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Watahiki H, Fujii K, Fukagawa T, Mita Y, Kitayama T, Mizuno N. Y chromosome haplogroup N in a Japanese population is classified into three subclades, and two DYS385 loci, a duplicated Y-STR, are duplicated again in subclade N-M1819. Leg Med (Tokyo) 2024; 67:102390. [PMID: 38190775 DOI: 10.1016/j.legalmed.2023.102390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/10/2024]
Abstract
DYS385 is one of the major Y chromosome short tandem repeats (Y-STRs) in forensic genetics and exists as 2 copies in the human Y chromosome palindrome P4 region. In this study, we found that some samples were estimated to have ≥ 4 copies of DYS385 in Y chromosome haplogroup N in a Japanese population. Y chromosome haplogroup N is distributed widely in eastern/central Asia, Siberia, and eastern/northern Europe, and is also observed in Japan; however, little is known about haplogroup N subclades in the Japanese population. To reveal the link between increased DYS385 copy number and haplogroup N subclades, we sequenced single nucleotide polymorphisms to classify the subclades. As a result, the Japanese Y chromosomes of haplogroup N were classified into three subclades, and an increased DYS385 copy number was specific to subclade N-M1819* (N1b2*). These results are of use in forensic DNA analysis because Y-STR copy number is important for the interpretation of Y-STR typing results of male DNA mixtures and kinship analysis. We also found that DYS458.1 microvariants (DYS458 intermediate alleles with single-nucleotide insertion) were observed only in subclade N-CTS962 (N1b1b∼) samples. Given that previous studies reported that DYS458.1 microvariants are observed in Y chromosomes of haplogroup N in other populations, DYS458.1 might be used to infer haplogroup N subclades without limitation to the Japanese population. The results of this study will be beneficial not only to forensic genetics but also to anthropological studies.
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Affiliation(s)
- Haruhiko Watahiki
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan.
| | - Koji Fujii
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Takashi Fukagawa
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Yusuke Mita
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Tetsushi Kitayama
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Natsuko Mizuno
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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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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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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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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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: 1] [Impact Index Per Article: 1.0] [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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Du Q, Ma G, Lu C, Wang Q, Fu L, Cong B, Li S. Development and evaluation of a novel panel containing 188 microhaplotypes for 2nd-degree kinship testing in the Hebei Han population. Forensic Sci Int Genet 2023; 65:102855. [PMID: 36947934 DOI: 10.1016/j.fsigen.2023.102855] [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: 09/23/2022] [Revised: 02/17/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
Distant kinship identification is one of the critical problems in forensic genetics. As a new type of genetic marker defined and discussed in the last decade, the microhaplotype (MH) has drawn much attention in such identification owing to its specific advantages to traditional short tandem repeat (STR) or single nucleotide polymorphism (SNP) markers. In this study, MH markers were screened step by step from the 1000 Genomes Project database, and a novel multiplex panel containing 188 MHs (in which 181 are reported the first time, while 1 was reported in a previous study and the other 6 have partial overlaps with known markers) was constructed for application in 2nd- and 3rd-degree kinship identification. Along with the construction, a novel MH nomenclature was proposed, in which the SNP position information they contained was taken into account to eliminate the possibility that the same locus was named differently interlaboratory. After a series of evaluations, the panel was shown to have good sequencing accuracy, high sensitivity, species specificity, and resistance to anti-PCR inhibitors or degradation. Population data of the 188 MHs were calculated based on the genetic information of 221 unrelated Hebei Han individuals, and the effective number of alleles (Ae) ranged from 2.0925 to 8.2634 (with an average of 2.9267). For the whole system, the cumulative matching probability (CMP), the cumulative power of exclusion in paternity testing of duos (CPEduo) and that of trios (CPEtrio) reached 2.8422 × 10-137, 1-1.3109 × 10-21, and 1-2.8975 × 10-39, respectively, indicating that this panel was satisfactory for individual identification and paternity testing. Then, the efficiency of the 188 MHs in 2nd- and 3rd-degree kinship testing was studied based on 30 extended families consisting of 179 2nd-degree and 121 3rd-degree relatives, as well as simulations of 0.5 million pairs of those two kinships. The results showed that clear opinions would be given in 83.36% of 2nd-degree identifications with a false rate less than 10-5, when the confirming and excluding thresholds of cumulative likelihood ratio (CLR) were set as 104 and 10-4, respectively. This panel is still not sufficient to solve the problem of 3rd-degree kinship identification alone, and approximately 300 or 870 MH loci would be needed in 2nd- or 3rd-degree kinship identification, respectively, to achieve a system efficiency not less than 0.99 with such a threshold set; such necessary numbers would be used only as a reference in further research.
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Affiliation(s)
- Qingqing Du
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Guanju Ma
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Chaolong Lu
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Qian Wang
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Lihong Fu
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Bin Cong
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Shujin Li
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China.
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Zhao M, Cui W, Zhang Y, Lan Q, Zhu B. Haplotypic polymorphisms and forensic applications in Chinese Hunan Han population based on a series of Y-STR loci: a perspective of paternal inheritance. Ann Hum Biol 2023; 50:52-55. [PMID: 36688836 DOI: 10.1080/03014460.2023.2171120] [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: 01/24/2023]
Abstract
BACKGROUND Hunan, a multinational province in China, possesses more than fifty ethnic groups, such as the Han, Yao, Tujia, Miao, and so on. AIMS To evaluate the forensic efficiency of the novel panel and investigate the genetic relationships between Hunan Han population and 12 other reference populations from China. SUBJECTS AND METHODS Haplotypic data of 153 unrelated males of Hunan Han population were investigated using the AGCU Y SUPP Plus amplification system containing 27 Y-chromosomal short tandem repeat (STR) loci. Forensic parameters were calculated to evaluate the application efficiency of this panel in Hunan Han population. RESULTS Haplotype diversity, discrimination capability, and match probability values were 0.9999999977, 1.0000, and 0.0065, respectively. Pairwise fixation index values demonstrated that the minimal genetic differentiation (0.0073) was found between Hunan Han population and Hunan Yao group, while the maximal genetic differentiation (0.0651) was observed between Hunan Han and Guangxi Yao group from the perspective of the patrilineal DNA analysis. CONCLUSIONS The haplotype distributions of 27 Y-STR loci in Hunan Han population exhibited remarkable polymorphisms. Moreover, this panel has potential advantages for the forensic applications regarding family investigations, paternity testing of the paternal line, and population genetics.
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Affiliation(s)
- Ming Zhao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yunying Zhang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
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Antão-Sousa S, Conde-Sousa E, Gusmão L, Amorim A, Pinto N. Estimations of Mutation Rates Depend on Population Allele Frequency Distribution: The Case of Autosomal Microsatellites. Genes (Basel) 2022; 13:genes13071248. [PMID: 35886031 PMCID: PMC9323320 DOI: 10.3390/genes13071248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/28/2022] [Accepted: 07/11/2022] [Indexed: 01/27/2023] Open
Abstract
Microsatellites (or short-tandem repeats (STRs)) are widely used in anthropology and evolutionary studies. Their extensive polymorphism and rapid evolution make them the ideal genetic marker for dating events, such as the age of a gene or a population. This usage requires the estimation of mutation rates, which are usually estimated by counting the observed Mendelian incompatibilities in one-generation familial configurations (typically parent(s)–child duos or trios). Underestimations are inevitable when using this approach, due to the occurrence of mutational events that do not lead to incompatibilities with the parental genotypes (‘hidden’ or ‘covert’ mutations). It is known that the likelihood that one mutation event leads to a Mendelian incompatibility depends on the mode of genetic transmission considered, the type of familial configuration (duos or trios) considered, and the genotype(s) of the progenitor(s). In this work, we show how the magnitude of the underestimation of autosomal microsatellite mutation rates varies with the populations’ allele frequency distribution spectrum. The Mendelian incompatibilities approach (MIA) was applied to simulated parent(s)/offspring duos and trios in different populational scenarios. The results showed that the magnitude and type of biases depend on the population allele frequency distribution, whatever the type of familial data considered, and are greater when duos, instead of trios, are used to obtain the estimates. The implications for molecular anthropology are discussed and a simple framework is presented to correct the naïf estimates, along with an informatics tool for the correction of incompatibility rates obtained through the MIA.
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Affiliation(s)
- Sofia Antão-Sousa
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal; (E.C.-S.); (A.A.); (N.P.)
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), 4200-465 Porto, Portugal
- Faculty of Sciences, University of Porto (FCUP), 4169-007 Porto, Portugal
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro 20550-013, Brazil;
- Correspondence:
| | - Eduardo Conde-Sousa
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal; (E.C.-S.); (A.A.); (N.P.)
- Instituto de Engenharia Biomédica (INEB), 4200-135 Porto, Portugal
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro 20550-013, Brazil;
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal; (E.C.-S.); (A.A.); (N.P.)
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), 4200-465 Porto, Portugal
- Faculty of Sciences, University of Porto (FCUP), 4169-007 Porto, Portugal
| | - Nádia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal; (E.C.-S.); (A.A.); (N.P.)
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), 4200-465 Porto, Portugal
- Center of Mathematics, University of Porto (CMUP), 4169-007 Porto, Portugal
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9
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Översti S, Palo JU. Variation in the substitution rates among the human mitochondrial haplogroup U sublineages. Genome Biol Evol 2022; 14:6613373. [PMID: 35731946 PMCID: PMC9250076 DOI: 10.1093/gbe/evac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2022] [Indexed: 11/22/2022] Open
Abstract
Resolving the absolute timescale of phylogenetic trees stipulates reliable estimates for the rate of DNA sequence evolution. For this end, various calibration methods have been developed and studied intensively. Intraspecific rate variation among distinct genetic lineages, however, has gained less attention. Here, we have assessed lineage-specific molecular rates of human mitochondrial DNA (mtDNA) by performing tip-calibrated Bayesian phylogenetic analyses. Tip-calibration, as opposed to traditional nodal time stamps from dated fossil evidence or geological events, is based on sample ages and becoming ever more feasible as ancient DNA data from radiocarbon-dated samples accumulate. We focus on subhaplogroups U2, U4, U5a, and U5b, the data including ancient mtDNA genomes from 14C-dated samples (n = 234), contemporary genomes (n = 301), and two outgroup sequences from haplogroup R. The obtained molecular rates depended on the data sets (with or without contemporary sequences), suggesting time-dependency. More notable was the rate variation between haplogroups: U4 and U5a stand out having a substantially higher rate than U5b. This is also reflected in the divergence times obtained (U5a: 17,700 years and U5b: 29,700 years), a disparity not reported previously. After ruling out various alternative causes (e.g., selection, sampling, and sequence quality), we propose that the substitution rates have been influenced by demographic histories, widely different among populations where U4/U5a or U5b are frequent. As with the Y-chromosomal subhaplogroup R1b, the mitochondrial U4 and U5a have been associated with remarkable range extensions of the Yamnaya culture in the Bronze Age.
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Affiliation(s)
- Sanni Översti
- Transmission, Infection, Diversification and Evolution Group, Max-Planck Institute for the Science of Human History, Jena, Germany Kahlaische Straße 10, 07745, Jena, Germany.,Organismal and Evolutionary Biology Research Programme, Faculty of Biological Sciences, University of Helsinki, Helsinki, Finland P.O. Box 56, FI-00014, Helsinki, Finland
| | - Jukka U Palo
- Department of Forensic Medicine, Faculty of Medicine, University of Helsinki, Helsinki, Finland P.O. Box 40, FI-00014, Helsinki, Finland.,Forensic Chemistry Unit, Forensic Genetics Team, Finnish Institute for Health and Welfare, Helsinki, Finland P.O. Box 30, FI-00271, Helsinki, Finland
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10
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Kharkov VN. Y-Chromosome Markers in Population Genetics: Fundamental and Applied Results of Ethnogenomic Research. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421090040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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11
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Improved Models of Coalescence Ages of Y-DNA Haplogroups. Genes (Basel) 2021; 12:genes12060862. [PMID: 34200049 PMCID: PMC8228294 DOI: 10.3390/genes12060862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 11/19/2022] Open
Abstract
Databases of commercial DNA-testing companies now contain more customers with sequenced DNA than any completed academic study, leading to growing interest from academic and forensic entities. An important result for both these entities and the test takers themselves is how closely two individuals are related in time, as calculated through one or more molecular clocks. For Y-DNA, existing interpretations of these clocks are insufficiently accurate to usefully measure relatedness in historic times. In this article, I update the methods used to calculate coalescence ages (times to most-recent common ancestor, or TMRCAs) using a new, probabilistic statistical model that includes Y-SNP, Y-STR and ancilliary historical data, and provide examples of its use.
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12
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Mutation analysis for 25 Y-STR markers in Japanese population. Leg Med (Tokyo) 2021; 50:101860. [PMID: 33607450 DOI: 10.1016/j.legalmed.2021.101860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/22/2021] [Accepted: 02/05/2021] [Indexed: 11/27/2022]
Abstract
In this study, we analyzed DNA samples from 213 Japanese father son pairs with 25 Y-chromosome short tandem repeat (Y-STR) (DYS576, DYS389I, DYS635, DYS389II, DYS627, DYS460, DYS458, DYS19, YGATAH4, DYS448, DYS391, DYS456, DYS390, DYS438, DYS392, DYS518, DYS570, DYS437, DYS385, DYS449, DYS393, DYS439, DYS481, DYF387S1, and DYS533) markers using the Yfiler™ Plus PCR amplification kit. We calculated Y-STR mutation rates for each locus to evaluate the efficacy of the 25 Y-STR markers for paternity testing and forensic identification using samples from male relatives. Six rapidly mutating Y-STR markers (DYS576, DYS627, DYS518, DYS570, DYS449 and DYF387S1), previously reported to have high mutation rates (>1.0 × 10-2), are included in the 25 Y-STR markers, but our findings revealed that the mutation rates for all Y-STR markers except for DYS576 and DYS458 were lower than 1.0 × 10-2. Therefore, the use of these 25 Y-STR markers may be useful for forensic identification in the Japanese population.
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13
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Staadig A, Tillmar A. Evaluation of microhaplotypes in forensic kinship analysis from a Swedish population perspective. Int J Legal Med 2021; 135:1151-1160. [PMID: 33506298 PMCID: PMC8205927 DOI: 10.1007/s00414-021-02509-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/08/2021] [Indexed: 11/28/2022]
Abstract
The development of massively parallel sequencing (MPS) technology has enabled the discovery of several new types of forensic markers where microhaplotypes are one of these promising novel genetic markers. Microhaplotypes are, commonly, less than 300 nucleotides in length and consist of two or more closely linked single-nucleotide polymorphisms (SNPs). In this study, we have examined a custom-made QIAseq Microhaplotype panel (Qiagen), including 45 different microhaplotype loci. DNA libraries were prepared according to the GeneRead DNAseq Targeted Panels V2 library preparation workflow (Qiagen) and sequenced on a MiSeq FGx instrument (Verogen). We evaluated the performance of the panel based on 75 samples of Swedish origin and haplotype frequencies were established. We performed sensitivity studies and could detect haplotypes at input amounts down to 0.8 ng. We also studied mixture samples with two contributors for which haplotypes, for the minor contributor, were detectable down to the level of 1:100. Furthermore, we executed kinship simulations to evaluate the usefulness of this panel in kinship analysis. The results showed that both paternity and full sibling cases can clearly be solved. When simulating a half sibling versus unrelated case scenario, there were, however, some overlap of the likelihood ratio distributions potentially resulting in inconclusiveness. To conclude, the results of this initial study are promising for further implementation of this microhaplotype assay into the forensic field, although we noticed some primer design issues that could be optimized, which possibly would increase the power of the assay.
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Affiliation(s)
- Adam Staadig
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden. .,Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology; Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden.
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden.,Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology; Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
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14
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Ralf A, Lubach D, Kousouri N, Winkler C, Schulz I, Roewer L, Purps J, Lessig R, Krajewski P, Ploski R, Dobosz T, Henke L, Henke J, Larmuseau MHD, Kayser M. Identification and characterization of novel rapidly mutating Y‐chromosomal short tandem repeat markers. Hum Mutat 2020; 41:1680-1696. [DOI: 10.1002/humu.24068] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/05/2020] [Accepted: 06/22/2020] [Indexed: 01/06/2023]
Affiliation(s)
- Arwin Ralf
- Department of Genetic Identification Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
| | - Delano Lubach
- Department of Genetic Identification Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
| | - Nefeli Kousouri
- Department of Genetic Identification Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
| | | | - Iris Schulz
- Institut für Blutgruppenforschung LGC GmbH Cologne Germany
| | - Lutz Roewer
- Abteilung für Forensische Genetik, Institut für Rechtsmedizin und Forensische Wissenschaften Charite ́‐Universitätsmedizin Berlin Berlin Germany
| | - Josephine Purps
- Abteilung für Forensische Genetik, Institut für Rechtsmedizin und Forensische Wissenschaften Charite ́‐Universitätsmedizin Berlin Berlin Germany
| | - Rüdiger Lessig
- Institut für Rechtsmedizin Universitätsklinikum Halle Halle/Saale Germany
| | - Pawel Krajewski
- Department of Medical Genetics and Department of Forensic Medicine Medical University Warsaw Warsaw Poland
| | - Rafal Ploski
- Department of Medical Genetics and Department of Forensic Medicine Medical University Warsaw Warsaw Poland
| | - Tadeusz Dobosz
- Department of Forensic Medicine Wroclaw Medical University Wroclaw Poland
| | - Lotte Henke
- Institut für Blutgruppenforschung LGC GmbH Cologne Germany
| | - Jürgen Henke
- Institut für Blutgruppenforschung LGC GmbH Cologne Germany
| | | | - Manfred Kayser
- Department of Genetic Identification Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
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15
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Ambrosio IB, Braganholi DF, Orlando LBM, Andrekenas NC, da Mota Pontes I, da Silva DA, Astolfi-Filho S, de Carvalho EF, Cicarelli RMB, Gusmão L. Mutational data and population profiling of 23 Y-STRs in three Brazilian populations. Forensic Sci Int Genet 2020; 48:102348. [PMID: 32707472 DOI: 10.1016/j.fsigen.2020.102348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/22/2020] [Accepted: 06/26/2020] [Indexed: 11/18/2022]
Abstract
Y-chromosomal STRs are important markers in forensic genetics, due to some peculiar characteristics. The absence of recombination makes them a useful tool to infer kinship in complex cases involving distant paternal relatives, or to infer paternal bio-geographic ancestry. The presence of a single copy, being transmitted from father to son, allow tracing mutational events in Y-STRs without ambiguity. For the statistical interpretation of forensic evidences based on Y-STR profiles, it is necessary to have estimates on both mutation rates and haplotype frequencies. In this work, 407 father-son duos from São Paulo and Rio de Janeiro states and 204 unrelated individuals from Manaus were analyzed. Haplotype frequencies and mutation rates for the Y-STRs from the PowerPlex Y23 commercial kit were estimated. Thirty-six mutations were observed in 15 of the 22 Y-STRs analyzed, for an average mutation rate of 3.84 × 10-3 (95 % CI 2.69 × 10-3 to 5.32 × 10-3). All mutations in GAAA repeats occurred in alleles with 13 or more uninterrupted units. Mutations in GATA repeats were observed in alleles with 9-17 uninterrupted units. An analysis carried out in different father's age groups showed an increase of 2.48 times the mutation rate in the age group of 40-50 years, when compared to the 20-30 age group, in agreement with the described for autosomal STRs. A high haplotype diversity was found in the three Brazilian populations. Pairwise genetic distance analysis (FST) showed no significant differences between the three populations in this study, which were also close to populations with strong European influence. The highest distances among the Brazilian populations were with São Gabriel da Cachoeira, which has a high Native American ancestry.
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Affiliation(s)
- Isabela Brunelli Ambrosio
- Laboratório de Investigação de Paternidade, NAC - Faculdade de Ciências Farmacêuticas (FCFAr), Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São Paulo, Brazil.
| | - Danilo Faustino Braganholi
- Laboratório de Investigação de Paternidade, NAC - Faculdade de Ciências Farmacêuticas (FCFAr), Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São Paulo, Brazil
| | - Larissa Barros Muniz Orlando
- Laboratório de Genética Forense, do Instituto de Criminalística "Lorena do Santos Baptista" da Polícia Civil do Estado do Amazonas, Manaus, AM, Brazil
| | - Natalia Carolina Andrekenas
- Laboratório de Investigação de Paternidade, NAC - Faculdade de Ciências Farmacêuticas (FCFAr), Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São Paulo, Brazil
| | - Isabel da Mota Pontes
- Laboratório de Diagnóstico Molecular, Universidade Federal do Amazonas/UFAM, Manaus, AM, Brazil
| | - Dayse Aparecida da Silva
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Spartaco Astolfi-Filho
- Laboratório de Diagnóstico Molecular, Universidade Federal do Amazonas/UFAM, Manaus, AM, Brazil
| | | | - Regina Maria Barretto Cicarelli
- Laboratório de Investigação de Paternidade, NAC - Faculdade de Ciências Farmacêuticas (FCFAr), Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São Paulo, Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
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16
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Xu W, Wang Y, Zhang D, Wang D, Zhou L, Ye X, Zhu C, Shi Y. Mutation analysis of 21 autosomal short tandem repeats in Han population from Hunan, China. Ann Hum Biol 2020; 46:254-260. [PMID: 31264462 DOI: 10.1080/03014460.2019.1638966] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Background: Short tandem repeats (STRs) are powerful genetic markers widely used in human genetics. Population data and locus-specific mutation rates of STRs are crucial for the evaluation and interpretation of genetic evidence in forensic and population genetics.Aim: To investigate the mutation rates of 21 autosomal STRs in a population from central south China.Subjects and methods: This study analysed 3420 paternity cases with a Combined Paternity Index >10,000 from Han population in Hunan. A total of 68,743 meiotic transfers were analysed and 62 mutations were identified.Results: The overall mutation rate of STR loci was 0.9 × 10-3 (95% CI, 0.0007-0.0011) and the locus-specific mutation rates were estimated ranging from 0.0000-0.0023. Locus D1S1656 exhibited the highest mutation rate of 2.3 × 10-3 (95% CI, 0.0005-0.0006), followed by D12S391 with a mutation rate of 2.0 × 10-3 (95% CI, 0.0007-0.0044). No mutation was observed at TPOX, D2S1338 or Penta D. One-step mutation cases accounted for 96.77% of total mutations and the ratio of paternal vs maternal mutations was ∼4.85:1. Inter-population comparisons of locus-specific mutation rates of several STRs revealed significant differences between Han in Hunan and Han in other regions of China. Conclusion: The data justified the use of geographical data in further genetic applications.
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Affiliation(s)
- Wei Xu
- Institute of Translational Medicine, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, PR China
| | - Yuequn Wang
- Institute of Life Science, Hunan Normal University, Changsha, PR China
| | - Dandan Zhang
- School of Public Health, University of South China, Hengyang, PR China
| | - Daixin Wang
- Center of Forensic Science, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan School of Physical Sciences, Changsha, PR China
| | - Liang Zhou
- School of Public Health, Changsha Normal University, Changsha, PR China
| | - Xiangli Ye
- School of Medicine, Hunan Normal University, Changsha, PR China
| | - Chaogeng Zhu
- Translational Medicine Laboratory of Pancreatic Diseases, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, PR China
| | - Yongzhong Shi
- Institute of Translational Medicine, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, PR China
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17
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Maduna SN, Vivian-Smith A, Jónsdóttir ÓDB, Imsland AKD, Klütsch CFC, Nyman T, Eiken HG, Hagen SB. Genome- and transcriptome-derived microsatellite loci in lumpfish Cyclopterus lumpus: molecular tools for aquaculture, conservation and fisheries management. Sci Rep 2020; 10:559. [PMID: 31953426 PMCID: PMC6968997 DOI: 10.1038/s41598-019-57071-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 12/17/2019] [Indexed: 12/16/2022] Open
Abstract
The lumpfish Cyclopterus lumpus is commercially exploited in numerous areas of its range in the North Atlantic Ocean, and is important in salmonid aquaculture as a biological agent for controlling sea lice. Despite the economic importance, few genetic resources for downstream applications, such as linkage mapping, parentage analysis, marker-assisted selection (MAS), quantitative trait loci (QTL) analysis, and assessing adaptive genetic diversity are currently available for the species. Here, we identify both genome- and transcriptome-derived microsatellites loci from C. lumpus to facilitate such applications. Across 2,346 genomic contigs, we detected a total of 3,067 microsatellite loci, of which 723 were the most suitable ones for primer design. From 116,555 transcriptomic unigenes, we identified a total of 231,556 microsatellite loci, which may indicate a high coverage of the available STRs. Out of these, primer pairs could only be designed for 6,203 loci. Dinucleotide repeats accounted for 89 percent and 52 percent of the genome- and transcriptome-derived microsatellites, respectively. The genetic composition of the dominant repeat motif types showed differences from other investigated fish species. In the genome-derived microsatellites AC/GT (67.8 percent), followed by AG/CT (15.1 percent) and AT/AT (5.6 percent) were the major motifs. Transcriptome-derived microsatellites showed also most dominantly the AC/GT repeat motif (33 percent), followed by A/T (26.6 percent) and AG/CT (11 percent). Functional annotation of microsatellite-containing transcriptomic sequences showed that the majority of the expressed sequence tags encode proteins involved in cellular and metabolic processes, binding activity and catalytic reactions. Importantly, STRs linked to genes involved in immune system process, growth, locomotion and reproduction were discovered in the present study. The extensive genomic marker information reported here will facilitate molecular ecology studies, conservation initiatives and will benefit many aspects of the breeding programmes of C. lumpus.
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Affiliation(s)
- Simo N Maduna
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Environment and Natural Resources, P.O. Box 115, NO-1431, Ås, Norway.
| | - Adam Vivian-Smith
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Forestry and Forest Resources, P.O. Box 115, NO-1431, Ås, Norway
| | | | - Albert K D Imsland
- Akvaplan-niva, Iceland Office, Akralind 4, 201, Kópavogur, Iceland.,Department of Biosciences, University of Bergen, 5020, Bergen, Norway
| | - Cornelya F C Klütsch
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Environment and Natural Resources, P.O. Box 115, NO-1431, Ås, Norway
| | - Tommi Nyman
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Environment and Natural Resources, P.O. Box 115, NO-1431, Ås, Norway
| | - Hans Geir Eiken
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Environment and Natural Resources, P.O. Box 115, NO-1431, Ås, Norway
| | - Snorre B Hagen
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Environment and Natural Resources, P.O. Box 115, NO-1431, Ås, Norway.
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18
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Michalak E, Abreu-Głowacka M, Konarzewska M, Pepiński W, Skawrońska M, Wójcik M, Sołtyszewski I, Żaba C. Population genetics of 30 insertion-deletion polymorphism in polish Populations. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Hamester FIR, da Silva DS, Leboute APM, Motta CHA, Alho CS. Slippage mutation rates in 15 autosomal short tandem repeat loci for forensic purposes in a Southeastern Brazilian population. Electrophoresis 2019; 40:2873-2876. [PMID: 31442316 DOI: 10.1002/elps.201800491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 07/24/2019] [Accepted: 08/13/2019] [Indexed: 11/06/2022]
Abstract
Well-defined estimates of mutation rates in highly polymorphic tetranucleotide STR loci are a prerequisite for human identification in genetics laboratory routines useful for civil and criminal investigations. Studying 15 autosomal STR loci of forensic interest (CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, TH01, TPOX, and vWA), we detected 193 slippage mutations (189 one-step and four two-step mutations) in 148 875 parent-child allelic transfers from 5171 paternity cases with true biological relationship (15 096 individuals; 4754 trios and 417 duos; 9925 meiosis) from the state of São Paulo, a very representative population of Brazil. The overall mutation rate was 1.3 × 10-3 and the highest rates were observed at loci vWA (2.8 × 10-3 ), FGA and D18S51 (2.7 × 10-3 for both), while loci TH01 and TPOX did not present any mutations. The mean slippage mutation rate of paternal origin (1.8 × 10-3 ) was six times higher than that observed for maternal origin (0.3 × 10-3 ).
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Affiliation(s)
- Fernanda Irma Remus Hamester
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Laboratório de Genética Humana e Molecular - Genética Forense, Porto Alegre, RS, Brazil.,Instituto-Geral de Perícias do Estado do Rio Grande do Sul (IGP-RS), Divisão de Genética Forense, Porto Alegre, RS, Brazil
| | - Débora Santos da Silva
- Instituto de Medicina Social e Criminologia (IMESC), Núcleo de Perícias Laboratoriais, São Paulo, SP, Brazil
| | - Ana Paula Magalhães Leboute
- Instituto-Geral de Perícias do Estado do Rio Grande do Sul (IGP-RS), Divisão de Genética Forense, Porto Alegre, RS, Brazil
| | - Carlos Henrique Ares Motta
- Instituto de Medicina Social e Criminologia (IMESC), Núcleo de Perícias Laboratoriais, São Paulo, SP, Brazil
| | - Clarice Sampaio Alho
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Laboratório de Genética Humana e Molecular - Genética Forense, Porto Alegre, RS, Brazil
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20
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A comprehensive mutation study in wide deep-rooted R1b Serbian pedigree: mutation rates and male relative differentiation capacity of 36 Y-STR markers. Forensic Sci Int Genet 2019; 41:137-144. [DOI: 10.1016/j.fsigen.2019.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/05/2019] [Accepted: 04/29/2019] [Indexed: 11/23/2022]
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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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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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Vieira TC, Duarte Gigonzac MA, Goulart Rodovalho R, Morais Cavalcanti L, Bernardes Minasi L, Melo Rodrigues F, da Cruz AD. Mutation rates in 21 autosomal short tandem repeat loci in a population from Goiás, Brazil. Electrophoresis 2017; 38:2791-2794. [DOI: 10.1002/elps.201700192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 06/20/2017] [Accepted: 07/29/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Thaís Cidália Vieira
- LaGene-Laboratory of Human Cytogenetics and Molecular Genetics; Secretary of State for Health of Goiás (LACEN/SESGO); Goiânia GO Brazil
- State University of Goiás (UEG); Goiânia GO Brazil
- Postgraduate Program in Genetics (MGene)/Replicon Research Center; Pontifical Catholic University of Goiás (PUC-GO); Goiânia GO Brazil
| | - Marc Alexandre Duarte Gigonzac
- LaGene-Laboratory of Human Cytogenetics and Molecular Genetics; Secretary of State for Health of Goiás (LACEN/SESGO); Goiânia GO Brazil
- State University of Goiás (UEG); Goiânia GO Brazil
- Postgraduate Program in Genetics (MGene)/Replicon Research Center; Pontifical Catholic University of Goiás (PUC-GO); Goiânia GO Brazil
| | | | | | - Lysa Bernardes Minasi
- Postgraduate Program in Genetics (MGene)/Replicon Research Center; Pontifical Catholic University of Goiás (PUC-GO); Goiânia GO Brazil
| | - Flávia Melo Rodrigues
- State University of Goiás (UEG); Goiânia GO Brazil
- Postgraduate Program in Genetics (MGene)/Replicon Research Center; Pontifical Catholic University of Goiás (PUC-GO); Goiânia GO Brazil
| | - Aparecido Divino da Cruz
- LaGene-Laboratory of Human Cytogenetics and Molecular Genetics; Secretary of State for Health of Goiás (LACEN/SESGO); Goiânia GO Brazil
- Postgraduate Program in Genetics (MGene)/Replicon Research Center; Pontifical Catholic University of Goiás (PUC-GO); Goiânia GO Brazil
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Sánchez M, Burgos G, Gaviria A, Aguirre V, Vela M, Leone P, Paz-y-Miño C. Y STRs mutation events in father-son pairs in Ecuadorian individuals. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Steele CD, Court DS, Balding DJ. Worldwide F(ST) estimates relative to five continental-scale populations. Ann Hum Genet 2015; 78:468-77. [PMID: 26460400 PMCID: PMC4223938 DOI: 10.1111/ahg.12081] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We estimate the population genetics parameter (also referred to as the fixation index) from short tandem repeat (STR) allele frequencies, comparing many worldwide human subpopulations at approximately the national level with continental-scale populations. is commonly used to measure population differentiation, and is important in forensic DNA analysis to account for remote shared ancestry between a suspect and an alternative source of the DNA. We estimate comparing subpopulations with a hypothetical ancestral population, which is the approach most widely used in population genetics, and also compare a subpopulation with a sampled reference population, which is more appropriate for forensic applications. Both estimation methods are likelihood-based, in which is related to the variance of the multinomial-Dirichlet distribution for allele counts. Overall, we find low values, with posterior 97.5 percentiles when comparing a subpopulation with the most appropriate population, and even for inter-population comparisons we find . These are much smaller than single nucleotide polymorphism-based inter-continental estimates, and are also about half the magnitude of STR-based estimates from population genetics surveys that focus on distinct ethnic groups rather than a general population. Our findings support the use of up to 3% in forensic calculations, which corresponds to some current practice.
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Nagle N, Ballantyne KN, van Oven M, Tyler-Smith C, Xue Y, Taylor D, Wilcox S, Wilcox L, Turkalov R, van Oorschot RA, McAllister P, Williams L, Kayser M, Mitchell RJ. Antiquity and diversity of aboriginal Australian Y-chromosomes. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 159:367-81. [DOI: 10.1002/ajpa.22886] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 10/01/2015] [Accepted: 10/08/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Nano Nagle
- Department of Biochemistry and Genetics; La Trobe Institute of Molecular Sciences, La Trobe University; Melbourne VIC Australia
| | - Kaye N. Ballantyne
- Victorian Police Forensic Services Department; Office of the Chief Forensic Scientist; Melbourne VIC Australia
- Department of Forensic Molecular Biology; Erasmus MC University Medical Center; Rotterdam The Netherlands
| | - Mannis van Oven
- Department of Forensic Molecular Biology; Erasmus MC University Medical Center; Rotterdam The Netherlands
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute; Welcome Trust Genome Campus; Hinxton Cambridgeshire UK
| | - Yali Xue
- The Wellcome Trust Sanger Institute; Welcome Trust Genome Campus; Hinxton Cambridgeshire UK
| | - Duncan Taylor
- Forensic Science South Australia; 21 Divett Place Adelaide SA 5000 Australia
- School of Biological Sciences; Flinders University; Adelaide SA 5001 Australia
| | - Stephen Wilcox
- Australian Genome Research Facility; Melbourne VIC Australia
| | - Leah Wilcox
- Department of Biochemistry and Genetics; La Trobe Institute of Molecular Sciences, La Trobe University; Melbourne VIC Australia
| | - Rust Turkalov
- Australian Genome Research Facility; Melbourne VIC Australia
| | - Roland A.H. van Oorschot
- Victorian Police Forensic Services Department; Office of the Chief Forensic Scientist; Melbourne VIC Australia
| | | | - Lesley Williams
- Department of Communities; Child Safety and Disability Services, Queensland Government; Brisbane QLD Australia
| | - Manfred Kayser
- Department of Forensic Molecular Biology; Erasmus MC University Medical Center; Rotterdam The Netherlands
| | - Robert J. Mitchell
- Department of Biochemistry and Genetics; La Trobe Institute of Molecular Sciences, La Trobe University; Melbourne VIC Australia
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27
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Forensic typing of short tandem repeat markers on the X and Y chromosomes. Forensic Sci Int Genet 2015; 18:140-51. [DOI: 10.1016/j.fsigen.2015.03.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/22/2015] [Accepted: 03/24/2015] [Indexed: 11/17/2022]
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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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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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30
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Da Fré NN, Rodenbusch R, Gastaldo AZ, Hanson E, Ballantyne J, Alho CS. Genetic data and de novo mutation rates in father-son pairs of 23 Y-STR loci in Southern Brazil population. Int J Legal Med 2014; 129:1221-3. [DOI: 10.1007/s00414-014-1101-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 10/29/2014] [Indexed: 10/24/2022]
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31
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Isolation, contact and social behavior shaped genetic diversity in West Timor. J Hum Genet 2014; 59:494-503. [PMID: 25078354 PMCID: PMC4521296 DOI: 10.1038/jhg.2014.62] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 06/25/2014] [Accepted: 06/27/2014] [Indexed: 01/17/2023]
Abstract
Timor, an eastern Indonesian island linking mainland Asia with Australia and the Pacific world, had a complex history, including its role as a contact zone between two language families (Austronesian and Trans-New Guinean), as well as preserving elements of a rich Austronesian cultural heritage, such as matrilocal marriage practices. Using an array of biparental (autosomal and X-chromosome single-nucleotide polymorphisms) and uniparental markers (Y chromosome and mitochondrial DNA), we reconstruct a broad genetic profile of Timorese in the Belu regency of West Timor, including the traditional princedom of Wehali, focusing on the effects of cultural practices, such as language and social change, on patterns of genetic diversity. Sex-linked data highlight the different histories and social pressures experienced by women and men. Measures of diversity and population structure show that Timorese men had greater local mobility than women, as expected in matrilocal communities, where women remain in their natal village, whereas men move to the home village of their wife. Reaching further back in time, maternal loci (mitochondrial DNA and the X chromosome) are dominated by lineages with immigrant Asian origins, whereas paternal loci (Y chromosome) tend to exhibit lineages of the earliest settlers in the eastern Indonesian region. The dominance of Asian female lineages is especially apparent in the X chromosome compared with the autosomes, suggesting that women played a paramount role during and after the period of Asian immigration into Timor, perhaps driven by the matrilocal marriage practices of expanding Austronesian communities.
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Trejaut JA, Poloni ES, Yen JC, Lai YH, Loo JH, Lee CL, He CL, Lin M. Taiwan Y-chromosomal DNA variation and its relationship with Island Southeast Asia. BMC Genet 2014; 15:77. [PMID: 24965575 PMCID: PMC4083334 DOI: 10.1186/1471-2156-15-77] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 06/10/2014] [Indexed: 01/12/2023] Open
Abstract
Background Much of the data resolution of the haploid non-recombining Y chromosome (NRY) haplogroup O in East Asia are still rudimentary and could be an explanatory factor for current debates on the settlement history of Island Southeast Asia (ISEA). Here, 81 slowly evolving markers (mostly SNPs) and 17 Y-chromosomal short tandem repeats were used to achieve higher level molecular resolution. Our aim is to investigate if the distribution of NRY DNA variation in Taiwan and ISEA is consistent with a single pre-Neolithic expansion scenario from Southeast China to all ISEA, or if it better fits an expansion model from Taiwan (the OOT model), or whether a more complex history of settlement and dispersals throughout ISEA should be envisioned. Results We examined DNA samples from 1658 individuals from Vietnam, Thailand, Fujian, Taiwan (Han, plain tribes and 14 indigenous groups), the Philippines and Indonesia. While haplogroups O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 follow a decreasing cline from Taiwan towards Western Indonesia, O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 decline northward from Western Indonesia towards Taiwan. Compared to the Taiwan plain tribe minority groups the Taiwanese Austronesian speaking groups show little genetic paternal contribution from Han. They are also characterized by low Y-chromosome diversity, thus testifying for fast drift in these populations. However, in contrast to data provided from other regions of the genome, Y-chromosome gene diversity in Taiwan mountain tribes significantly increases from North to South. Conclusion The geographic distribution and the diversity accumulated in the O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 haplogroups on one hand, and in the O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 haplogroups on the other, support a pincer model of dispersals and gene flow from the mainland to the islands which likely started during the late upper Paleolithic, 18,000 to 15,000 years ago. The branches of the pincer contributed separately to the paternal gene pool of the Philippines and conjointly to the gene pools of Madagascar and the Solomon Islands. The North to South increase in diversity found for Taiwanese Austronesian speaking groups contrasts with observations based on mitochondrial DNA, thus hinting to a differentiated demographic history of men and women in these populations.
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Affiliation(s)
- Jean A Trejaut
- Mackay Memorial Hospital, Taipei, Molecular Anthropology Laboratory, 45 Min-Sheng Road,225115 Tamsui, New Taipei city, Taiwan.
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Mutation rates of 15 X chromosomal short tandem repeat markers. Int J Legal Med 2014; 128:579-87. [DOI: 10.1007/s00414-014-1016-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 04/30/2014] [Indexed: 11/25/2022]
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Mutation rates, spectra, and genome-wide distribution of spontaneous mutations in mismatch repair deficient yeast. G3-GENES GENOMES GENETICS 2013; 3:1453-65. [PMID: 23821616 PMCID: PMC3755907 DOI: 10.1534/g3.113.006429] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
DNA mismatch repair is a highly conserved DNA repair pathway. In humans, germline mutations in hMSH2 or hMLH1, key components of mismatch repair, have been associated with Lynch syndrome, a leading cause of inherited cancer mortality. Current estimates of the mutation rate and the mutational spectra in mismatch repair defective cells are primarily limited to a small number of individual reporter loci. Here we use the yeast Saccharomyces cerevisiae to generate a genome-wide view of the rates, spectra, and distribution of mutation in the absence of mismatch repair. We performed mutation accumulation assays and next generation sequencing on 19 strains, including 16 msh2 missense variants implicated in Lynch cancer syndrome. The mutation rate for DNA mismatch repair null strains was approximately 1 mutation per genome per generation, 225-fold greater than the wild-type rate. The mutations were distributed randomly throughout the genome, independent of replication timing. The mutation spectra included insertions/deletions at homopolymeric runs (87.7%) and at larger microsatellites (5.9%), as well as transitions (4.5%) and transversions (1.9%). Additionally, repeat regions with proximal repeats are more likely to be mutated. A bias toward deletions at homopolymers and insertions at (AT)n microsatellites suggests a different mechanism for mismatch generation at these sites. Interestingly, 5% of the single base pair substitutions might represent double-slippage events that occurred at the junction of immediately adjacent repeats, resulting in a shift in the repeat boundary. These data suggest a closer scrutiny of tumor suppressors with homopolymeric runs with proximal repeats as the potential drivers of oncogenesis in mismatch repair defective cells.
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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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Haas C, Shved N, Rühli FJ, Papageorgopoulou C, Purps J, Geppert M, Willuweit S, Roewer L, Krawczak M. Y-chromosomal analysis identifies the skeletal remains of Swiss national hero Jörg Jenatsch (1596-1639). Forensic Sci Int Genet 2013; 7:610-617. [PMID: 24035510 DOI: 10.1016/j.fsigen.2013.08.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 08/13/2013] [Accepted: 08/14/2013] [Indexed: 10/26/2022]
Abstract
Jörg Jenatsch was a Swiss defender of independence and a fighter for liberty in the 17th century. With the help of three living male members of the Jenatsch family, we successfully identified a skeleton exhumed from Chur cathedral as the remains of Jörg Jenatsch. Our conclusion was based upon complete Y-STR and Y-SNP profiles that could be generated by replicate analyses of a bone sample available to us. The skeleton and the three living family members carried the same Y-SNP haplogroup, but were discordant at three of 23 Y-STR loci. This notwithstanding, conservative biostatistical evaluation of the data suggests that the Chur skeleton is at least 20 times more likely than not to be Jörg Jenatsch.
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Affiliation(s)
- Cordula Haas
- Institute of Legal Medicine, University of Zurich, Switzerland.
| | - Natallia Shved
- Centre for Evolutionary Medicine, Institute of Anatomy, University of Zurich, Switzerland
| | - Frank Jakobus Rühli
- Centre for Evolutionary Medicine, Institute of Anatomy, University of Zurich, Switzerland
| | - Christina Papageorgopoulou
- Laboratory of Anthropology, Department of History and Ethnology, Demokritus University of Thrace, Greece
| | - Josephine Purps
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Maria Geppert
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Sascha Willuweit
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University of Kiel, Germany
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Pepinski W, Abreu-Glowacka M, Koralewska-Kordel M, Michalak E, Kordel K, Niemcunowicz-Janica A, Szeremeta M, Konarzewska M. Population genetics of 30 INDELs in populations of Poland and Taiwan. Mol Biol Rep 2013; 40:4333-8. [PMID: 23690203 PMCID: PMC3685699 DOI: 10.1007/s11033-013-2521-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 04/27/2013] [Indexed: 11/30/2022]
Abstract
The Investigator DIPplex® kit (Qiagen) contain components for the simultaneous amplification and analysis of 30 biallelic autosomal INDELs and amelogenin. The objective of this study was to estimate the diversity of the 30 markers in Polish (NP = 122) and Taiwanese (NT = 126) population samples and to evaluate their usefulness in forensic genetics. All amplicon lengths were shorter than 160 base pairs. The DIPplex genotype distributions showed no significant deviation from Hardy–Weinberg rule expectations (Bonferroni corrected) except for DLH39 in the Taiwanese population. Among the Poles and the Taiwanese the mean observed heterozygosity values are 0.4385 and 0.4079, and the combined matching probability values are 7.98 × 10−14 and 1.22 × 10−11, respectively. The investigated marker set has been confirmed as a potential extension to standard short tandem repeat-based kits or a separate informative system for individual identification and kinship analysis. Eight INDELs have been selected as possible ancestry informative single-nucleotide polymorphisms for further analyses.
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Affiliation(s)
- Witold Pepinski
- Department of Forensic Medicine, Medical University of Bialystok, Bialystok, Poland.
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Tumonggor MK, Karafet TM, Hallmark B, Lansing JS, Sudoyo H, Hammer MF, Cox MP. The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific. J Hum Genet 2013; 58:165-73. [PMID: 23344321 DOI: 10.1038/jhg.2012.154] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Indonesia, an island nation linking mainland Asia with the Pacific world, hosts a wide range of linguistic, ethnic and genetic diversity. Despite the complexity of this cultural environment, genetic studies in Indonesia remain surprisingly sparse. Here, we report mitochondrial DNA (mtDNA) and associated Y-chromosome diversity for the largest cohort of Indonesians examined to date-2740 individuals from 70 communities spanning 12 islands across the breadth of the Indonesian archipelago. We reconstruct 50 000 years of population movements, from mitochondrial lineages reflecting the very earliest settlers in island southeast Asia, to Neolithic population dispersals. Historic contacts from Chinese, Indians, Arabs and Europeans comprise a noticeable fraction of Y-chromosome variation, but are not reflected in the maternally inherited mtDNA. While this historic immigration favored men, patterns of genetic diversity show that women moved more widely in earlier times. However, measures of population differentiation signal that Indonesian communities are trending away from the matri- or ambilocality of early Austronesian societies toward the more common practice of patrilocal residence today. Such sex-specific dispersal patterns remain even after correcting for the different mutation rates of mtDNA and the Y chromosome. This detailed palimpsest of Indonesian genetic diversity is a direct outcome of the region's complex history of immigration, transitory migrants and populations that have endured in situ since the region's first settlement.
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Rajeevan H, Soundararajan U, Pakstis AJ, Kidd KK. Introducing the Forensic Research/Reference on Genetics knowledge base, FROG-kb. INVESTIGATIVE GENETICS 2012; 3:18. [PMID: 22938150 PMCID: PMC3488007 DOI: 10.1186/2041-2223-3-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 06/22/2012] [Indexed: 11/18/2022]
Abstract
BACKGROUND Online tools and databases based on multi-allelic short tandem repeat polymorphisms (STRPs) are actively used in forensic teaching, research, and investigations. The Fst value of each CODIS marker tends to be low across the populations of the world and most populations typically have all the common STRP alleles present diminishing the ability of these systems to discriminate ethnicity. Recently, considerable research is being conducted on single nucleotide polymorphisms (SNPs) to be considered for human identification and description. However, online tools and databases that can be used for forensic research and investigation are limited. METHODS The back end DBMS (Database Management System) for FROG-kb is Oracle version 10. The front end is implemented with specific code using technologies such as Java, Java Servlet, JSP, JQuery, and GoogleCharts. RESULTS We present an open access web application, FROG-kb (Forensic Research/Reference on Genetics-knowledge base, http://frog.med.yale.edu), that is useful for teaching and research relevant to forensics and can serve as a tool facilitating forensic practice. The underlying data for FROG-kb are provided by the already extensively used and referenced ALlele FREquency Database, ALFRED (http://alfred.med.yale.edu). In addition to displaying data in an organized manner, computational tools that use the underlying allele frequencies with user-provided data are implemented in FROG-kb. These tools are organized by the different published SNP/marker panels available. This web tool currently has implemented general functions possible for two types of SNP panels, individual identification and ancestry inference, and a prediction function specific to a phenotype informative panel for eye color. CONCLUSION The current online version of FROG-kb already provides new and useful functionality. We expect FROG-kb to grow and expand in capabilities and welcome input from the forensic community in identifying datasets and functionalities that will be most helpful and useful. Thus, the structure and functionality of FROG-kb will be revised in an ongoing process of improvement. This paper describes the state as of early June 2012.
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Affiliation(s)
- Haseena Rajeevan
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, P.O.Box 208005, New Haven, CT 06520-8005, USA
- Center for Medical Informatics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Usha Soundararajan
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, P.O.Box 208005, New Haven, CT 06520-8005, USA
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, P.O.Box 208005, New Haven, CT 06520-8005, USA
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, P.O.Box 208005, New Haven, CT 06520-8005, USA
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Abstract
We propose that haplotyped loci with high heterozygosity can be useful in human identification, especially within families, if recombination is very low among the sites. Three or more SNPs extending over small molecular intervals (<10 KB) can be identified in the human genome to define miniature haplotypes with moderate levels of linkage disequilibrium. Properly selected, these mini-haplotypes (or minihaps) consist of multiple haplotype lineages (alleles) that have evolved from the ancestral human haplotype but show no evidence of recurring recombination, allowing each distinct haplotype to be equated with an allele, all copies of which are essentially identical by descent. Historic recombinants, representing rare events that have drifted to common frequencies over many generations, can be identified in some cases, they do not equate to frequently recurring recombination. We have identified examples in our data collected on various projects and present eight such mini-haplotypes comprised of informative SNPs. We also discuss the ideal characteristics and advantages of minihaps for human familial identification and ancestry inference, and compare them to other types of forensic markers in use and/or that have been proposed. We expect that it is possible to carry out a systematic search and identify a useful panel of mini-haplotypes, with even better properties than the examples presented here.
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Mitochondrial DNA and Y chromosome variation provides evidence for a recent common ancestry between Native Americans and Indigenous Altaians. Am J Hum Genet 2012; 90:229-46. [PMID: 22281367 DOI: 10.1016/j.ajhg.2011.12.014] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 12/06/2011] [Accepted: 12/19/2011] [Indexed: 11/20/2022] Open
Abstract
The Altai region of southern Siberia has played a critical role in the peopling of northern Asia as an entry point into Siberia and a possible homeland for ancestral Native Americans. It has an old and rich history because humans have inhabited this area since the Paleolithic. Today, the Altai region is home to numerous Turkic-speaking ethnic groups, which have been divided into northern and southern clusters based on linguistic, cultural, and anthropological traits. To untangle Altaian genetic histories, we analyzed mtDNA and Y chromosome variation in northern and southern Altaian populations. All mtDNAs were assayed by PCR-RFLP analysis and control region sequencing, and the nonrecombining portion of the Y chromosome was scored for more than 100 biallelic markers and 17 Y-STRs. Based on these data, we noted differences in the origin and population history of Altaian ethnic groups, with northern Altaians appearing more like Yeniseian, Ugric, and Samoyedic speakers to the north, and southern Altaians having greater affinities to other Turkic speaking populations of southern Siberia and Central Asia. Moreover, high-resolution analysis of Y chromosome haplogroup Q has allowed us to reshape the phylogeny of this branch, making connections between populations of the New World and Old World more apparent and demonstrating that southern Altaians and Native Americans share a recent common ancestor. These results greatly enhance our understanding of the peopling of Siberia and the Americas.
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Lu D, Liu Q, Wu W, Zhao H. Mutation analysis of 24 short tandem repeats in Chinese Han population. Int J Legal Med 2011; 126:331-5. [DOI: 10.1007/s00414-011-0630-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 10/04/2011] [Indexed: 10/16/2022]
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Current genetic methodologies in the identification of disaster victims and in forensic analysis. J Appl Genet 2011; 53:41-60. [PMID: 22002120 PMCID: PMC3265735 DOI: 10.1007/s13353-011-0068-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2011] [Revised: 09/22/2011] [Accepted: 09/23/2011] [Indexed: 12/16/2022]
Abstract
This review presents the basic problems and currently available molecular techniques used for genetic profiling in disaster victim identification (DVI). The environmental conditions of a mass disaster often result in severe fragmentation, decomposition and intermixing of the remains of victims. In such cases, traditional identification based on the anthropological and physical characteristics of the victims is frequently inconclusive. This is the reason why DNA profiling became the gold standard for victim identification in mass-casualty incidents (MCIs) or any forensic cases where human remains are highly fragmented and/or degraded beyond recognition. The review provides general information about the sources of genetic material for DNA profiling, the genetic markers routinely used during genetic profiling (STR markers, mtDNA and single-nucleotide polymorphisms [SNP]) and the basic statistical approaches used in DNA-based disaster victim identification. Automated technological platforms that allow the simultaneous analysis of a multitude of genetic markers used in genetic identification (oligonucleotide microarray techniques and next-generation sequencing) are also presented. Forensic and population databases containing information on human variability, routinely used for statistical analyses, are discussed. The final part of this review is focused on recent developments, which offer particularly promising tools for forensic applications (mRNA analysis, transcriptome variation in individuals/populations and genetic profiling of specific cells separated from mixtures).
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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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Cooper DN, Bacolla A, Férec C, Vasquez KM, Kehrer-Sawatzki H, Chen JM. On the sequence-directed nature of human gene mutation: the role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease. Hum Mutat 2011; 32:1075-99. [PMID: 21853507 DOI: 10.1002/humu.21557] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Accepted: 06/17/2011] [Indexed: 12/21/2022]
Abstract
Different types of human gene mutation may vary in size, from structural variants (SVs) to single base-pair substitutions, but what they all have in common is that their nature, size and location are often determined either by specific characteristics of the local DNA sequence environment or by higher order features of the genomic architecture. The human genome is now recognized to contain "pervasive architectural flaws" in that certain DNA sequences are inherently mutation prone by virtue of their base composition, sequence repetitivity and/or epigenetic modification. Here, we explore how the nature, location and frequency of different types of mutation causing inherited disease are shaped in large part, and often in remarkably predictable ways, by the local DNA sequence environment. The mutability of a given gene or genomic region may also be influenced indirectly by a variety of noncanonical (non-B) secondary structures whose formation is facilitated by the underlying DNA sequence. Since these non-B DNA structures can interfere with subsequent DNA replication and repair and may serve to increase mutation frequencies in generalized fashion (i.e., both in the context of subtle mutations and SVs), they have the potential to serve as a unifying concept in studies of mutational mechanisms underlying human inherited disease.
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Affiliation(s)
- David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom.
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Y-chromosome variation in Altaian Kazakhs reveals a common paternal gene pool for Kazakhs and the influence of Mongolian expansions. PLoS One 2011; 6:e17548. [PMID: 21412412 PMCID: PMC3055870 DOI: 10.1371/journal.pone.0017548] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 02/08/2011] [Indexed: 12/28/2022] Open
Abstract
Kazakh populations have traditionally lived as nomadic pastoralists that seasonally migrate across the steppe and surrounding mountain ranges in Kazakhstan and southern Siberia. To clarify their population history from a paternal perspective, we analyzed the non-recombining portion of the Y-chromosome from Kazakh populations living in southern Altai Republic, Russia, using a high-resolution analysis of 60 biallelic markers and 17 STRs. We noted distinct differences in the patterns of genetic variation between maternal and paternal genetic systems in the Altaian Kazakhs. While they possess a variety of East and West Eurasian mtDNA haplogroups, only three East Eurasian paternal haplogroups appear at significant frequencies (C3*, C3c and O3a3c*). In addition, the Y-STR data revealed low genetic diversity within these lineages. Analysis of the combined biallelic and STR data also demonstrated genetic differences among Kazakh populations from across Central Asia. The observed differences between Altaian Kazakhs and indigenous Kazakhs were not the result of admixture between Altaian Kazakhs and indigenous Altaians. Overall, the shared paternal ancestry of Kazakhs differentiates them from other Central Asian populations. In addition, all of them showed evidence of genetic influence by the 13th century CE Mongol Empire. Ultimately, the social and cultural traditions of the Kazakhs shaped their current pattern of genetic variation.
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Giardina E, Spinella A, Novelli G. Past, present and future of forensic DNA typing. Nanomedicine (Lond) 2011; 6:257-70. [DOI: 10.2217/nnm.10.160] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Recent advances in our ability to dissect the human genome and the availability of platforms for genome-wide analysis and whole-genome sequencing are expected to develop new tools for both biomedical and forensic DNA analyses. Nowadays, we can individualize single cells left at the crime scene or analyze ancient human remains. Here, we provide a general view on the past, current and likely future directions of forensic DNA analysis.
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Affiliation(s)
| | - Aldo Spinella
- Direzione Centrale Anticrimine, Servizio di Polizia Scientifica, Rome, Italy
| | - Giuseppe Novelli
- Centre of Excellence for Genomic Risk Assessment in Multifactorial & Complex Diseases, School of Medicine, University of Rome Tor Vergata, Via Montpellier, 1–00133 Rome, Italy
- Division of Cardiovascular Medicine, Department of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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Burgarella C, Navascués M. Mutation rate estimates for 110 Y-chromosome STRs combining population and father-son pair data. Eur J Hum Genet 2011; 19:70-5. [PMID: 20823913 PMCID: PMC3039515 DOI: 10.1038/ejhg.2010.154] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 06/01/2010] [Accepted: 08/05/2010] [Indexed: 11/09/2022] Open
Abstract
Y-chromosome microsatellites (Y-STRs) are typically used for kinship analysis and forensic identification, as well as for inferences on population history and evolution. All applications would greatly benefit from reliable locus-specific mutation rates, to improve forensic probability calculations and interpretations of diversity data. However, estimates of mutation rate from father-son transmissions are available for few loci and have large confidence intervals, because of the small number of meiosis usually observed. By contrast, population data exist for many more Y-STRs, holding unused information about their mutation rates. To incorporate single locus diversity information into Y-STR mutation rate estimation, we performed a meta-analysis using pedigree data for 80 loci and individual haplotypes for 110 loci, from 29 and 93 published studies, respectively. By means of logistic regression we found that relative genetic diversity, motif size and repeat structure explain the variance of observed rates of mutations from meiosis. This model allowed us to predict locus-specific mutation rates (mean predicted mutation rate 2.12 × 10(-3), SD=1.58 × 10(-3)), including estimates for 30 loci lacking meiosis observations and 41 with a previous estimate of zero. These estimates are more accurate than meiosis-based estimates when a small number of meiosis is available. We argue that our methodological approach, by taking into account locus diversity, could be also adapted to estimate population or lineage-specific mutation rates. Such adjusted estimates would represent valuable information for selecting the most reliable markers for a wide range of applications.
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Affiliation(s)
- Concetta Burgarella
- CNRS UMR 7625 Écologie et Évolution, École Normale Supérieure, Paris, France
- INIA, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Miguel Navascués
- CNRS UMR 7625 Écologie et Évolution, École Normale Supérieure, Paris, France
- INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, Montferrier-sur-Lez Cedex, France
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Phylogeography and conservation of the bull shark (Carcharhinus leucas) inferred from mitochondrial and microsatellite DNA. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0145-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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50
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Ballantyne KN, Goedbloed M, Fang R, Schaap O, Lao O, Wollstein A, Choi Y, van Duijn K, Vermeulen M, Brauer S, Decorte R, Poetsch M, von Wurmb-Schwark N, de Knijff P, Labuda D, Vézina H, Knoblauch H, Lessig R, Roewer L, Ploski R, Dobosz T, Henke L, Henke J, Furtado MR, Kayser M. Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications. Am J Hum Genet 2010; 87:341-53. [PMID: 20817138 DOI: 10.1016/j.ajhg.2010.08.006] [Citation(s) in RCA: 271] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 08/02/2010] [Accepted: 08/13/2010] [Indexed: 11/24/2022] Open
Abstract
Nonrecombining Y-chromosomal microsatellites (Y-STRs) are widely used to infer population histories, discover genealogical relationships, and identify males for criminal justice purposes. Although a key requirement for their application is reliable mutability knowledge, empirical data are only available for a small number of Y-STRs thus far. To rectify this, we analyzed a large number of 186 Y-STR markers in nearly 2000 DNA-confirmed father-son pairs, covering an overall number of 352,999 meiotic transfers. Following confirmation by DNA sequence analysis, the retrieved mutation data were modeled via a Bayesian approach, resulting in mutation rates from 3.78 × 10(-4) (95% credible interval [CI], 1.38 × 10(-5) - 2.02 × 10(-3)) to 7.44 × 10(-2) (95% CI, 6.51 × 10(-2) - 9.09 × 10(-2)) per marker per generation. With the 924 mutations at 120 Y-STR markers, a nonsignificant excess of repeat losses versus gains (1.16:1), as well as a strong and significant excess of single-repeat versus multirepeat changes (25.23:1), was observed. Although the total repeat number influenced Y-STR locus mutability most strongly, repeat complexity, the length in base pairs of the repeated motif, and the father's age also contributed to Y-STR mutability. To exemplify how to practically utilize this knowledge, we analyzed the 13 most mutable Y-STRs in an independent sample set and empirically proved their suitability for distinguishing close and distantly related males. This finding is expected to revolutionize Y-chromosomal applications in forensic biology, from previous male lineage differentiation toward future male individual identification.
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