 43 of the 49 Y-STRs analyzed, pedigree-based mutation rates were similar to previous father-son based estimates, while for six markers significant differences were observed. Male relative differentiation rates from the 30 RMplex Y-STRs were 43%, 84%, 96%, 99%, and 100% for relatives separated by one, four, six, nine, and twelve meioses, respectively, which largely exceeded rates obtained by 25 standard Y-STRs. Machine learning based models for predicting the degree of patrilineal consanguinity yielded accurate and reasonably precise predictions when using RM Y-STRs. Fully matching haplotypes resulted in a 95% confidence interval of 1-6 meioses with RMplex compared to 1-25 with Yfiler Plus. Our comprehensive pedigree study demonstrates the value of RM Y-STRs for differentiating male relatives of various types, in many cases achieving individual identification, thereby overcoming the largest limitation of forensic Y-chromosome analysis.
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Thompson JM. Amplification of Extracted DNA and Direct Amplification with the PowerPlex ® Y23 System. Methods Mol Biol 2023; 2685:227-239. [PMID: 37439985 DOI: 10.1007/978-1-0716-3295-6_14] [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] [Indexed: 07/14/2023]
Abstract
The PowerPlex® Y23 System offered by Promega Corporation contains 23 Y-STR loci (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS481, DYS533, DYS549, DYS570, DYS576, DYS635, DYS643, and Y-GATA-H4). The PowerPlex® Y23 System is designed to amplify DNA from purified extracts as well as direct amplification from substrates used to collect database samples (e.g., swabs and storage cards). Protocols are provided for full-volume reactions for DNA extracts, as well as half-volume reactions for direct amplifications from different substrates.
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10
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Development and validation of a new multiplex for upgrading Y-STRs population databases from 12 to 23 markers and its forensic casework application. Sci Rep 2022; 12:21734. [PMID: 36526709 PMCID: PMC9758231 DOI: 10.1038/s41598-022-25785-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Y chromosomal short tandem repeats (Y-STRs) are used in forensic investigations as a useful complementary tool to autosomal markers. The ongoing development of new kits with an increasing number of markers makes it necessary to update populations typed in the Y-STR Haplotype Reference Database to reach at least 23 Y-STRs. A novel Y-STR multiplex panel was developed to offer a cost-efficient alternative to update Y-STR haplotypes from 12 to 23 loci. This panel includes the eleven markers, DYS448, DYS456, DYS458, DYS635, Y-GATA H4, DYS576, DYS481, DYS549, DYS533, DYS570 and DYS643, as well as DYS385a/b for traceability purpose. Developmental validation of this panel was conducted following the recommendations of the Scientific Working Group on DNA Analysis Methods (SWGDAM), showing high sensitivity, tolerance to common inhibitors as well as high species specificity. It was efficient for degraded DNA samples and for detection of male mixtures. When applying it for extending the current data of the Ibiza population, both the discrimination capacity and the haplotype diversity increased from 0.5952 to 0.9048 and from 0.9808 to 0.9977, respectively. Together, the study demonstrates the suitability of this panel in forensic casework.
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Soldati G, Turrina S, De Leo D. Forensic assessment on the application of a virtual pool of 30 Y-STRs. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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12
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Zhou Y, Cui W, Wu B, Zhu B. Development and validation of a new multiplex Y-STR panel designed to increase the power of discrimination. Electrophoresis 2022; 43:1899-1910. [PMID: 35856743 DOI: 10.1002/elps.202100313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/28/2022] [Accepted: 07/08/2022] [Indexed: 12/14/2022]
Abstract
In an attempt to increase the discrimination capacity (DC) and reduce the adventitious match probability, a 6-dye multiplex Y-chromosomal short tandem repeat (Y-STR) panel named Y34plex was constructed that combined 25 Y-chromosomal markers (DYS456, DYS627, DYS390, DYS570, DYS635, DYS385a/b, DYS448, DYS437, DYS533, DYS449, DYS481, DYS392, DYS391, DYS389I, DYS460, YGATAH4, DYS438, DYS389II, DYS19, DYS458, DYF387S1a/b, DYS439, DYS393, DYS576, and DYS518) in widely used commercial kits, with nine highly polymorphic Y-STR loci (DYS557, DYS527a/b, DYS593, DYS444, DYS596, DYS643, DYS447, DYS549, and DYS645). The Y34plex is a promising type system to distinguish both unrelated and related male individuals due to the incorporation of rapidly mutated Y-STR loci. A validation study of the Y34plex was performed and followed the guidelines of the Scientific Working Group on DNA analysis methods. Results show that full Y-STR profiles were obtained from male/female DNA mixtures with 125 pg of male DNA in the presence of 50 ng of female DNA. The ability to tolerate polymerase chain reaction inhibitors commonly contained in forensic casework samples demonstrated the applicability and robustness of the Y34plex. Compared with the Yfiler Plus kit, the novel panel showed an increased power of discrimination in Chinese Wuxi Han population (n = 434). The overall haplotype diversity of the Y34plex was 0.999606, whereas DC value was 0.956221, which is suitable for use on forensic paternal investigation.
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Affiliation(s)
- Yongsong Zhou
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, P. R. China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Buling Wu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, P. R. China
| | - Bofeng Zhu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, P. R. China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, P. R. China
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13
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de Knijff P. On the Forensic Use of Y-Chromosome Polymorphisms. Genes (Basel) 2022; 13:genes13050898. [PMID: 35627283 PMCID: PMC9141910 DOI: 10.3390/genes13050898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 12/26/2022] Open
Abstract
Nowadays, the use of Y-chromosome polymorphisms forms an essential part of many forensic DNA investigations. However, this was not always the case. Only since 1992 have we seen that some forensic scientists started to have an interest in this chromosome. In this review, I will sketch a brief history focusing on the forensic use of Y-chromosome polymorphisms. Before describing the various applications of short-tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) on the Y-chromosome, I will discuss a few often ignored aspects influencing proper use and interpretation of Y-chromosome information: (i) genotyping Y-SNPs and Y-STRs, (ii) Y-STR haplotypes shared identical by state (IBS) or identical by descent (IBD), and (iii) Y-haplotype database frequencies.
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Affiliation(s)
- Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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14
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Y-SNP Haplogroup Hierarchy Finder: a web tool for Y-SNP haplogroup assignment. J Hum Genet 2022; 67:487-493. [DOI: 10.1038/s10038-022-01033-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/03/2022] [Accepted: 03/09/2022] [Indexed: 11/08/2022]
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15
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A multi-dimensional evaluation of the 'NIST 1032' sample set across four forensic Y-STR multiplexes. Forensic Sci Int Genet 2022; 57:102655. [PMID: 35007854 PMCID: PMC9901497 DOI: 10.1016/j.fsigen.2021.102655] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/09/2021] [Accepted: 12/12/2021] [Indexed: 02/08/2023]
Abstract
This manuscript reports Y-chromosomal short tandem repeat (Y-STR) haplotypes for 1032 male U.S. population samples across 30 Y-STR loci characterized by three capillary electrophoresis (CE) length-based kits (PowerPlex Y23 System, Yfiler Plus PCR Amplification Kit, and Investigator Argus Y-28 QS Kit) and one sequence-based kit (ForenSeq DNA Signature Prep Kit): DYF387S1, DYS19, DYS385 a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS505, DYS518, DYS522, DYS533, DYS549, DYS570, DYS576, DYS612, DYS627, DYS635, DYS643, and Y-GATA-H4. The length-based Y-STR haplotypes include six loci that are not reported in the sequence-based kit (DYS393, DYS449, DYS456, DYS458, DYS518, and DYS627), whereas three loci included in the sequence-based kit are not present in length-based kits (DYS505, DYS522, and DYS612). For the latter, a custom multiplex was used to generate CE length-based data, allowing 1032 samples to be evaluated for concordance across the 30 Y-STR loci included in these four commercial Y-STR typing kits. Discordances between typing methods were analyzed further to assess underlying causes such as primer binding site mutations and flanking region insertions/deletions. Allele-level frequency and statistical information is provided for sequenced loci, excluding the multi-copy loci DYF387S1 and DYS385 a/b, for which locus-specific haplotype-level frequencies are provided instead. The resulting data reveals the degree of information gained through sequencing: 88% of sequenced Y-STR loci contain additional sequence-based alleles compared to length-based data, with the DYS389II locus containing the most additional alleles (51) observed by sequencing. Despite these allelic increases, only minimal improvement was observed in haplotype resolution by sequence, with all four commercial kits providing a similar ability to differentiate length-based haplotypes in this sample set. Finally, a subset of 369 male samples were compared to their corresponding additionally sequenced father samples, revealing the sequence basis for the 50 length-based changes observed, and no additional sequence-based mutations. GenBank accession numbers are reported for each unique sequence, and associated records are available in the STRSeq Y-Chromosomal STR Loci National Center for Biotechnology Information (NCBI) BioProject, accession PRJNA380347. Haplotype data is updated in the Y-STR Haplotype Reference Database (YHRD) for the 'NIST 1032' data set to now achieve the level of maximal haplotype of YHRD. All supplementary files including revisions to previously published Y-STR data are available in the NIST Public Data Repository: U.S. population data for human identification markers, DOI 10.18434/t4/1500024.
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16
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Improving the regional Y-STR haplotype resolution utilizing haplogroup-determining Y-SNPs and the application of machine learning in Y-SNP haplogroup prediction in a forensic Y-STR database: A pilot study on male Chinese Yunnan Zhaoyang Han population. Forensic Sci Int Genet 2021; 57:102659. [PMID: 35007855 DOI: 10.1016/j.fsigen.2021.102659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 12/14/2021] [Accepted: 12/27/2021] [Indexed: 11/23/2022]
Abstract
Improving the resolution of the current widely used Y-chromosomal short tandem repeat (Y-STR) dataset is of great importance for forensic investigators, and the current approach is limited, except for the addition of more Y-STR loci. In this research, a regional Y-DNA database was investigated to improve the Y-STR haplotype resolution utilizing a Y-SNP Pedigree Tagging System that includes 24 Y-chromosomal single nucleotide polymorphism (Y-SNP) loci. This pilot study was conducted in the Chinese Yunnan Zhaoyang Han population, and 3473 unrelated male individuals were enrolled. Based on data on the male haplogroups under different panels, the matched or near-matching (NM) Y-STR haplotype pairs from different haplogroups indicated the critical roles of haplogroups in improving the regional Y-STR haplotype resolution. A classic median-joining network analysis was performed using Y-STR or Y-STR/Y-SNP data to reconstruct population substructures, which revealed the ability of Y-SNPs to correct misclassifications from Y-STRs. Additionally, population substructures were reconstructed using multiple unsupervised or supervised dimensionality reduction methods, which indicated the potential of Y-STR haplotypes in predicting Y-SNP haplogroups. Haplogroup prediction models were built based on nine publicly accessible machine-learning (ML) approaches. The results showed that the best prediction accuracy score could reach 99.71% for major haplogroups and 98.54% for detailed haplogroups. Potential influences on prediction accuracy were assessed by adjusting the Y-STR locus numbers, selecting Y-STR loci with various mutabilities, and performing data processing. ML-based predictors generally presented a better prediction accuracy than two available predictors (Nevgen and EA-YPredictor). Three tree models were developed based on the Yfiler Plus panel with unprocessed input data, which showed their strong generalization ability in classifying various Chinese Han subgroups (validation dataset). In conclusion, this study revealed the significance and application prospects of Y-SNP haplogroups in improving regional Y-STR databases. Y-SNP haplogroups can be used to discriminate NM Y-STR haplotype pairs, and it is important for forensic Y-STR databases to develop haplogroup prediction tools to improve the accuracy of biogeographic ancestry inferences.
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17
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Lemos MP, Nandi V, Dragavon J, Fleming I, Krishnan K, Musuruana M, Kramer M, Glantz H, Andrasik M, Coombs RW, McElrath MJ, Tieu HV. HIV-1 Nucleic Acids Identify Rectal HIV Exposures in Self-Collected Rectal Swabs, Whereas Y-Chromosome Single Tandem Repeat Mixtures Are Not Reliable Biomarkers of Condomless Receptive Anal Intercourse. J Acquir Immune Defic Syndr 2021; 88:138-148. [PMID: 34506358 PMCID: PMC8439546 DOI: 10.1097/qai.0000000000002748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 05/10/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND To focus interventions, biomarkers of HIV-1 exposure could help in identifying subpopulations at highest risk of acquisition. We assessed whether Y-chromosome single tandem repeat (YSTR) mixtures obtained from rectal swabs could serve as a biomarker of condomless receptive anal intercourse (CRAI) among men who have sex with men and transgender women and evaluated the feasibility of detecting HIV-1 virions to assess exposures. METHODS Twenty-nine sexually active HIV-seronegative men who have sex with men and one transgender woman from New York City answered on-site and mobile app sexual behavior questionnaires. They were randomized to collecting self-administered rectal swabs every morning or after receptive anal intercourse (RAI). YSTR profiles were assessed from blood sample and swabs; HIV-1 exposure was measured by conducting quantitative polymerase chain reaction in swabs. RESULTS After 2 months, the daily mobile survey had 135%-201% more instances of anal sex acts and 170%-193% more RAI than on-site surveys. Daily mobile reporting had 11%-35% less CRAI events than those reported on-site (Pdaily = 0.001; Pper-sex = 0.047). The daily swabbing arm reported less RAI (P < 0.001) and CRAI (P < 0.038) and had 2.95 lower odds of detecting YSTR mixtures (P = 0.021) than the per-sex-event arm. Surprisingly, YSTR detection was not significantly modified by report of bowel movements and lubricant, enema, or condom use. No participant became HIV-1 infected, yet HIV-1 total nucleic acids were detected in 6 independent episodes of CRAI in 2 participants taking pre-exposure prophylaxis. CONCLUSIONS YSTR mixtures demonstrated 80% specificity but only 30% sensitivity as a biomarker of CRAI in self-collected rectal swabs. However, detection of HIV-1 exposures in self-collected swabs may help in identifying those needing further HIV risk reduction strategies.
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Affiliation(s)
- Maria P. Lemos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Vijay Nandi
- Laboratory of Data Analytics, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY
| | - Joan Dragavon
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Ira Fleming
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Keertana Krishnan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Martin Musuruana
- Laboratory of Data Analytics, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY
| | - Madeline Kramer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hayley Glantz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michele Andrasik
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert W. Coombs
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
- Department of Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Hong-Van Tieu
- Laboratory of Infectious Disease Prevention, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY
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18
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Smith G, Mathews D, Sander-Effron S, Requesens D, Turan N, Scheinfeldt L. Microsatellite Markers in Biobanking: A New Multiplexed Assay. Biopreserv Biobank 2021; 19:438-443. [PMID: 34468209 PMCID: PMC8665806 DOI: 10.1089/bio.2021.0042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microsatellites, or MSATs, offer a fast and cost-effective way for biobanks to establish a biospecimen genetic profile. Importantly, this genetic profile can be used to authenticate multiple submissions derived from the same individual as well as biospecimens derived from the same original sample submission over time. While the Certificate of Confidentiality provided by the National Institutes of Health offers some meaningful protection to prevent the disclosure of potentially identifiable information to entities within the United States, we consider, in this study, the potential to offer additional protection to participants who choose to donate to biobanks by minimizing the use of forensic Combined DNA Index System (CODIS) MSAT markers in biobanking. To this end, we report the design and validation of a new multiplexed MSAT assay that does not include CODIS markers for use in biobanking operations and quality control management.
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Affiliation(s)
- Gretchen Smith
- Coriell Institute for Medical Research, Camden, New Jersey, USA
| | - Debra Mathews
- Berman Institute of Bioethics, Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Deborah Requesens
- Coriell Institute for Medical Research, Camden, New Jersey, USA.,The Orphan Disease Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Nahid Turan
- Coriell Institute for Medical Research, Camden, New Jersey, USA
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19
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Adnan A, Rakha A, Nazir S, Alghafri R, Hassan Q, Wang CC, Lu J. Forensic features and genetic legacy of the Baloch population of Pakistan and the Hazara population across Durand line revealed by Y-chromosomal STRs. Int J Legal Med 2021; 135:1777-1784. [PMID: 33818632 DOI: 10.1007/s00414-021-02591-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/26/2021] [Indexed: 11/27/2022]
Abstract
The Hazara population across Durand line has experienced extensive interaction with Central Asian and East Asian populations. Hazara individuals have typical Mongolian facial appearances and they called themselves descendants of Genghis Khan's army. The people who speak the Balochi language are called Baloch. Previously, a worldwide analysis of Y-chromosomal haplotype diversity for rapidly mutating (RM) Y-STRs and with PowerPlex Y23 System (Promega Corporation Madison, USA) kit was created with collaborative efforts, but Baloch and Hazara population from Pakistan and Hazara population from Afghanistan were missing. In the current study, Yfiler Plus PCR Amplification Kit loci were examined in 260 unrelated Hazara individuals from Afghanistan, 153 Hazara individuals, and 111 Balochi individuals from Baluchistan Pakistan. For the Hazara population from Afghanistan and Pakistan overall, 380 different haplotypes were observed on these 27 Y-STR loci, gene diversities ranged from 0.51288 (DYS389I) to 0.9257 (DYF387S1), and haplotype diversity was 0.9992. For the Baloch population, every individual was unique at 27 Y-STR loci; gene diversity ranged from 0.5718 (DYS460) to 0.9371(DYF387S1). Twelve haplotypes were shared between 178 individuals, while only two haplotypes among these twelve were shared between 87 individuals in Hazara populations. Rst and Fst pairwise genetic distance analyses, multidimensional scaling plot, neighbor-joining tree, linear discriminatory analysis, and median-joining network were performed, which shed light on the history of Hazara and Baloch populations. The results of our study showed that the Yfiler Plus PCR Amplification Kit marker set provided substantially stronger discriminatory power in the Baloch population of Pakistan and the Hazara population across the Durand line.
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Affiliation(s)
- Atif Adnan
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, Liaoning, 110122, People's Republic of China.
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences Lahore, Lahore, 54600, Pakistan
| | - Shahid Nazir
- Department of Forensic Sciences, University of Health Sciences Lahore, Lahore, 54600, Pakistan
| | - Rashed Alghafri
- General Department of Forensic Sciences and Criminology, Dubai Police General Head Quarters, Dubai, United Arab Emirates
| | - Qudsia Hassan
- Department of Forensic Medicine & Toxicology, Ziauddin Medical College Clifton, Karachi, Pakistan
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Jie Lu
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, Liaoning, 110122, People's Republic of China.
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20
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Zhao Y, Yao X, Li Y, Chen C, Guo D, Jiao Z, Yang Z, Yu Z, Ma W, Zhang Q. Developmental validation of the Microreader™ Y Prime Plus ID System: An advanced Y-STR 38-plex system for forensic applications. Sci Justice 2021; 61:260-270. [PMID: 33985674 DOI: 10.1016/j.scijus.2021.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 12/24/2020] [Accepted: 01/23/2021] [Indexed: 11/16/2022]
Abstract
Y-STR is widely used in sexual assaults and familial searches of suspects. Here, we reported a novel 38-plex STR genotyping system designed for forensic applications. Microreader™ Y Prime Plus ID System (YPP) amplifies 38 loci in one reaction, including 29 loci from commonly used Yfiler® Plus PCR Amplification Kit & PowerPlex® Y23 System (DYS393, DYS570, DYS19, DYS392, DYS549, Y GATA H4, DYS460, DYS458, DYS481, DYS635, DYS448, DYS533, DYS449, DYS456, DYS389I, DYS390, DYS389Ⅱ, DYS438, DYS391, DYS439, DYS437, DYS385a/b, DYS643, DYS518, DYS576, DYF387S1a/b, and DYS627), 6 commonly used loci for the Y-STR database (DYS444, DYS447, DYS596, DYF404a/b, DYS527a/b, DYS557) and one Y-indel specific for the Chinese population. YPP is designed for different types of samples, such as blood card and swabs. In this work, YPP was validated following SWGDAM guidelines (2016) and guidelines from Ministry of Public Security of the People's Republic of China, including PCR-based, sensitivity, accuracy and precision, mixture, stability and inhibitor, and species specificity. The results indicate that the Microreader™ Y Prime Plus ID System is a powerful identification kit designed for forensic databases.
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Affiliation(s)
- Yi Zhao
- Forensic Science Service of the Beijing Public Security Bureau, 100192 Beijing, China
| | - Xiaojuan Yao
- Forensic Science Service of the Xinzhou Public Security Bureau, 034000 Shanxi, China
| | - Yifan Li
- Beijing Microread Genetics, 100045 Beijing, China
| | - Chengjian Chen
- Forensic Science Service of the Beijing Public Security Bureau, 100192 Beijing, China
| | - Dan Guo
- Beijing Microread Genetics, 100045 Beijing, China
| | - Zhangping Jiao
- Forensic Science Service of the Beijing Public Security Bureau, 100192 Beijing, China
| | - Zhipan Yang
- Beijing Microread Genetics, 100045 Beijing, China
| | - Zailiang Yu
- Beijing Microread Genetics, 100045 Beijing, China.
| | - Wanshan Ma
- Suzhou Microread Genetics, 215163 Suzhou, China.
| | - Qingxia Zhang
- Forensic Science Service of the Beijing Public Security Bureau, 100192 Beijing, China.
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21
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Ahmad SF, Singchat W, Jehangir M, Suntronpong A, Panthum T, Malaivijitnond S, Srikulnath K. Dark Matter of Primate Genomes: Satellite DNA Repeats and Their Evolutionary Dynamics. Cells 2020; 9:E2714. [PMID: 33352976 PMCID: PMC7767330 DOI: 10.3390/cells9122714] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
A substantial portion of the primate genome is composed of non-coding regions, so-called "dark matter", which includes an abundance of tandemly repeated sequences called satellite DNA. Collectively known as the satellitome, this genomic component offers exciting evolutionary insights into aspects of primate genome biology that raise new questions and challenge existing paradigms. A complete human reference genome was recently reported with telomere-to-telomere human X chromosome assembly that resolved hundreds of dark regions, encompassing a 3.1 Mb centromeric satellite array that had not been identified previously. With the recent exponential increase in the availability of primate genomes, and the development of modern genomic and bioinformatics tools, extensive growth in our knowledge concerning the structure, function, and evolution of satellite elements is expected. The current state of knowledge on this topic is summarized, highlighting various types of primate-specific satellite repeats to compare their proportions across diverse lineages. Inter- and intraspecific variation of satellite repeats in the primate genome are reviewed. The functional significance of these sequences is discussed by describing how the transcriptional activity of satellite repeats can affect gene expression during different cellular processes. Sex-linked satellites are outlined, together with their respective genomic organization. Mechanisms are proposed whereby satellite repeats might have emerged as novel sequences during different evolutionary phases. Finally, the main challenges that hinder the detection of satellite DNA are outlined and an overview of the latest methodologies to address technological limitations is presented.
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Affiliation(s)
- Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Maryam Jehangir
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo 18618-689, Brazil
| | - Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Suchinda Malaivijitnond
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand;
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand;
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
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22
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Population genetic data of 4 multicopy Y-STR markers in Chinese. Leg Med (Tokyo) 2020; 47:101788. [PMID: 32950019 DOI: 10.1016/j.legalmed.2020.101788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/31/2020] [Accepted: 09/07/2020] [Indexed: 11/23/2022]
Abstract
Novel Y chromosomal STR (Y-STR) markers have been continuously discovered during the past decades, promoting the widely application of Y-STRs in the area of forensic science. Here, four multicopy Y-STR markers were focused, including DYF383S1, DYF409S1, DYF411S1 and DYF371, which are rarely reported in China and differ in the number of copies on Y chromosome. Characterization of the markers was performed in population of Hunan province, China, based on sequence analysis. Allele nomenclature and allelic ladder were then developed to avoid the disunity of typing standard. To evaluate their forensic performance, gene diversity of the four loci was investigated in 548 unrelated male individuals from Hunan population. The number of haplotype was analyzed by both conservative (C-type) and expanded approach (E-type) for markers containing more than 2 copies. As detected, there were 7, 9, 13 alleles and 15, 22, 23 haplotypes for DYF383S1, DYF409S1 and DYF411S1, respectively. Thirty-two C-types and 56 E-types were found in DYF371, indicating the highest haplotype diversity (HD) among all tested loci (0.871 and 0.888 for C-type and E-type, respectively). Two other Y-STRs (DYF409S1, DYF411S1) also showed high haplotype diversity (>0.8) in the population. Combining the four loci, discrimination capacity reached 0.505 (C-type) or 0.533 (E-type), and the total HD values exceeded 0.991. The results inferred great potential of the multicopy markers to improve the resolution of paternal identification in China population.
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Zhou Y, Yao Y, Liu B, Yang Q, Zhou Z, Shao C, Li S, Tang Q, Xie J. Characterizing Y-STRs in the Evaluation of Population Differentiation Using the Mean of Allele Frequency Difference between Populations. Genes (Basel) 2020; 11:genes11050566. [PMID: 32438591 PMCID: PMC7290957 DOI: 10.3390/genes11050566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/18/2020] [Accepted: 05/13/2020] [Indexed: 01/17/2023] Open
Abstract
Y-chromosomal short tandem repeats (Y-STRs) are widely used in human research for the evaluation of population substructure or population differentiation. Previous studies show that several haplotype sets can be used for the evaluation of population differentiation. However, little is known about whether each Y-STR in these sets performs well during this procedure. In this study, a total of 20,927 haplotypes of a Yfiler Plus set were collected from 41 global populations. Different configurations were observed in multidimensional scaling (MDS) plots based on pairwise genetic distances evaluated using a Yfiler set and a Yfiler Plus set, respectively. Subsequently, 23 single-copy Y-STRs were characterized in the evaluation of population differentiation using the mean of allele frequency difference (mAFD) between populations. Our results indicated that DYS392 had the largest mAFD value (0.3802) and YGATAH4 had the smallest value (0.1845). On the whole, larger pairwise genetic distances could be obtained using the set with the top fifteen markers from these 23 single-copy Y-STRs, and clear clustering or separation of populations could be observed in the MDS plot in comparison with those using the set with the minimum fifteen markers. In conclusion, the mAFD value is reliable to characterize Y-STRs for efficiency in the evaluation of population differentiation.
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Affiliation(s)
- Yuxiang Zhou
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; (Y.Z.); (Y.Y.); (B.L.); (Q.Y.); (Z.Z.); (C.S.)
| | - Yining Yao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; (Y.Z.); (Y.Y.); (B.L.); (Q.Y.); (Z.Z.); (C.S.)
| | - Baonian Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; (Y.Z.); (Y.Y.); (B.L.); (Q.Y.); (Z.Z.); (C.S.)
| | - Qinrui Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; (Y.Z.); (Y.Y.); (B.L.); (Q.Y.); (Z.Z.); (C.S.)
| | - Zhihan Zhou
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; (Y.Z.); (Y.Y.); (B.L.); (Q.Y.); (Z.Z.); (C.S.)
| | - Chengchen Shao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; (Y.Z.); (Y.Y.); (B.L.); (Q.Y.); (Z.Z.); (C.S.)
| | - Shilin Li
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China;
| | - Qiqun Tang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China;
| | - Jianhui Xie
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; (Y.Z.); (Y.Y.); (B.L.); (Q.Y.); (Z.Z.); (C.S.)
- Correspondence: ; Tel.: +86-21-54237569
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Genetic structure of Mataco-Guaycurú speakers from Argentina and the extent of their genetic admixture with neighbouring urban populations. Sci Rep 2019; 9:17559. [PMID: 31772268 PMCID: PMC6879578 DOI: 10.1038/s41598-019-54146-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/08/2019] [Indexed: 11/25/2022] Open
Abstract
Argentina hosts more than 30 Native American groups, who are widely distributed throughout the country. Mataco-Guaycurú speakers settled in the ecoregion of Gran Chaco and represent 26.7% of the extant aboriginal population of the country. To further investigate the genetic attributes of these speakers, we focused our attention on four aboriginal groups, namely, Wichí, Toba, Pilagá and Mocoví, belonging to the Mataco-Guaycurú linguistic group. Our main goal was to evaluate the interrelationships among the groups and the relationships of these groups with admixed urban populations and to assess correspondences between molecular analysis and historical information. A total of 890 samples (282 Native Americans and 608 inhabitants of admixed urban areas) were analysed. Genetic information was gathered from 15 autosomal STRs, 17 Y-STRs, entire mtDNA control region sequences, 24 AIM-SNPs and 46 AIM-DIPs. Native American signatures were detected in 97.9% of mtDNA lineages, 89.1% of Y-haplotypes and 90.3% to 96.9% of autosomal markers. Wichí exhibited the genetic composition with the largest Native American contribution among the groups and a weak signal of gene flow. This work provides extended genetic information of potential interest in the fields of molecular anthropology and forensic genetics.
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Oldoni F, Podini D. Forensic molecular biomarkers for mixture analysis. Forensic Sci Int Genet 2019; 41:107-119. [DOI: 10.1016/j.fsigen.2019.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/06/2019] [Accepted: 04/17/2019] [Indexed: 01/10/2023]
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Roewer L. Y‐chromosome short tandem repeats in forensics—Sexing, profiling, and matching male DNA. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/wfs2.1336] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences Corporate Member of Freie Universität Berlin, Humboldt‐Universität zu Berlin and Berlin Institute of Health, Charité‐Universitätsmedizin Berlin 13353 Berlin Germany
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Novel Y-chromosome short tandem repeat sequence variation for loci DYS710, DYS518, DYS385, DYS644, DYS612, DYS626, DYS504, DYS481, DYS447 and DYS449. Int J Legal Med 2019; 133:1681-1689. [PMID: 30982129 DOI: 10.1007/s00414-019-02056-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/29/2019] [Indexed: 10/27/2022]
Abstract
In forensic casework, Y-chromosome short tandem repeats (Y-STRs) are essential for differentiating between unrelated males and resolving the male component of admixed biological evidence. While the majority of Y-STRs are adequate for discriminating between different paternal lineages, rapidly mutating Y-STRs are necessary for improving discrimination between males within populations of low Y-chromosome diversity and between paternal relatives. Alternatively, sequencing of Y-STRs may also improve the discrimination between isometric Y-STR alleles by identifying variation in the repeat unit pattern arrangements and by identifying SNPs in the flanking region or within the STR repeat unit itself. In this report, a total of 153 DNA sequences are presented across the Y-STR loci DYS710, DYS518, DYS385, DYS644, DYS612, DYS626, DYS504, DYS481, DYS447 and DYS449. A total of 94 Y-STR sequences provided herein are reported for the first time, of which 37 sequences represent alleles showing size homoplasy, 34 sequences of known alleles for which sequence data has been unavailable and a total of 23 novel allele sequences across loci DYS644, DS447, DYS710 and DYS504. This study further encountered a rare sequence variant in the 5' flanking region of DYS385 and a total of two SNPs in the repeat structure at DYS481 and DYS449.
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Carney C, Whitney S, Vaidyanathan J, Persick R, Noel F, Vallone PM, Romsos EL, Tan E, Grover R, Turingan RS, French JL, Selden RF. Developmental validation of the ANDE™ rapid DNA system with FlexPlex™ assay for arrestee and reference buccal swab processing and database searching. Forensic Sci Int Genet 2019; 40:120-130. [PMID: 30818156 DOI: 10.1016/j.fsigen.2019.02.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 12/20/2022]
Abstract
A developmental validation was performed to demonstrate reliability, reproducibility and robustness of the ANDE System with the FlexPlex assay, including an integrated Expert System, across a number of laboratories and buccal sample variations. Previously, the related DNAscan™/ANDE 4C Rapid DNA System using the PowerPlex®16 assay and integrated Expert System Software received NDIS approval in March 2016. The enhanced ANDE instrument, referred to as ANDE 6C, and the accompanying 6-dye, 27-locus STR assay, referred to as FlexPlex, have been developed to be compatible with all widely used global loci, including the expanded set of the CODIS core 20 loci. Six forensic and research laboratories participated in the FlexPlex Rapid DNA developmental validation experiments, testing a total of 2045 swabs, including those obtained from 1387 unique individuals. The goal of this extensive and comprehensive validation was to thoroughly evaluate and document the ANDE System and its internal Expert System to reliably genotype reference buccal swab samples in a manner compliant with the FBI's Quality Assurance Standards and the NDIS Operational Procedures. The ANDE System, including automated Expert System analysis, generated reproducible and concordant results for buccal swabs when testing various instruments at different laboratories by a number of different operators. When testing a number of non-human DNAs, including oral bacteria, the ANDE System and FlexPlex assay demonstrated limited cross-reactivity. Potential PCR inhibitors were evaluated as part of the validation and no inhibition was detected. Reproducible and concordant profiles were generated from buccal swab samples collected with a limit of detection appropriate for buccal swab collections from arrestees. The precision and resolution of the System met industry standards for detection of microvariants and single base resolution. The integrated Expert System appropriately demonstrated the ability to correctly pass or fail profiles for CODIS upload without human review. During this comprehensive developmental validation, the ANDE System successfully interpreted over 2000 samples tested with over 99.99% concordant alleles. The data package described herein led to the ANDE System with the FlexPlex assay receiving NDIS approval in June 2018.
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Affiliation(s)
- Christopher Carney
- Florida Department of Law Enforcement DNA Investigative Support Database, 2331 Phillips Road, Tallahassee, FL, 32308, USA
| | - Scott Whitney
- Florida Department of Law Enforcement DNA Investigative Support Database, 2331 Phillips Road, Tallahassee, FL, 32308, USA
| | | | - Rebekah Persick
- Louisiana State Police, 376 East Airport Road, Baton Rouge, LA, 70806, USA
| | - Fabrice Noel
- National Institute of Criminalistics and Criminology, Chaussée de Vilvorde, 100, 1120, Bruxelles, Belgium
| | - Peter M Vallone
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899-8314, USA
| | - Erica L Romsos
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899-8314, USA
| | - Eugene Tan
- ANDE Corporation, 266 Second Avenue, Waltham, MA, 02451, USA
| | - Ranjana Grover
- ANDE Corporation, 266 Second Avenue, Waltham, MA, 02451, USA
| | | | - Julie L French
- ANDE Corporation, 266 Second Avenue, Waltham, MA, 02451, USA.
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Xuan JF, Adnan A, Khan RA, Xing JX, Yao J, Wang BJ. Population genetics of 19 Y-STR loci in Yanbian Korean samples from China. Ann Hum Genet 2018; 83:134-140. [PMID: 30506867 DOI: 10.1111/ahg.12296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/18/2018] [Accepted: 11/20/2018] [Indexed: 11/28/2022]
Abstract
BACKGROUND China harbors 56 ethnic groups, including Korean, with a population size of approximately 1.92 million at the 2010 census. Most of the Koreans live in Northeastern parts of China, including Jilin (59.64%), Heilongjiang (20.21%), and Liaoning (12.55%) provinces, and the rest are spread to other parts of China. Koreans across China share a common culture, which is similar to Korea. METHODS We have explored the genetic characteristics of 20 Y-chromosomal short tandem repeat (Y-STR) loci in 252 unrelated Chinese Korean male individuals from Jilin Province, using a Goldeneye 20Y amplification kit. Moreover, phylogenetic analysis was performed between the Korean population and other relevant populations based on the Y-STR haplotypes. RESULTS We have found 237 different haplotypes among 252 unrelated individuals. The haplotype frequencies ranged from 0.0238 to 0.0040, while gene diversity ranged from 0.9666 (DYS385a/b) to 0.2260 (DYS391). The random match probability was 0.0048, the haplotype diversity was 0.9992 ± 0.0006 and discrimination capacity was 0.9405. Population comparison revealed that Korean populations are lining up together with other Korean populations from East Asia. CONCLUSION Our results showed that the 20 Y-STR loci in the Yanbian Korean population are valuable for forensic application and human genetics. The Yanbian Koreans have lined up with other Korean population from China and Korea while showing significant differences from other East Asian populations.
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Affiliation(s)
- Jin-Feng Xuan
- School of Forensic Medicine, China Medical University, Shenyang, 110122, China
| | - Atif Adnan
- School of Forensic Medicine, China Medical University, Shenyang, 110122, China
| | - Rehan Ali Khan
- School of International Education, China Medical University, Shenyang, 110122, China
| | - Jia-Xin Xing
- School of Forensic Medicine, China Medical University, Shenyang, 110122, China
| | - Jun Yao
- School of Forensic Medicine, China Medical University, Shenyang, 110122, China
| | - Bao-Jie Wang
- School of Forensic Medicine, China Medical University, Shenyang, 110122, China
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Park HC, Lee EJ, Nam YH, Cho NS, Lim SK, Kim W. Genetic variation for three Y-STR loci: DYS390, DYS518, and DYS643. Int J Legal Med 2018; 133:1007-1013. [PMID: 30334084 DOI: 10.1007/s00414-018-1947-9] [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: 05/02/2018] [Accepted: 10/10/2018] [Indexed: 11/26/2022]
Abstract
Y chromosome short tandem repeats (Y-STRs) are commonly used to analyze male-specific DNA. Although biallelic patterns due to duplication events have been detected at some loci, Y-STRs generally appear as a single peak except for DYS385 because the Y chromosome is haploid. STR loci in regions of segmental duplication by homologous recombination on the Y chromosome exhibit double allelic peaks, rather than single peaks. In this study, we report a bi- and triallelic pattern observed simultaneously in DYS390, DYS518, and DYS643. A bi- and triallelic pattern has not previously been observed simultaneously for these three loci. We also identified the copy number variation in the region including these loci by the microarray-based analysis. Given the peak balance pattern, the copy number variation, and the close position of these three loci on the Y chromosome, we consider that this phenomenon is caused by a segmental duplication in the euchromatin region. By ruling out mixed samples, a common interpretation of multiple peaks, these results have practical implications for the interpretation of Y-STR results in forensics analyses.
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Affiliation(s)
- Hyun-Chul Park
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Eun-Jung Lee
- Forensic Medicine Division, National Forensic Service Gwangju Institute, Gwangju, 57248, Republic of Korea
| | - Youn-Hyung Nam
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea
| | - Nam-Soo Cho
- Forensic Medicine Division, National Forensic Service Daejeon Institute, Daejeon, 34054, Republic of Korea
| | - Si-Keun Lim
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea.
| | - Won Kim
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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Discriminating power of rapidly mutating Y-STRs in deep rooted endogamous pedigrees from Sindhi population of Pakistan. Leg Med (Tokyo) 2018; 34:17-20. [PMID: 30098581 DOI: 10.1016/j.legalmed.2018.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/19/2018] [Accepted: 08/03/2018] [Indexed: 11/23/2022]
Abstract
Rapidly mutating Y-STRs (RM Y-STRs) have been paid much attention in recent years. The 13 RM Y-STRs (DYF387S1, DYF399S1, DYF403S1a/b, DYF404S1, DYS449, DYS518, DYS526I/II, DYS547, DYS570, DYS576, DYS612, DYS626, and DYS627) 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 in endogamous populations, separation of which is usually impossible with standard Y-STRs. In current study, we analyzed the RM Y-STRs and PowerPlex® Y23 System in 216 male relatives from 18 deep rooted endogamous Sindhi families from Pakistan. Mutations were frequently observed at DYF399S1, DYS449, DYS518DYS547 and DYF403S1b2 loci, which are known to mutate more rapidly than other RM Y-STRs. Overall differentiation rate with RM Y-STRs was as high as 32.88%, while those with PowerPlex® Y23 System and AmpFℓSTR® Yfiler™ kit were 6.85% and 3.65% respectively. The differentiation rate of RM Y-STRs was 29.22% and 26.03% higher than those of AmpFlSTR® Yfiler™ kit and PowerPlex® Y23 System, respectively.
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Sala A, Caputo M, Ginart S, Theiler G, Parolin ML, Carnese RF, Fainboim L, Corach D. Historical records under the genetic evidence: "Chiriguano" tribe genesis as a test case. Mol Biol Rep 2018; 45:987-1000. [PMID: 30003508 DOI: 10.1007/s11033-018-4246-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/08/2018] [Indexed: 10/28/2022]
Abstract
Historical records suggest that Chiriguano tribe is the result of a genetic admixture event. The process involved the arrival of Guaraní tribesmen descending from Amazonian region of Brazil along with groups of Arawak origin that inhabited the foothill plains of Bolivia. Later they arrived in Argentina at the beginning of the twentieth century. Aiming to test the historical records, we analysed a set of 46 samples collected at San Ramon de la Nueva Orán, Province of Salta, Argentina. A wide set of uni- and biparentally transmitted genetic markers were analysed, including 23 autosomal STRs; 46 AIM-DIPs and 24 AIM-SNPs all located at diverse autosomal chromosome locations; 23 Y-STRs and the entire mtDNA D-Loop sequence. Ancestry informative markers allowed for the detection of a strong Native American component in the genomes (> 94%), while all mtDNA haplotypes showed Native American characteristic motives, and 93% of Y-haplotypes belonged to the Q1a3a Y-haplogroup. The analysis of mitochondrial haplotypes and Y chromosome, although they did not match other populations, revealed a relationship between the Chiriguano and other groups of Guaraní and Arawak origin inhabiting Brazil and Bolivia, confirming, at least in part, the historical records describing the origins of Chiriguano tribal settlements in northwestern Argentina.
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Affiliation(s)
- Andrea Sala
- Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina. .,CONICET-Consejo Nacional de Investigaciones Científicas y Tecnológicas, C1033AAJ, Buenos Aires, Argentina.
| | - Mariela Caputo
- Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina.,CONICET-Consejo Nacional de Investigaciones Científicas y Tecnológicas, C1033AAJ, Buenos Aires, Argentina
| | - Santiago Ginart
- Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina.,CONICET-Consejo Nacional de Investigaciones Científicas y Tecnológicas, C1033AAJ, Buenos Aires, Argentina
| | - Graciela Theiler
- Instituto de Inmunología, Genética y Metabolismo (INIGEM-CONICET), Hospital de Clínicas "José de San Martín", University of Buenos Aires, Buenos Aires, Argentina
| | - María Laura Parolin
- Instituto de Diversidad y Evolución Austral (IDEAus) CCT CENPAT-CONICET, Puerto Madryn, Argentina
| | - Raúl Francisco Carnese
- Sección Antropología Biológica, Instituto de Ciencias Antropológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Leonardo Fainboim
- CONICET-Consejo Nacional de Investigaciones Científicas y Tecnológicas, C1033AAJ, Buenos Aires, Argentina.,Instituto de Inmunología, Genética y Metabolismo (INIGEM-CONICET), Hospital de Clínicas "José de San Martín", University of Buenos Aires, Buenos Aires, Argentina
| | - Daniel Corach
- Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina.,CONICET-Consejo Nacional de Investigaciones Científicas y Tecnológicas, C1033AAJ, Buenos Aires, Argentina
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Technical note: developmental validation of a novel 6-dye typing system with 36 Y-STR loci. Int J Legal Med 2018; 133:1015-1027. [DOI: 10.1007/s00414-018-1864-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 05/14/2018] [Indexed: 10/16/2022]
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Ly G, Alard B, Laurent R, Lafosse S, Toupance B, Monidarin C, Diffloth G, Bourdier F, Evrard O, Pavard S, Chaix R. Residence rule flexibility and descent groups dynamics shape uniparental genetic diversities in South East Asia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 165:480-491. [PMID: 29359511 DOI: 10.1002/ajpa.23374] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 11/09/2017] [Accepted: 12/04/2017] [Indexed: 11/08/2022]
Abstract
OBJECTIVES Social organization plays a major role in shaping human population genetic diversity. In particular, matrilocal populations tend to exhibit less mitochondrial diversity than patrilocal populations, and the other way around for Y chromosome diversity. However, several studies have not replicated such findings. The objective of this study is to understand the reasons for such inconsistencies and further evaluate the influence of social organization on genetic diversity. MATERIALS AND METHODS We explored uniparental diversity patterns using mitochondrial HV1 sequences and 17 Y-linked short tandem repeats (STRs) in 12 populations (n = 619) from mainland South-East Asia exhibiting a wide range of social organizations, along with quantitative ethno-demographic information sampled at the individual level. RESULTS MtDNA diversity was lower in matrilocal than in multilocal and patrilocal populations while Y chromosome diversity was similar among these social organizations. The reasons for such asymmetry at the genetic level were understood by quantifying sex-specific migration rates from our ethno-demographic data: while female migration rates varied between social organizations, male migration rates did not. This unexpected lack of difference in male migrations resulted from a higher flexibility in residence rule in patrilocal than in matrilocal populations. In addition, our data suggested an impact of clan fission process on uniparental genetic patterns. CONCLUSIONS The observed lack of signature of patrilocality on Y chromosome patterns might be attributed to the higher residence flexibility in the studied patrilocal populations, thus providing a potential explanation for the apparent discrepancies between social and genetic structures. Altogether, this study highlights the need to quantify the actual residence and descent patterns to fit social to genetic structures.
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Affiliation(s)
- Goki Ly
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Paris, F-75016, France
| | - Bérénice Alard
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Paris, F-75016, France
| | - Romain Laurent
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Paris, F-75016, France
| | - Sophie Lafosse
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Paris, F-75016, France
| | - Bruno Toupance
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Paris, F-75016, France
| | - Chou Monidarin
- Faculty of Pharmacy and Rodolphe Mérieux Laboratory, University of Health Sciences, Phnom Penh, Cambodia
| | | | - Frédéric Bourdier
- Développement et Sociétés, UMR 201, Panthéon Sorbonne, IEDES, IRD, Paris, France
| | - Olivier Evrard
- Patrimoines Locaux et Gouvernance, UMR 208, IRD, MNHN, Paris, France
| | - Samuel Pavard
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Paris, F-75016, France
| | - Raphaëlle Chaix
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Paris, F-75016, France
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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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Liu Z, Jia D, Zhang J, Li C, Zhang X, Yang Y, Yang M, Chen M, Yu Z, Wang Y, Yan J. Inconsistent genotyping call at DYS389 locus and implications for interpretation. Int J Legal Med 2017; 132:1043-1048. [PMID: 29177704 DOI: 10.1007/s00414-017-1735-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 11/08/2017] [Indexed: 11/26/2022]
Abstract
The male-specific Y chromosome short tandem repeat (STR) locus is used widely in forensic case, which are useful molecular tool to providing the biological evidence for male/female mixture and paternal lineage cases. The Y-STR analysis has been greatly facilitated by advent of commercial multiplex kit. However, even with well-designed robust multiplex kit, abnormal genotyping profile may be observed when encountering with mutations, such as deletion/duplication within the target region or mutation at the primer binding site. In this study, a single-allele shift by five nucleotides for the DYS389I marker between the AmpFlSTR® Yfiler® and Yfiler® Plus PCR amplification kits while the same allele count for DYS389II was observed in eight unrelated Chinese male individuals. After further investigations by re-amplified with three additional multiplex kits, sanger, and next-generation sequencing, the discordance was finally proven caused by existing rare mutation in those sample, which contained two adjacent SNPs only one base apart in the sequence. This paper describes the molecular basis of the discordance at DYS389I genotyping between different commercial multiplex kits and could provide available information for enhancing of interpretation of abnormal Y-STR genotyping in forensic practice.
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Affiliation(s)
- Zhiyong Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, 100101, Beijing, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Dongtao Jia
- Nantong Bureau of Public Safety, 226000, Nantong, Jiangsu, People's Republic of China
| | - Jingjing Zhang
- Beijing 3i Forensics Technology Co., Ltd, 100192, Beijing, People's Republic of China
| | - Chen Li
- Beijing Microread Genetics Co., Ltd, 100089, Beijing, People's Republic of China
| | - Xi Zhang
- Beijing 3i Forensics Technology Co., Ltd, 100192, Beijing, People's Republic of China
| | - Yaran Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, 100101, Beijing, People's Republic of China
| | - Meng Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, 100101, Beijing, People's Republic of China
| | - Man Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, 100101, Beijing, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Zailiang Yu
- Beijing Microread Genetics Co., Ltd, 100089, Beijing, People's Republic of China
| | - Yan Wang
- Beijing 3i Forensics Technology Co., Ltd, 100192, Beijing, People's Republic of China
| | - Jiangwei Yan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, 100101, Beijing, People's Republic of China.
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China.
- Shanxi Medical University, 030009, Taiyuan, People's Republic of China.
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SharifahNany RahayuKarmilla S, Aedrianee AR, Nur Haslindawaty AR, Nur Azeelah A, Panneerchelvam S, Norazmi MN, Zafarina Z. Paternal lineage affinity of the Malay subethnic and Orang Asli populations in Peninsular Malaysia. Int J Legal Med 2017; 132:1087-1090. [DOI: 10.1007/s00414-017-1697-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/20/2017] [Indexed: 10/18/2022]
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39
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Qian X, Hou J, Wang Z, Ye Y, Lang M, Gao T, Liu J, Hou Y. Next Generation Sequencing Plus (NGS+) with Y-chromosomal Markers for Forensic Pedigree Searches. Sci Rep 2017; 7:11324. [PMID: 28900279 PMCID: PMC5595879 DOI: 10.1038/s41598-017-11955-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/01/2017] [Indexed: 11/17/2022] Open
Abstract
There is high demand for forensic pedigree searches with Y-chromosome short tandem repeat (Y-STR) profiling in large-scale crime investigations. However, when two Y-STR haplotypes have a few mismatched loci, it is difficult to determine if they are from the same male lineage because of the high mutation rate of Y-STRs. Here we design a new strategy to handle cases in which none of pedigree samples shares identical Y-STR haplotype. We combine next generation sequencing (NGS), capillary electrophoresis and pyrosequencing under the term ‘NGS+’ for typing Y-STRs and Y-chromosomal single nucleotide polymorphisms (Y-SNPs). The high-resolution Y-SNP haplogroup and Y-STR haplotype can be obtained with NGS+. We further developed a new data-driven decision rule, FSindex, for estimating the likelihood for each retrieved pedigree. Our approach enables positive identification of pedigree from mismatched Y-STR haplotypes. It is envisaged that NGS+ will revolutionize forensic pedigree searches, especially when the person of interest was not recorded in forensic DNA database.
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Affiliation(s)
- Xiaoqin Qian
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Jiayi Hou
- Clinical and Translational Research Institute, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yi Ye
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Min Lang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Tianzhen Gao
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China.
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López S, Thomas MG, van Dorp L, Ansari-Pour N, Stewart S, Jones AL, Jelinek E, Chikhi L, Parfitt T, Bradman N, Weale ME, Hellenthal G. The Genetic Legacy of Zoroastrianism in Iran and India: Insights into Population Structure, Gene Flow, and Selection. Am J Hum Genet 2017; 101:353-368. [PMID: 28844488 PMCID: PMC5590844 DOI: 10.1016/j.ajhg.2017.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/24/2017] [Indexed: 11/24/2022] Open
Abstract
Zoroastrianism is one of the oldest extant religions in the world, originating in Persia (present-day Iran) during the second millennium BCE. Historical records indicate that migrants from Persia brought Zoroastrianism to India, but there is debate over the timing of these migrations. Here we present genome-wide autosomal, Y chromosome, and mitochondrial DNA data from Iranian and Indian Zoroastrians and neighboring modern-day Indian and Iranian populations and conduct a comprehensive genome-wide genetic analysis in these groups. Using powerful haplotype-based techniques, we find that Zoroastrians in Iran and India have increased genetic homogeneity relative to other sampled groups in their respective countries, consistent with their current practices of endogamy. Despite this, we infer that Indian Zoroastrians (Parsis) intermixed with local groups sometime after their arrival in India, dating this mixture to 690–1390 CE and providing strong evidence that Iranian Zoroastrian ancestry was maintained primarily through the male line. By making use of the rich information in DNA from ancient human remains, we also highlight admixture in the ancestors of Iranian Zoroastrians dated to 570 BCE–746 CE, older than admixture seen in any other sampled Iranian group, consistent with a long-standing isolation of Zoroastrians from outside groups. Finally, we report results, and challenges, from a genome-wide scan to identify genomic regions showing signatures of positive selection in present-day Zoroastrians that might correlate to the prevalence of particular diseases among these communities.
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Woerner AE, King JL, Budowle B. Fast STR allele identification with STRait Razor 3.0. Forensic Sci Int Genet 2017; 30:18-23. [PMID: 28605651 DOI: 10.1016/j.fsigen.2017.05.008] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/08/2017] [Accepted: 05/29/2017] [Indexed: 10/19/2022]
Abstract
The short tandem repeat allele identification tool (STRait Razor), a program used to characterize the haplotypes of short tandem repeats (STRs) in massively parallel sequencing (MPS) data, was redesigned. STRait Razor v3.0 performs ∼660× faster allele identification than its previous version (v2s), a speedup that is largely due to a novel indexing strategy used to perform "fuzzy" (approximate) string matching of anchor sequences. Written in a portable compiled language, C++, STRait Razor v3.0 functions on all major operating systems including Microsoft Windows, and it has cross-platform multithreading support. In silico estimates of precision and accuracy of STRait Razor v3.0 were 100% in this evaluation and results were highly concordant with those of Strait Razor v2s. STRait Razor v3.0 adds several key features that simplify the haplotype reporting process, including simple filters to remove low frequency haplotypes as well as merging haplotypes within a locus encoded on opposite strands of the DNA molecule.
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Affiliation(s)
- August E Woerner
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA.
| | - Jonathan L King
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; Center of Excellence in Genomic Medicine (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
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Kayser M. Forensic use of Y-chromosome DNA: a general overview. Hum Genet 2017; 136:621-635. [PMID: 28315050 PMCID: PMC5418305 DOI: 10.1007/s00439-017-1776-9] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 03/08/2017] [Indexed: 11/19/2022]
Abstract
The male-specific part of the human Y chromosome is widely used in forensic DNA analysis, particularly in cases where standard autosomal DNA profiling is not informative. A Y-chromosomal gene fragment is applied for inferring the biological sex of a crime scene trace donor. Haplotypes composed of Y-chromosomal short tandem repeat polymorphisms (Y-STRs) are used to characterise paternal lineages of unknown male trace donors, especially suitable when males and females have contributed to the same trace, such as in sexual assault cases. Y-STR haplotyping applied in crime scene investigation can (i) exclude male suspects from involvement in crime, (ii) identify the paternal lineage of male perpetrators, (iii) highlight multiple male contributors to a trace, and (iv) provide investigative leads for finding unknown male perpetrators. Y-STR haplotype analysis is employed in paternity disputes of male offspring and other types of paternal kinship testing, including historical cases, as well as in special cases of missing person and disaster victim identification involving men. Y-chromosome polymorphisms are applied for inferring the paternal bio-geographic ancestry of unknown trace donors or missing persons, in cases where autosomal DNA profiling is uninformative. In this overview, all different forensic applications of Y-chromosome DNA are described. To illustrate the necessity of forensic Y-chromosome analysis, the investigation of a prominent murder case is described, which initiated two changes in national forensic DNA legislation both covering Y-chromosome use, and was finally solved via an innovative Y-STR dragnet involving thousands of volunteers after 14 years. Finally, expectations for the future of forensic Y-chromosome DNA analysis are discussed.
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Affiliation(s)
- Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
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44
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Choi EJ, Park KW, Lee YH, Nam YH, Suren G, Ganbold U, Kim JA, Kim SY, Kim HM, Kim K, Kim W. Forensic and population genetic analyses of the GlobalFiler STR loci in the Mongolian population. Genes Genomics 2017. [DOI: 10.1007/s13258-016-0511-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Adnan A, Ralf A, Rakha A, Kousouri N, Kayser M. Improving empirical evidence on differentiating closely related men with RM Y-STRs: A comprehensive pedigree study from Pakistan. Forensic Sci Int Genet 2016; 25:45-51. [DOI: 10.1016/j.fsigen.2016.07.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 06/07/2016] [Accepted: 07/07/2016] [Indexed: 11/17/2022]
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46
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Koganebuchi K, Haneji K, Toma T, Joh K, Soejima H, Fujimoto K, Ishida H, Ogawa M, Hanihara T, Harada S, Kawamura S, Oota H. The allele frequency of ALDH2*Glu504Lys and ADH1B*Arg47His for the Ryukyu islanders and their history of expansion among East Asians. Am J Hum Biol 2016; 29. [PMID: 27801545 DOI: 10.1002/ajhb.22933] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/09/2016] [Accepted: 10/04/2016] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVES A cline of frequencies of the derived allele of the ALDH2 gene, which causes a deficiency of an enzyme and "facial flushing" in humans who drink alcohol, has been known among the people of the Japanese archipelago. This cline is conventionally explained by admixture with immigrants from the Asian continent occurring during the Yayoi period. Previous studies lack sufficient data from the peripheral regions of the indigenous Jomon people, and those data the ADH1B gene that is involved in the Class I ADH gene cluster and contains another variant leading to a functional change. METHODS We focused on the southwestern-most people from the Ryukyu Islands (n = 218) and those from northern Kyushu (n = 21) where the Yayoi immigrants likely arrived. We investigated both the Class I ADH and ALDH2 loci, as well as neutral genetic markers. RESULTS In the Ryukyu Islands, the frequencies of the ancestral alleles in both loci were always higher than those in mainland Japan, while the frequencies of ADH1B were less than those of the derived allele. A haplotype block was not observed in ALDH2 but was in Class I ADH. DISCUSSION Our data suggest that the derived allele of ALDH2 came with the Yayoi immigrants from the Asian continent to the Japanese archipelago. However, the derived allele of ADH1B is unlikely to be related to the Yayoi migration. Therefore, we postulate that the expansion of the derived allele of ADHIB in East Asia could be traced back to the last glacial period.
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Affiliation(s)
- Kae Koganebuchi
- Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Kanagawa, 252-0373, Japan.,Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Kuniaki Haneji
- Haneji Oral Surgery Clinic, Medical Corporation Hayamakai, Okinawa, 906-0015, Japan.,Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, 903-0215, Japan
| | - Takashi Toma
- Department of Oral and Maxillofacial Surgery, Adventist Medical Center, Okinawa, 903-0201, Japan.,Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, 903-0215, Japan
| | - Keiichiro Joh
- Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Hidenobu Soejima
- Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Kazuma Fujimoto
- Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, 903-0215, Japan
| | - Motoyuki Ogawa
- Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Kanagawa, 252-0373, Japan.,Department of Anatomy, Kitasato University School of Medicine, Kanagawa, 252-0374, Japan
| | - Tsunehiko Hanihara
- Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Kanagawa, 252-0373, Japan.,Department of Anatomy, Kitasato University School of Medicine, Kanagawa, 252-0374, Japan.,The University Museum, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Shoji Harada
- Ex-Institute of Community Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Hiroki Oota
- Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Kanagawa, 252-0373, Japan.,Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.,Department of Anatomy, Kitasato University School of Medicine, Kanagawa, 252-0374, Japan
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47
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Vatandoost N, Salehi AR, Kazemi M, Khosravi S, Eslami G, Kamali S, Salehi R. Genetic polymorphism of 8 Y-STR loci in native population of Isfahan province in central part of Iran. Ann Hum Biol 2016; 44:175-179. [PMID: 27282193 DOI: 10.1080/03014460.2016.1200671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND Y-chromosome short tandem repeats (Y-STRs) are genetic markers with practical applications in human identification and population studies. AIM Here we present the allelic and haplotype frequencies of 8 Y-STR loci most commonly used in forensic medicine in 103 unrelated native males of Isfahan province, central part of Iran. SUBJECTS AND METHODS The cases were selected on the basis of strict criteria to assure pure native populations of Isfahan origin. DNA extracted from peripheral blood samples and PCR amplified for each marker. Y-specific STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393 were included in this study. RESULTS The most common alleles for each locus were: DYS19, allele 12; DYS385, allele 12; DYS389I, allele 13; DYS389II, allele 29; DYS390, allele 24; DYS391, allele 10; DYS392, allele 11; and DYS393, allele 13. Gene diversity value was calculated from the allelic frequency for each locus. The average gene diversity was 0.6518. A total of 101 haplotypes were observed in eight Y-specific STR loci, the haplotype diversity was raised to 0.986. CONCLUSION The results revealed that a set of eight Y-specific STR loci were able to discriminate most of the male individuals in the population studied. A search through the Y Haplotype Reference Database demonstrated 21 matched haplotypes to 160,693 haplotypes, exclusively with Eurasian-European, Eurasian, and Eurasian-Indo Iranian populations.
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Affiliation(s)
- Nasimeh Vatandoost
- a Department of Genetics and Molecular Biology , School of Medicine, Isfahan University of Medical Sciences , Isfahan, Iran
| | - Ahmad Reza Salehi
- a Department of Genetics and Molecular Biology , School of Medicine, Isfahan University of Medical Sciences , Isfahan, Iran
| | - Mohammad Kazemi
- a Department of Genetics and Molecular Biology , School of Medicine, Isfahan University of Medical Sciences , Isfahan, Iran
| | - Sharifeh Khosravi
- a Department of Genetics and Molecular Biology , School of Medicine, Isfahan University of Medical Sciences , Isfahan, Iran
| | - Gilda Eslami
- b Department of Parasitology and Mycology, Faculty of Medicine , Shahid Sadoughi University of Medical Sciences , Yazd , Iran
| | - Sara Kamali
- a Department of Genetics and Molecular Biology , School of Medicine, Isfahan University of Medical Sciences , Isfahan, Iran
| | - Rasoul Salehi
- a Department of Genetics and Molecular Biology , School of Medicine, Isfahan University of Medical Sciences , Isfahan, Iran.,c Acquired Immunodeficiency Research Center, Isfahan University of Medical Sciences , Isfahan , Iran.,d Gerfa Namayesh Azmayesh (GENAZMA) Research & Science Institute , Isfahan, Iran
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48
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Kimmel M, Wojdyła T. Genetic demographic networks: Mathematical model and applications. Theor Popul Biol 2016; 111:75-86. [PMID: 27378746 DOI: 10.1016/j.tpb.2016.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 06/21/2016] [Accepted: 06/24/2016] [Indexed: 10/21/2022]
Abstract
Recent improvement in the quality of genetic data obtained from extinct human populations and their ancestors encourages searching for answers to basic questions regarding human population history. The most common and successful are model-based approaches, in which genetic data are compared to the data obtained from the assumed demography model. Using such approach, it is possible to either validate or adjust assumed demography. Model fit to data can be obtained based on reverse-time coalescent simulations or forward-time simulations. In this paper we introduce a computational method based on mathematical equation that allows obtaining joint distributions of pairs of individuals under a specified demography model, each of them characterized by a genetic variant at a chosen locus. The two individuals are randomly sampled from either the same or two different populations. The model assumes three types of demographic events (split, merge and migration). Populations evolve according to the time-continuous Moran model with drift and Markov-process mutation. This latter process is described by the Lyapunov-type equation introduced by O'Brien and generalized in our previous works. Application of this equation constitutes an original contribution. In the result section of the paper we present sample applications of our model to both simulated and literature-based demographies. Among other we include a study of the Slavs-Balts-Finns genetic relationship, in which we model split and migrations between the Balts and Slavs. We also include another example that involves the migration rates between farmers and hunters-gatherers, based on modern and ancient DNA samples. This latter process was previously studied using coalescent simulations. Our results are in general agreement with the previous method, which provides validation of our approach. Although our model is not an alternative to simulation methods in the practical sense, it provides an algorithm to compute pairwise distributions of alleles, in the case of haploid non-recombining loci such as mitochondrial and Y-chromosome loci in humans.
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Affiliation(s)
- Marek Kimmel
- Department of Statistics, Rice University, 6100 Main Street, Houston, TX 77005, USA; Systems Engineering Group, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland.
| | - Tomasz Wojdyła
- Institute of Automatic Control, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland.
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49
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Liu H, Li X, Mulero J, Carbonaro A, Short M, Ge J. A convenient guideline to determine if two Y-STR profiles are from the same lineage. Electrophoresis 2016; 37:1659-68. [DOI: 10.1002/elps.201500566] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 02/22/2016] [Accepted: 03/24/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Hai Liu
- The Institute of Forensic Science and Technology; Henan Provincial Public Security Bureau; Zhengzhou P. R. China
| | - Xiaoyang Li
- The Institute of Forensic Science and Technology; Henan Provincial Public Security Bureau; Zhengzhou P. R. China
| | - Julio Mulero
- Human Identification Division; Thermo Fisher Scientific; South San Francisco CA USA
| | - Andrea Carbonaro
- Human Identification Division; Thermo Fisher Scientific; South San Francisco CA USA
| | - Marc Short
- Human Identification Division; Thermo Fisher Scientific; South San Francisco CA USA
| | - Jianye Ge
- Human Identification Division; Thermo Fisher Scientific; South San Francisco CA USA
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50
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Analysis of genetic admixture in Uyghur using the 26 Y-STR loci system. Sci Rep 2016; 6:19998. [PMID: 26842947 PMCID: PMC4740765 DOI: 10.1038/srep19998] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/22/2015] [Indexed: 11/24/2022] Open
Abstract
The Uyghur population has experienced extensive interaction with European and Eastern Asian populations historically. A set of high-resolution genetic markers could be useful to infer the genetic relationships between the Uyghur population and European and Asian populations. In this study we typed 100 unrelated Uyghur males living in southern Xinjiang at 26 Y-STR loci. Using the high-resolution 26 Y-STR loci system, we investigated genetic and phylogenetic relationship between the Uyghur population and 23 reference European or Asian populations. We found that the Uyghur population exhibited a genetic admixture of Eastern Asian and European populations, and had a slightly closer relationship with the selected European populations than the Eastern Asian populations. We also demonstrated that the 26 Y-STR loci system was potentially useful in forensic sciences because it has a large power of discrimination and rarely exhibits common haplotypes. However, ancestry inference of Uyghur samples could be challenging due to the admixed nature of the population.
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