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Antão-Sousa S, Gusmão L, Modesti NM, Feliziani S, Faustino M, Marcucci V, Sarapura C, Ribeiro J, Carvalho E, Pereira V, Tomas C, de Pancorbo MM, Baeta M, Alghafri R, Almheiri R, Builes JJ, Gouveia N, Burgos G, Pontes MDL, Ibarra A, da Silva CV, Parveen R, Benitez M, Amorim A, Pinto N. Microsatellites' mutation modeling through the analysis of the Y-chromosomal transmission: Results of a GHEP-ISFG collaborative study. Forensic Sci Int Genet 2024; 69:102999. [PMID: 38181588 DOI: 10.1016/j.fsigen.2023.102999] [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: 05/08/2023] [Revised: 10/25/2023] [Accepted: 12/10/2023] [Indexed: 01/07/2024]
Abstract
The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) organized a collaborative study on mutations of Y-chromosomal short tandem repeats (Y-STRs). New data from 2225 father-son duos and data from 44 previously published reports, corresponding to 25,729 duos, were collected and analyzed. Marker-specific mutation rates were estimated for 33 Y-STRs. Although highly dependent on the analyzed marker, mutations compatible with the gain or loss of a single repeat were 23.2 times more likely than those involving a greater number of repeats. Longer alleles (relatively to the modal one) showed to be nearly twice more mutable than the shorter ones. Within the subset of longer alleles, the loss of repeats showed to be nearly twice more likely than the gain. Conversely, shorter alleles showed a symmetrical trend, with repeat gains being twofold more frequent than reductions. A positive correlation between the paternal age and the mutation rate was observed, strengthening previous findings. The results of a machine learning approach, via logistic regression analyses, allowed the establishment of algebraic formulas for estimating the probability of mutation depending on paternal age and allele length for DYS389I, DYS393 and DYS627. Algebraic formulas could also be established considering only the allele length as predictor for DYS19, DYS389I, DYS389II-I, DYS390, DYS391, DYS393, DYS437, DYS439, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS533, DYS576, DYS626 and DYS627 loci. For the remaining Y-STRs, a lack of statistical significance was observed, probably as a consequence of the small effective size of the subsets available, a common difficulty in the modeling of rare events as is the case of mutations. The amount of data used in the different analyses varied widely, depending on how the data were reported in the publications analyzed. This shows a regrettable waste of produced data, due to inadequate communication of the results, supporting an urgent need of publication guidelines for mutation studies.
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Affiliation(s)
- Sofia Antão-Sousa
- Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal; Faculty of Sciences of the University of Porto (FCUP), Porto, Portugal; DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Nidia M Modesti
- Centro de Genética Forense, Poder Judicial de Córdoba, Argentina
| | - Sofía Feliziani
- Centro de Genética Forense, Poder Judicial de Córdoba, Argentina
| | - Marisa Faustino
- Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Faculty of Sciences of the University of Porto (FCUP), Porto, Portugal
| | - Valeria Marcucci
- Laboratorio Regional de Investigación Forense, Tribunal Superior de Justicia de Santa Cruz, Argentina
| | - Claudia Sarapura
- Laboratorio Regional de Investigación Forense, Tribunal Superior de Justicia de Santa Cruz, Argentina
| | - Julyana Ribeiro
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Elizeu Carvalho
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Carmen Tomas
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Lascaray Research Center, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Rashed Alghafri
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Reem Almheiri
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Juan José Builes
- GENES SAS Laboratory, Medellín, Colombia; Institute of Biology, University of Antioquia, Medellín, Colombia
| | - Nair Gouveia
- Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. / Serviço de Genética e Biologia Forenses, Delegação do Centro, Portugal
| | - German Burgos
- One Health Global Research Group, Facultad de Medicina, Universidad de Las Américas (UDLA), Quito, Ecuador; Grupo de Medicina Xenómica, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Maria de Lurdes Pontes
- Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. / Serviço de Genética e Biologia Forenses, Delegação do Norte, Portugal
| | - Adriana Ibarra
- Laboratorio IDENTIGEN, Universidad de Antioquia, Colombia
| | - Claudia Vieira da Silva
- Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. / Serviço de Genética e Biologia Forenses, Delegação do Sul, Portugal
| | - Rukhsana Parveen
- Forensic Services Laboratory, Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Marc Benitez
- Policia de la Generalitat de Catalunya - Mossos d'Esquadra. Unitat Central del Laboratori Biològic, Barcelona, Spain
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal; Faculty of Sciences of the University of Porto (FCUP), Porto, Portugal
| | - Nadia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal; Centre of Mathematics of the University of Porto, Porto, Portugal.
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2
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Mitchell MR, Chaseling J, Jones L, White T, Bernie A, Haupt LM, Griffiths LR, Wright KM. Improving the strategy to identify historical military remains: a literature review and Y-STR meta-analysis. Forensic Sci Res 2024; 9:owad050. [PMID: 38562552 PMCID: PMC10982847 DOI: 10.1093/fsr/owad050] [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: 09/08/2022] [Accepted: 09/26/2023] [Indexed: 04/04/2024] Open
Abstract
The identification of historical military remains by Unrecovered War Casualties-Army (UWC-A) currently relies on Y-chromosome Short Tandem Repeat (Y-STR) testing when maternal relatives are not available, or when a mitochondrial DNA match does not provide sufficient certainty of identification. However, common Y-STR profiles (using Yfiler™) between sets of remains or families often prevent identification. To resolve these cases, an investigation of additional Y-DNA markers is needed for their potential inclusion into the DNA identification strategy. The number of genetic transmissions between missing soldiers and their living relatives needs to be considered to avoid false exclusions between paternal relatives. Analysis of 236 World War I/II (WWI/II) era pairs of relatives identified up to seven genetic transmissions between WWII soldiers and their living relatives, and nine for WWI. Previous Y-STR meta-analyses were published approximately 10 years ago when rapidly mutating markers were relatively new. This paper reports a contemporary literature review and meta-analysis of 35 studies (which includes 23 studies not previously used in meta-analysis) and 23 commonly used Y-STR's mutation rates to inform the inclusion of additional loci to UWC-A's DNA identification strategy. Meta-analysis found mutation data for a given Y-STR locus could be pooled between studies and that the mutation rates were significantly different between some loci (at P < 0.05). Based on this meta-analysis, we have identified two additional markers from PowerPlex® Y23 for potential inclusion in UWC-A's identification strategy. Further avenues for potential experimental exploration are discussed. Key points From 236 UWC-A pairs of relatives, we observed up to nine genetic transmissions between WWI soldiers and their living relatives, and seven for WWII.MedCalc® software for meta-analysis utilizing the Freeman-Tukey transformation was run, which analysed 35 published studies and 23 commonly used loci. Previous Y-STR mutation rate meta-analyses are now 10 years old; this paper includes 23 studies that were not included in previous meta-analyses.Through meta-analysis, we identify two markers from PowerPlex® Y23 for potential inclusion in UWC-A's historical remains identification strategy (alongside Yfiler™). We discuss potential next steps for experimental exploration of additional Y-DNA markers.
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Affiliation(s)
- Melinda R Mitchell
- Queensland University of Technology (QUT), Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Janet Chaseling
- Queensland University of Technology (QUT), Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Lee Jones
- Queensland University of Technology (QUT), Research Methods Group, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Toni White
- Queensland University of Technology (QUT), Defence Innovation Hub, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Andrew Bernie
- Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Russell, Australian Capital Territory, Australia
| | - Larisa M Haupt
- Queensland University of Technology (QUT), Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Lyn R Griffiths
- Queensland University of Technology (QUT), Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Kirsty M Wright
- Queensland University of Technology (QUT), Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
- Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Russell, Australian Capital Territory, Australia
- Royal Australian Air Force (RAAF), No 2 Expeditionary Health Squadron, RAAF Base Williamtown, Williamtown, New South Wales, Australia
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3
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Antão-Sousa S, Pinto N, Rende P, Amorim A, Gusmão L. The sequence of the repetitive motif influences the frequency of multistep mutations in Short Tandem Repeats. Sci Rep 2023; 13:10251. [PMID: 37355683 PMCID: PMC10290632 DOI: 10.1038/s41598-023-32137-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 03/23/2023] [Indexed: 06/26/2023] Open
Abstract
Microsatellites, or Short Tandem Repeats (STRs), are subject to frequent length mutations that involve the loss or gain of an integer number of repeats. This work aimed to investigate the correlation between STRs' specific repetitive motif composition and mutational dynamics, specifically the occurrence of single- or multistep mutations. Allelic transmission data, comprising 323,818 allele transfers and 1,297 mutations, were gathered for 35 Y-chromosomal STRs with simple structure. Six structure groups were established: ATT, CTT, TCTA/GATA, GAAA/CTTT, CTTTT, and AGAGAT, according to the repetitive motif present in the DNA leading strand of the markers. Results show that the occurrence of multistep mutations varies significantly among groups of markers defined by the repetitive motif. The group of markers with the highest frequency of multistep mutations was the one with repetitive motif CTTTT (25% of the detected mutations) and the lowest frequency corresponding to the group with repetitive motifs TCTA/GATA (0.93%). Statistically significant differences (α = 0.05) were found between groups with repetitive motifs with different lengths, as is the case of TCTA/GATA and ATT (p = 0.0168), CTT (p < 0.0001) and CTTTT (p < 0.0001), as well as between GAAA/CTTT and CTTTT (p = 0.0102). The same occurred between the two tetrameric groups GAAA/CTTT and TCTA/GATA (p < 0.0001) - the first showing 5.7 times more multistep mutations than the second. When considering the number of repeats of the mutated paternal alleles, statistically significant differences were found for alleles with 10 or 12 repeats, between GATA and ATT structure groups. These results, which demonstrate the heterogeneity of mutational dynamics across repeat motifs, have implications in the fields of population genetics, epidemiology, or phylogeography, and whenever STR mutation models are used in evolutionary studies in general.
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Affiliation(s)
- Sofia Antão-Sousa
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal.
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
- Department of Biology, Faculty of Sciences of University of Porto (FCUP), Porto, Portugal.
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil.
| | - Nádia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Center of Mathematics of University of Porto (CMUP), Porto, Portugal
| | - Pablo Rende
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences of University of Porto (FCUP), Porto, Portugal
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Department of Biology, Faculty of Sciences of University of Porto (FCUP), Porto, Portugal
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
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Lee DG, Kim SJ, Cho WC, Cho Y, Park JH, Lee J, Jung JY. Analysis of mutation rates and haplotypes of 23 Y-chromosomal STRs in Korean father-son pairs. Forensic Sci Int Genet 2023; 65:102875. [PMID: 37084624 DOI: 10.1016/j.fsigen.2023.102875] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 04/10/2023] [Accepted: 04/16/2023] [Indexed: 04/23/2023]
Abstract
Y-chromosomal short tandem repeats (Y-STRs) have been widely used in forensic genetics, and accurate knowledge of mutation rates at Y-STR loci is essential in kinship analysis. The main aim of this study was to estimate Y-STR mutation rates in Korean males. To obtain locus-specific mutations and haplotypes at 23 Y-STRs, we analyzed samples from 620 Korean father-son pairs. In addition, we also analyzed 476 unrelated individuals using the PowerPlex® Y23 System, with the aim of augmenting the available data for the Korean population. The PowerPlex® Y23 system facilitates analysis of the 23 Y-STR loci (DYS576, DYS570, DYS458, DYS635, DYS389 II, DYS549, DYS385, DYS481, DYS439, DYS456, DYS389 I, DYS19, DYS393, DYS391, DYS533, DYS437, DYS390, Y GATA H4, DYS448, DYS438, DYS392, and DYS643). Locus-specific mutation rate estimates varied from 0.00 to 8.06 × 10-3 per generation, with an average mutation rate of 2.17 × 10-3 (95% CI, 1.5-3.1 × 10-3). To obtain comprehensive genetic values for the Korean population, we combined data obtained in this study with previously reported values, thereby enabling us to estimate the locus-specific mutation rates regarding 22,711 allele transmissions. By combining these data, we obtained an overall average mutation rate of 2.91 × 10-3 (95% CI, 2.3-3.7 × 10-3). In addition, among the 476 unrelated Korean males, we detected 467 different haplotypes, with an overall haplotype diversity value of 0.9999. By extracting haplotypes of Y-STRs described in previous literature on 23 Y-STR reported in Korea, we obtained gene diversities for 1133 Korean individuals. We believe that the values and characteristics of the 23 Y-STRs analyzed in this study will contribute to establishing criteria for forensic genetic interpretation, including kinship analysis.
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Affiliation(s)
- Dong Gyu Lee
- Forensic DNA Division, National Forensic Service, Wonju, South Korea; Department of forensics Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Su Jin Kim
- Forensic DNA Division, National Forensic Service, Wonju, South Korea
| | - Woo-Cheol Cho
- Forensic DNA Division, National Forensic Service, Wonju, South Korea
| | - Yoonjung Cho
- Forensic DNA Division, National Forensic Service, Wonju, South Korea
| | - Ji Hwan Park
- Forensic DNA Division, National Forensic Service, Wonju, South Korea
| | - Jinmyung Lee
- DNA Analysis Division, National Forensic Service Busan Institute, Busan, South Korea
| | - Ju Yeon Jung
- Forensic DNA Section, National Forensic Service Jeju Branch, Jeju, South Korea; Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea.
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Biogeographic origin and genetic characteristics of the peopling of Jeju Island based on lineage markers. Genes Genomics 2023; 45:307-318. [PMID: 36607592 DOI: 10.1007/s13258-022-01363-5] [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: 07/31/2022] [Accepted: 12/26/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Jeju Island is the largest island of South Korea, located southwest far from the mainland of Korea, and has a unique history and its own cultures that are distinguished from those of the other regions of the Korean mainland. However, the Jeju population has not been deeply investigated to date to understand their genetic structure, which may reflect their historical and geographical background. OBJECTIVE To identify the genetic characteristics and biogeographic origin of people of Jeju Island based on the statistical analysis of genetic data using lineage markers. METHODS 17 Y-STRs data for 615 unrelated males and mitochondrial DNA haplogroup data for 799 unrelated individuals residing on Jeju Island were generated, and analyzed to investigate genetic diversity and genetic characteristics using statistical methods including pairwise Fst or Rst, Analysis of molecular variance (AMOVA) and Multidimensional scaling (MDS). RESULTS For male individuals of Jeju Island, unique genetic characteristics were observed in the analysis of Y-STRs, including low haplotype diversity, strong association with surnames, genetic difference from other regions of Korea, and common genetic variation of the Y-STR loci known to be predominant in Northern populations, such as Mongolians. Statistical analysis of the mitochondrial DNA haplogroups also revealed similar results that showed low haplogroup diversity and high frequency of haplogroup Y prevalent mostly in ethnic populations around the Sea of Okhotsk in Northeastern Asia. All these results suggest that Jeju Island is genetically distinct from other regions of Korea, possibly being a subpopulation in Korea, and related closely to Northern Asian populations. CONCLUSION The findings in the genetic approach could support understanding of the historical background of Jeju Island that is consistent with evidence from other multidisciplinary studies.
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Messaoudi SA, Babu SR, Alsaleh AB, Albujja M, Al-Snan NR, Chaudhary AR, Kassab AC, Assidi M. Population genetic data for 12 X-STR loci in the Central Saudi region using investigator Argus X-12 amplification kit. Ann Hum Biol 2021; 48:321-326. [PMID: 34340612 DOI: 10.1080/03014460.2021.1957147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND X-chromosome short tandem repeat (X-STR) markers are important in forensic identity investigations and kinship analysis. SUBJECT AND METHODS In the current study, the distribution of 12 X-STR loci located in four linkage groups was evaluated using Investigator® Argus X-12 Amplification Kit in 200 unrelated healthy individuals (105 males and 95 females) from the central region of Saudi Arabia in order to develop an allelic frequency database for the markers included in the kit. RESULTS DXS10146 locus was the most informative with 21 alleles, while DXS8378 locus was the least with five alleles. Forensic parameters showed that all X-STRs loci, either as individual markers or as linkage groups, provide genetic information with high discrimination that is appropriate for forensic purposes with polymorphism information content (PIC), power of exclusion (PE), and paternity index (PI) varying from 0.61211 to 0.917979, 0.38722 to 0.842949, and 0.038416 to 0.16367, respectively. The pairwise genetic distance fixation index (Fst) results showed that the Saudi population is genetically closer to the Egyptian and Emirati populations and distant to the Turkish population. CONCLUSION The current study revealed that Investigator® Argus 12 X-STR kit would support the forensic application, kinship testing involving female offspring, and human identification in the Saudi population.
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Affiliation(s)
- Safia A Messaoudi
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Saranya R Babu
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Abrar B Alsaleh
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed Albujja
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Noora R Al-Snan
- Forensic Science Laboratory, Directorate of Forensic Science, General Directorate of Criminal Investigation and Forensic Science, Ministry of Interior, Manama, Kingdom of Bahrain
| | - Abdul Rauf Chaudhary
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Ahmed Ch Kassab
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Mourad Assidi
- Center of Excellence in Genomic Medicine Research (CEGMR), Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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Tang J, Yang M, Wang X, Wang Q, Wang Q, Zhang H, Qian E, Zhang H, Ji J, Ren Z, Wu Y, Huang J. Genetic structure and forensic characterisation of 36 Y-chromosomal STR loci in Hmong-Mien-speaking Miao population. Ann Hum Biol 2020; 47:541-548. [PMID: 32597239 DOI: 10.1080/03014460.2020.1788159] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
BACKGROUND Y-chromosomal short tandem repeats (Y-STRs) are widely used in paternity identification, pedigree investigation, and human population genetic history. AIM To investigate the Y-STR polymorphisms in a typical Miao population, and explore the genetic differentiation between the Miao population and reference groups. SUBJECTS AND METHODS We detected 36 Y-STRs genotyping in 455 unrelated Miao individuals from Guizhou province, and analysed genetic differentiation between the Miao population and 76 reference groups. RESULTS A total of 369 alleles were obtained, and the allele frequencies ranged from 0.0022 to 0.9802. In addition, the haplotype diversity, random match probability, and discrimination capacity values were 0.99997, 0.0022, and 0.9934, respectively. Moreover, the genetic relationships between Guizhou Miao and 76 ethnic populations showed that the population stratification was almost consistent with geographic distribution and language-family. CONCLUSIONS The 36 Y-STR loci in this study have good polymorphism distributions in the Guizhou Miao population, and therefore would be a useful tool in forensic identification and male parentage testing and even pedigree investigation.
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Affiliation(s)
- Jing Tang
- Guiyang Judicial Expertise Center of Public Security, Guiyang, Guizhou, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaojuan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qian Wang
- Guiyang Judicial Expertise Center of Public Security, Guiyang, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Enfang Qian
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yan Wu
- Guiyang Judicial Expertise Center of Public Security, Guiyang, Guizhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
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Wu Q, Ying J, Xue C, Lv Q, Song F, Wang J, Song X, Chen J. Genetic analysis of 29 Y-STR loci in Qiang population from Beichuan Qiang Autonomous County in China. Leg Med (Tokyo) 2020; 45:101714. [PMID: 32403023 DOI: 10.1016/j.legalmed.2020.101714] [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: 01/29/2020] [Revised: 04/10/2020] [Accepted: 05/03/2020] [Indexed: 02/08/2023]
Abstract
This study reported the forensic parameters of the 29 Y-STR loci of 242 unrelated Qiang males in Beichuan Qiang Autonomous County. Qiang population is a minority with small size populations and has never been reported. The overall haplotype diversity of Qiang population was measured to be 0.9992 while a discrimination capacity was 0.9215. According to the haplotypic analysis of the 29 Y-STR loci, 223 different haplotypes were obtained, of which 207 (92.83%) were unique. A total of 242 different alleles were checked at all loci, the corresponding allele frequencies ranged from 0.0041 to 0.7603. In addition, pairwise genetic distances, multidimensional scaling plots and neighbor-joining dendrogram were performed to analyze interpopulation differentiation between Qiang population and 16 other ethnic groups. These data can fill the gap in the Y-STR Haplotype Reference Database of the Qiang population and may be of reference value for forensic and population genetic analysis.
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Affiliation(s)
- Qian Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jun Ying
- Department of Clinical Laboratory, Santai People's Hospital, Santai 621100, Sichuan, China
| | - Chenglan Xue
- Sichuan Forensic Expertises Center in Southwest China, Chengdu 610041, China
| | - Qiang Lv
- Department of Clinical Laboratory, People's Hospital of Beichuan Qiang Autonomous County, Beichuan 622750, Sichuan, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jun Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xingbo Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Jie Chen
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China.
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Hakim HM, Khan HO, Ismail SA, Lalung J, Kofi AE, Nelson BR, Abdullah MT, Chambers GK, Edinur HA. Population data for 23 Y chromosome STR loci using the Powerplex® Y23 STR kit for the Kedayan population in Malaysia. Int J Legal Med 2020; 134:1335-1337. [PMID: 31897667 DOI: 10.1007/s00414-019-02237-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/11/2019] [Indexed: 11/25/2022]
Abstract
Genetic polymorphisms at 23 Y chromosome short tandem repeat (STRs) loci included in the Powerplex® Y23 PCR kit were successfully scored in 128 unrelated Kedayan individuals living in Sabah, East Malaysia. Complete haplotypes were recorded for all individuals and included 92 different types with 72 being unique to single male subjects. Three important forensic statistics were calculated from these data; haplotype diversity = 0.993, discriminating capacity = 0.719, and match probability = 0.015. The Kedayan appear to be most closely related to Malays and Filipinos in a multidimensional scaling plot and are separated from other mainland Asia populations including Thais and Hakka Han. These new data for Kedayan have been deposited in the YHRD database (accession number: YA004621). Our statistical analyses showed the reliability of Y-STR loci for geographically extended use in forensic casework and for studying human population history.
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Affiliation(s)
- Hashom Mohd Hakim
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 43200, Cheras, Selangor, Malaysia.
- School of Industrial Technology, Universiti Sains Malaysia, Jalan Sungai 2, 11800, Gelugor, Pulau Pinang, Malaysia.
| | - Hussein Omar Khan
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 43200, Cheras, Selangor, Malaysia
| | - Siti Afifah Ismail
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 43200, Cheras, Selangor, Malaysia
| | - Japareng Lalung
- School of Industrial Technology, Universiti Sains Malaysia, Jalan Sungai 2, 11800, Gelugor, Pulau Pinang, Malaysia
| | - Abban Edward Kofi
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Bryan Raveen Nelson
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Mohd Tajuddin Abdullah
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Geoffrey Keith Chambers
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Hisham Atan Edinur
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, 4111, Australia.
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Luo Y, Wu Y, Qian E, Wang Q, Wang Q, Zhang H, Wang X, Zhang H, Yang M, Ji J, Ren Z, Zhang Y, Tang J, Huang J. Population genetic analysis of 36 Y-chromosomal STRs yields comprehensive insights into the forensic features and phylogenetic relationship of Chinese Tai-Kadai-speaking Bouyei. PLoS One 2019; 14:e0224601. [PMID: 31703068 PMCID: PMC6839857 DOI: 10.1371/journal.pone.0224601] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/17/2019] [Indexed: 11/18/2022] Open
Abstract
Male-specifically inherited Y-STRs, harboring the features of haploidy and lack of crossing over, have gained considerable attention in population genetics and forensic investigations. Goldeneye® Y-PLUS kit was a recently developed amplification system focused on the genetic diversity of 36 Y-chromosomal short tandem repeats (Y-STRs) in East Asians. However, no population data and corresponding forensic features were reported in China. Here, 36 Y-STRs were first genotyped in 400 unrelated healthy Tai-Kadai-speaking Bouyei male individuals. A total of 371 alleles and 396 haplotypes could be detected, and the allelic frequencies ranged from 0.0025 to 0.9875. The haplotype diversity, random match probability and discrimination capacity values were 0.9999, 0.0026 and 0.9900, respectively. The gene diversity (GD) of 36 Y-STR loci in the studied group ranged from 0.0248 (DYS645) to 0.9601 (DYS385a/b). Population comparisons between the Guizhou Bouyei and 80 reference groups were performed via the AMOVA, MDS, and phylogenetic relationship reconstruction. The results showed that the population stratification was almost consistent with the geographic distribution and language-family, both among Chinese and worldwide ethnic groups. Our newly genotyped Bouyei samples show a close affinity with other Tai-Kadai-speaking groups in China and Southeast Asia. Our data may provide useful information for paternal lineage in the forensic application and population genetics, as well as evidence for archaeological and historical research.
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Affiliation(s)
- Ya Luo
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yan Wu
- Guiyang Judicial Expertise Center of Public Security, Guiyang, Guizhou, China
| | - Enfang Qian
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qian Wang
- Guiyang Judicial Expertise Center of Public Security, Guiyang, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaojuan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Ying Zhang
- Guiyang Judicial Expertise Center of Public Security, Guiyang, Guizhou, China
| | - Jing Tang
- Guiyang Judicial Expertise Center of Public Security, Guiyang, Guizhou, China
- * E-mail: (JT); (JH)
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
- * E-mail: (JT); (JH)
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11
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Genetic diversity and haplotype structure of 27 Y-STR loci in a Yanbian Korean population from Jilin Province, Northeast China. Leg Med (Tokyo) 2019; 36:110-112. [DOI: 10.1016/j.legalmed.2018.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 09/18/2018] [Accepted: 11/22/2018] [Indexed: 11/17/2022]
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12
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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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13
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Bugoye FC, Mulima E, Misinzo G. Analysis of Mutation Rate of 17 Y-Chromosome Short Tandem Repeats Loci Using Tanzanian Father-Son Paired Samples. GENETICS RESEARCH INTERNATIONAL 2018; 2018:8090469. [PMID: 30174958 PMCID: PMC6106792 DOI: 10.1155/2018/8090469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/24/2018] [Indexed: 11/17/2022]
Abstract
Hundred unrelated father-son buccal swab sample pairs collected from consented Tanzanian population were examined to establish mutation rates using 17 Y-STRs loci DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4 of the AmpFlSTRYfiler kit used in forensics and paternity testing. Prior to 17 Y-STRs analysis, father-son pair biological relationships were confirmed using 15 autosomal STRs markers and found to be paternally related. A total of four single repeat mutational events were observed between father and sons. Two mutations resulted in the gain of a repeat and the other two resulted in a loss of a repeat in the son. All observed mutations occurred at tetranucleotide loci DYS389II, DYS385a, and DYS385b. The locus specific mutation rate varied between 0 and 1.176 x10-3 and the average mutation rate of 17Y-STRs loci in the present study was 2.353x10-3 (6.41x10-4 - 6.013x10-3) at 95% CI. Furthermore the mean fathers' age with at least one mutation at son's birth was 32 years with standard error of 2.387 while the average age of all fathers without mutation in a sampled population at son's birth was 26.781 years with standard error of 0.609. The results shows that fathers' age at son's birth may have an effect on Y-STRs mutation rate analysis, though this age difference was statistically not significant using unpaired samples t-test (p = 0.05). As a consequence of observed mutation rates in this study, the precise and reliable understanding of mutation rate at Y-chromosome STR loci is necessary for a correct evaluation and interpretation of DNA typing results in forensics and paternity testing involving males. The criterion for exclusion in paternity testing should be defined, so that an exclusion from paternity has to be based on exclusion constellations at a minimum of two 17 Y-STRs loci.
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Affiliation(s)
- Fidelis Charles Bugoye
- Department of Forensic Science and DNA Services, Government Chemist Laboratory Authority, Dar es Salaam, Tanzania
| | - Elias Mulima
- Department of Forensic Science and DNA Services, Government Chemist Laboratory Authority, Dar es Salaam, Tanzania
| | - Gerald Misinzo
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro, Tanzania
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14
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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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15
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Claerhout S, Vandenbosch M, Nivelle K, Gruyters L, Peeters A, Larmuseau MH, Decorte R. Determining Y-STR mutation rates in deep-routing genealogies: Identification of haplogroup differences. Forensic Sci Int Genet 2018; 34:1-10. [DOI: 10.1016/j.fsigen.2018.01.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/10/2018] [Accepted: 01/14/2018] [Indexed: 10/18/2022]
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16
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He G, Chen P, Zou X, Chen X, Song F, Yan J, Hou Y. Genetic polymorphism investigation of the Chinese Yi minority using PowerPlex® Y23 STR amplification system. Int J Legal Med 2017; 131:663-666. [DOI: 10.1007/s00414-017-1537-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 01/10/2017] [Indexed: 11/25/2022]
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17
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Guo F, Song L, Zhang L. Population genetics for 17 Y-STR loci in Korean ethnic minority from Liaoning Province, Northeast China. Forensic Sci Int Genet 2016; 22:e9-e11. [PMID: 26818791 DOI: 10.1016/j.fsigen.2016.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 01/15/2016] [Accepted: 01/15/2016] [Indexed: 11/18/2022]
Affiliation(s)
- Fei Guo
- National Police University of China, No.83, Tawan Street, Huanggu District, Shenyang, Liaoning 110854, China.
| | - Liqu Song
- National Police University of China, No.83, Tawan Street, Huanggu District, Shenyang, Liaoning 110854, China
| | - Longnian Zhang
- National Police University of China, No.83, Tawan Street, Huanggu District, Shenyang, Liaoning 110854, China
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18
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Qian XQ, Yin CY, Ji Q, Li K, Fan HT, Yu YF, Bu FL, Hu LL, Wang JW, Mu HF, Haigh S, Chen F. Mutation rate analysis at 19 autosomal microsatellites. Electrophoresis 2015; 36:1633-9. [DOI: 10.1002/elps.201400558] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/09/2015] [Accepted: 03/13/2015] [Indexed: 11/05/2022]
Affiliation(s)
- Xiao-Qin Qian
- Department of Forensic Medicine; Nanjing Medical University; Nanjing Jiangsu P. R. China
| | - Cai-Yong Yin
- Department of Forensic Medicine; Nanjing Medical University; Nanjing Jiangsu P. R. China
| | - Qiang Ji
- Department of Forensic Medicine; Nanjing Medical University; Nanjing Jiangsu P. R. China
| | - Kai Li
- Department of Forensic Medicine; Nanjing Medical University; Nanjing Jiangsu P. R. China
| | - Han-Ting Fan
- Department of Forensic Medicine; Nanjing Medical University; Nanjing Jiangsu P. R. China
| | - Yan-Fang Yu
- Department of Forensic Medicine; Nanjing Medical University; Nanjing Jiangsu P. R. China
| | - Fan-Li Bu
- Department of Forensic Medicine; Nanjing Medical University; Nanjing Jiangsu P. R. China
| | - Ling-Li Hu
- Department of Forensic Medicine; Nanjing Medical University; Nanjing Jiangsu P. R. China
| | - Jian-Wen Wang
- Department of Forensic Medicine; Nanjing Medical University; Nanjing Jiangsu P. R. China
| | - Hao-Fang Mu
- Center of Forensic Sciences; Beijing Genomics Institute; Beijing P. R. China
| | - Steven Haigh
- Vascular Biology Center; Georgia Regents University; Augusta GA USA
| | - Feng Chen
- Department of Forensic Medicine; Nanjing Medical University; Nanjing Jiangsu P. R. China
- Vascular Biology Center; Georgia Regents University; Augusta GA USA
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19
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Oh YN, Lee HY, Lee EY, Kim EH, Yang WI, Shin KJ. Haplotype and mutation analysis for newly suggested Y-STRs in Korean father–son pairs. Forensic Sci Int Genet 2015; 15:64-8. [DOI: 10.1016/j.fsigen.2014.09.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/17/2014] [Accepted: 09/18/2014] [Indexed: 11/30/2022]
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20
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Balaresque P, King TE, Parkin EJ, Heyer E, Carvalho-Silva D, Kraaijenbrink T, de Knijff P, Tyler-Smith C, Jobling MA. Gene conversion violates the stepwise mutation model for microsatellites in y-chromosomal palindromic repeats. Hum Mutat 2014; 35:609-17. [PMID: 24610746 PMCID: PMC4233959 DOI: 10.1002/humu.22542] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 02/25/2014] [Indexed: 01/19/2023]
Abstract
The male-specific region of the human Y chromosome (MSY) contains eight large inverted repeats (palindromes), in which high-sequence similarity between repeat arms is maintained by gene conversion. These palindromes also harbor microsatellites, considered to evolve via a stepwise mutation model (SMM). Here, we ask whether gene conversion between palindrome microsatellites contributes to their mutational dynamics. First, we study the duplicated tetranucleotide microsatellite DYS385a,b lying in palindrome P4. We show, by comparing observed data with simulated data under a SMM within haplogroups, that observed heteroallelic combinations in which the modal repeat number difference between copies was large, can give rise to homoallelic combinations with zero-repeats difference, equivalent to many single-step mutations. These are unlikely to be generated under a strict SMM, suggesting the action of gene conversion. Second, we show that the intercopy repeat number difference for a large set of duplicated microsatellites in all palindromes in the MSY reference sequence is significantly reduced compared with that for nonpalindrome-duplicated microsatellites, suggesting that the former are characterized by unusual evolutionary dynamics. These observations indicate that gene conversion violates the SMM for microsatellites in palindromes, homogenizing copies within individual Y chromosomes, but increasing overall haplotype diversity among chromosomes within related groups.
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Affiliation(s)
- Patricia Balaresque
- UMR5288 CNRS/UPS-AMIS-Université Paul Sabatier, Toulouse, France; Department of Genetics, University of Leicester, Leicester, UK
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21
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Lee EY, Shin KJ, Rakha A, Sim JE, Park MJ, Kim NY, Yang WI, Lee HY. Analysis of 22 Y chromosomal STR haplotypes and Y haplogroup distribution in Pathans of Pakistan. Forensic Sci Int Genet 2014; 11:111-6. [DOI: 10.1016/j.fsigen.2014.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 03/03/2014] [Accepted: 03/04/2014] [Indexed: 10/25/2022]
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22
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Laouina A, Nadifi S, Boulouiz R, El Arji M, Talbi J, El Houate B, Yahia H, Chbel F. Mutation rate at 17 Y-STR loci in “Father/Son” pairs from moroccan population. Leg Med (Tokyo) 2013; 15:269-71. [DOI: 10.1016/j.legalmed.2013.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 01/31/2013] [Accepted: 03/15/2013] [Indexed: 11/29/2022]
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23
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Understanding the Y chromosome variation in Korea—relevance of combined haplogroup and haplotype analyses. Int J Legal Med 2012; 126:589-99. [DOI: 10.1007/s00414-012-0703-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 04/26/2012] [Indexed: 11/26/2022]
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24
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Nurieva NI, Medvinsky AB. The impact of population dynamics on Y-chromosome microsatellite polymorphism. Mathematical modeling. Biophysics (Nagoya-shi) 2012. [DOI: 10.1134/s0006350912030189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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25
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Martínez-González LJ, Saiz M, Álvarez-Cubero MJ, Gómez-Martín A, Álvarez JC, Martínez-Labarga C, Lorente JA. Distribution of Y chromosomal STRs loci in Mayan and Mestizo populations from Guatemala. Forensic Sci Int Genet 2012; 6:136-42. [DOI: 10.1016/j.fsigen.2011.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 02/18/2011] [Accepted: 04/02/2011] [Indexed: 11/28/2022]
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26
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Genetic diversity of 17 Y-chromosomal short tandem repeat loci in northeast Germany. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.08.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Empirical evaluation reveals best fit of a logistic mutation model for human Y-chromosomal microsatellites. Genetics 2011; 189:1403-11. [PMID: 21968190 DOI: 10.1534/genetics.111.132308] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rate of microsatellite mutation is dependent upon both the allele length and the repeat motif, but the exact nature of this relationship is still unknown. We analyzed data on the inheritance of human Y-chromosomal microsatellites in father-son duos, taken from 24 published reports and comprising 15,285 directly observable meioses. At the six microsatellites analyzed (DYS19, DYS389I, DYS390, DYS391, DYS392, and DYS393), a total of 162 mutations were observed. For each locus, we employed a maximum-likelihood approach to evaluate one of several single-step mutation models on the basis of the data. For five of the six loci considered, a novel logistic mutation model was found to provide the best fit according to Akaike's information criterion. This implies that the mutation probability at the loci increases (nonlinearly) with allele length at a rate that differs between upward and downward mutations. For DYS392, the best fit was provided by a linear model in which upward and downward mutation probabilities increase equally with allele length. This is the first study to empirically compare different microsatellite mutation models in a locus-specific fashion.
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28
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Hedman M, Neuvonen A, Sajantila A, Palo J. Dissecting the Finnish male uniformity: The value of additional Y-STR loci. Forensic Sci Int Genet 2011; 5:199-201. [DOI: 10.1016/j.fsigen.2010.03.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 03/18/2010] [Accepted: 03/18/2010] [Indexed: 11/29/2022]
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29
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Vieira-Silva C, Dario P, Ribeiro T, Lucas I, Geada H, Espinheira R. Y-STR mutational rates determination in South Portugal Caucasian population. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2009. [DOI: 10.1016/j.fsigss.2009.08.159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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30
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Haplotype-assisted characterization of germline mutations at short tandem repeat loci. Int J Legal Med 2009; 124:177-82. [DOI: 10.1007/s00414-009-0377-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 10/08/2009] [Indexed: 10/20/2022]
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31
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Shi W, Ayub Q, Vermeulen M, Shao RG, Zuniga S, van der Gaag K, de Knijff P, Kayser M, Xue Y, Tyler-Smith C. A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP-CEPH populations. Mol Biol Evol 2009; 27:385-93. [PMID: 19822636 PMCID: PMC2806244 DOI: 10.1093/molbev/msp243] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have investigated human male demographic history using 590 males from 51 populations in the Human Genome Diversity Project - Centre d’Étude du Polymorphisme Humain worldwide panel, typed with 37 Y-chromosomal Single Nucleotide Polymorphisms and 65 Y-chromosomal Short Tandem Repeats and analyzed with the program Bayesian Analysis of Trees With Internal Node Generation. The general patterns we observe show a gradient from the oldest population time to the most recent common ancestors (TMRCAs) and expansion times together with the largest effective population sizes in Africa, to the youngest times and smallest effective population sizes in the Americas. These parameters are significantly negatively correlated with distance from East Africa, and the patterns are consistent with most other studies of human variation and history. In contrast, growth rate showed a weaker correlation in the opposite direction. Y-lineage diversity and TMRCA also decrease with distance from East Africa, supporting a model of expansion with serial founder events starting from this source. A number of individual populations diverge from these general patterns, including previously documented examples such as recent expansions of the Yoruba in Africa, Basques in Europe, and Yakut in Northern Asia. However, some unexpected demographic histories were also found, including low growth rates in the Hazara and Kalash from Pakistan and recent expansion of the Mozabites in North Africa.
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Affiliation(s)
- Wentao Shi
- The Wellcome Trust Sanger Institute, Hinxton, Cambs., United Kingdom
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Reduced-volume and low-volume typing of Y-chromosomal SNPs to obtain Finnish Y-chromosomal compound haplotypes. Int J Legal Med 2009; 123:413-8. [DOI: 10.1007/s00414-009-0358-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 05/19/2009] [Indexed: 10/20/2022]
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Ge J, Budowle B, Aranda XG, Planz JV, Eisenberg AJ, Chakraborty R. Mutation rates at Y chromosome short tandem repeats in Texas populations. Forensic Sci Int Genet 2009; 3:179-84. [DOI: 10.1016/j.fsigen.2009.01.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 12/23/2008] [Accepted: 01/06/2009] [Indexed: 11/24/2022]
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Goedbloed M, Vermeulen M, Fang RN, Lembring M, Wollstein A, Ballantyne K, Lao O, Brauer S, Krüger C, Roewer L, Lessig R, Ploski R, Dobosz T, Henke L, Henke J, Furtado MR, Kayser M. Comprehensive mutation analysis of 17 Y-chromosomal short tandem repeat polymorphisms included in the AmpFlSTR Yfiler PCR amplification kit. Int J Legal Med 2009; 123:471-82. [PMID: 19322579 PMCID: PMC2766043 DOI: 10.1007/s00414-009-0342-y] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 03/13/2009] [Indexed: 11/28/2022]
Abstract
The Y-chromosomal short tandem repeat (Y-STR) polymorphisms included in the AmpFlSTR Yfiler polymerase chain reaction amplification kit have become widely used for forensic and evolutionary applications where a reliable knowledge on mutation properties is necessary for correct data interpretation. Therefore, we investigated the 17 Yfiler Y-STRs in 1,730-1,764 DNA-confirmed father-son pairs per locus and found 84 sequence-confirmed mutations among the 29,792 meiotic transfers covered. Of the 84 mutations, 83 (98.8%) were single-repeat changes and one (1.2%) was a double-repeat change (ratio, 1:0.01), as well as 43 (51.2%) were repeat gains and 41 (48.8%) repeat losses (ratio, 1:0.95). Medians from Bayesian estimation of locus-specific mutation rates ranged from 0.0003 for DYS448 to 0.0074 for DYS458, with a median rate across all 17 Y-STRs of 0.0025. The mean age (at the time of son's birth) of fathers with mutations was with 34.40 (+/-11.63) years higher than that of fathers without ones at 30.32 (+/-10.22) years, a difference that is highly statistically significant (p < 0.001). A Poisson-based modeling revealed that the Y-STR mutation rate increased with increasing father's age on a statistically significant level (alpha = 0.0294, 2.5% quantile = 0.0001). From combining our data with those previously published, considering all together 135,212 meiotic events and 331 mutations, we conclude for the Yfiler Y-STRs that (1) none had a mutation rate of >1%, 12 had mutation rates of >0.1% and four of <0.1%, (2) single-repeat changes were strongly favored over multiple-repeat ones for all loci but 1 and (3) considerable variation existed among loci in the ratio of repeat gains versus losses. Our finding of three Y-STR mutations in one father-son pair (and two pairs with two mutations each) has consequences for determining the threshold of allelic differences to conclude exclusion constellations in future applications of Y-STRs in paternity testing and pedigree analyses.
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Affiliation(s)
- Miriam Goedbloed
- Department of Forensic Molecular Biology, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam The Netherlands
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Sánchez-Diz P, Alves C, Carvalho E, Carvalho M, Espinheira R, García O, Pinheiro MF, Pontes L, Porto MJ, Santapa O, Silva C, Sumita D, Valente S, Whittle M, Yurrebaso I, Carracedo A, Amorim A, Gusmão L. Population and segregation data on 17 Y-STRs: results of a GEP-ISFG collaborative study. Int J Legal Med 2008; 122:529-33. [DOI: 10.1007/s00414-008-0265-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Accepted: 06/10/2008] [Indexed: 11/29/2022]
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Tariq MA, Ullah O, Riazuddin SA, Riazuddin S. Allele frequency distribution of 13 X-chromosomal STR loci in Pakistani population. Int J Legal Med 2008; 122:525-8. [PMID: 18629532 DOI: 10.1007/s00414-008-0263-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Accepted: 06/09/2008] [Indexed: 10/21/2022]
Abstract
Short tandem repeat (STR) markers are extensively being used for human identification as well as paternity and forensic case work. X-chromosome STR (X-STR) markers are a powerful complementary system especially in deficiency paternity testing. Many X-linked microsatellites have been evaluated but further studies are required to determine population specific statistics. Here, we report allele frequencies of 13 X-linked microsatellites (DXS8378, DXS9902, DXS6810, DXS7132, DXS981, DXS6793, DXS6801, DXS6789, GATA172D05, HPRTB, GATA31E08, DXS8377, and DXS7423) in the Pakistani population. Blood samples were collected from individuals representing all major ethnic groups of the Pakistan population. A total of 5-18 alleles were observed for each locus and altogether 109 alleles for all 13 X-STR loci. Heterozygosity in females ranged from 0.524 to 0.884. No significant deviation was observed from Hardy-Weinberg equilibrium for all 13 microsatellites. In addition, there was no evidence of linkage disequilibrium in any pairs of these markers. These results strongly suggest that the X-linked microsatellites described here can potentially serve as an extension to autosomal systems currently used in parentage analysis and forensic case work.
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Affiliation(s)
- Muhammad Akram Tariq
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
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The rate and spectrum of microsatellite mutation in Caenorhabditis elegans and Daphnia pulex. Genetics 2008; 178:2113-21. [PMID: 18430937 DOI: 10.1534/genetics.107.081927] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The effective use of microsatellite loci as tools for microevolutionary analysis requires knowledge of the factors influencing the rate and pattern of mutation, much of which is derived from indirect inference from population samples. Interspecific variation in microsatellite stability also provides a glimpse into aspects of phylogenetic constancy of mutational processes. Using long-term series of mutation-accumulation lines, we have obtained direct estimates of the spectrum of microsatellite mutations in two model systems: the nematode Caenorhabditis elegans and the microcrustacean Daphnia pulex. Although the scaling of the mutation rate with the number of tandem repeats is highly consistent across distantly related species, including yeast and human, the per-cell-division mutation rate appears to be elevated in multicellular species. Contrary to the expectations under the stepwise mutation model, most microsatellite mutations in C. elegans and D. pulex involve changes of multiple repeat units, with expansions being much more common than contractions.
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Decker AE, Kline MC, Redman JW, Reid TM, Butler JM. Analysis of mutations in father–son pairs with 17 Y-STR loci. Forensic Sci Int Genet 2008; 2:e31-5. [DOI: 10.1016/j.fsigen.2007.08.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Revised: 08/22/2007] [Accepted: 08/30/2007] [Indexed: 11/26/2022]
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Population data and mutation rate of nine Y-STRs in a mestizo Mexican population from Guadalajara, Jalisco, México. Leg Med (Tokyo) 2008; 10:319-20. [PMID: 18486519 DOI: 10.1016/j.legalmed.2008.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Revised: 02/25/2008] [Accepted: 03/19/2008] [Indexed: 10/22/2022]
Abstract
Nine Y-STR (DYS19, DYS390, DYS391, DYS392, DYS446, DYS447, DYS448, DYS456 and DYS458) were analyzed in a male sample of 285 unrelated individuals from Guadalajara, Jalisco, México. The haplotype diversity (0.996) and discrimination capacity (0.986) were calculated. A family study of around 200 father/son pairs and among 1828 meiosis showed five mutational events. All mutations were single step. The overall mutation rate estimated across the nine Y-STRs was 2.7 x 10(-3) (95% CI 1.2-6.4 x 10(-3))/locus/meiosis. The results indicate that these nine loci are useful Y-linked markers for forensic applications.
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Park MJ, Shin KJ, Kim NY, Yang WI, Cho SH, Lee HY. Characterization of Deletions in the DYS385 Flanking Region and Null Alleles Associated with AZFc Microdeletions in Koreans. J Forensic Sci 2008; 53:331-4. [DOI: 10.1111/j.1556-4029.2008.00660.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Pollin TI, McBride DJ, Agarwala R, Schäffer AA, Shuldiner AR, Mitchell BD, O'Connell JR. Investigations of the Y chromosome, male founder structure and YSTR mutation rates in the Old Order Amish. Hum Hered 2007; 65:91-104. [PMID: 17898540 PMCID: PMC2857628 DOI: 10.1159/000108941] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2007] [Accepted: 06/06/2007] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES Using Y chromosome short tandem repeat (YSTR) genotypes, (1) evaluate the accuracy and completeness of the Lancaster County Old Order Amish (OOA) genealogical records and (2) estimate YSTR mutation rates. METHODS Nine YSTR markers were genotyped in 739 Old Order Amish males who participated in several ongoing genetic studies of complex traits and could be connected into one of 28 all-male lineage pedigrees constructed using the Anabaptist Genealogy Database and the query software Ped-Hunter. A putative founder YSTR haplotype was constructed for each pedigree, and observed and inferred father-son transmissions were used to estimate YSTR mutation rates. RESULTS We inferred 27 distinct founder Y chromosome haplotypes in the 28 male lineages, which encompassed 27 surnames accounting for 98% of Lancaster OOA households. Nearly all deviations from founder haplotypes were consistent with mutation events rather than errors. The estimated marker-specific mutation rates ranged from 0 to 1.09% (average 0.33% using up to 283 observed meioses only and 0.28% using up to 1,232 observed and inferred meioses combined). CONCLUSIONS These data confirm the accuracy and completeness of the male lineage portion of the Anabaptist Genealogy Database and contribute mutation rate estimates for several commonly used Y chromosome STR markers.
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Affiliation(s)
- Toni I Pollin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
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