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Hajiesmaeil M, Ravasini F, Risi F, Magnarini G, Olivieri A, D'Atanasio E, Galehdari H, Trombetta B, Cruciani F. High incidence of AZF duplications in clan-structured Iranian populations detected through Y chromosome sequencing read depth analysis. Sci Rep 2023; 13:11857. [PMID: 37481605 PMCID: PMC10363161 DOI: 10.1038/s41598-023-39069-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/19/2023] [Indexed: 07/24/2023] Open
Abstract
The ampliconic region of the human Y chromosome consists of large duplicated sequences that can undergo non-allelic homologous recombination (NAHR), resulting in structural rearrangements that may cause infertility, especially when they occur in the azoospermia factor b/c (AZFb/c) region. Although AZF duplications have long been neglected due to the technical limitations of STS-based studies that focused mainly on deletions, recent next generation sequencing (NGS) technologies provided evidence for their importance in fertility. In this study, a NGS read depth approach was used to detect AZFb/c rearrangements in 87 Iranians from different ethnic groups. The duplication frequency in Iran proved to be twice as high as in the "1000 Genomes" dataset. Interestingly, most duplications were found in patrilineal ethnic groups, possibly as a consequence of their lower male effective population size which can counteract negative selection. Moreover, we found a large 8.0 Mb duplication, resulting in a fourfold increase in the copy number of AZFc genes, which to our knowledge is the largest duplication ever reported in this region. Overall, our results suggest that it is important to consider not only AZF deletions but also duplications to investigate the causes of male infertility, especially in patrilineal clan-based populations.
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Affiliation(s)
- Mogge Hajiesmaeil
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Francesco Ravasini
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Flavia Risi
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Giorgia Magnarini
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology 'Lazzaro Spallanzani', Pavia University, Pavia, Italy
- NBFC, National Biodiversity Future Center, 90133, Palermo, Italy
| | - Eugenia D'Atanasio
- Institute of Molecular Biology and Pathology (IBPM), CNR, 00185, Rome, Italy
| | - Hamid Galehdari
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Beniamino Trombetta
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Fulvio Cruciani
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy.
- Institute of Molecular Biology and Pathology (IBPM), CNR, 00185, Rome, Italy.
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Guo F, Liu Z, Long G, Zhang B, Dong X, Liu D, Yu S. High-resolution genotyping of 58 STRs in 635 Northern Han Chinese with MiSeq FGx ® Forensic Genomics System. Forensic Sci Int Genet 2023; 65:102879. [PMID: 37150076 DOI: 10.1016/j.fsigen.2023.102879] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/16/2023] [Accepted: 04/22/2023] [Indexed: 05/09/2023]
Abstract
Sequence polymorphisms were characterized at 27 autosomal STRs (A-STRs), 7 X chromosomal STRs (X-STRs), and 24 Y chromosomal STRs (Y-STRs) in 635 Northern Han Chinese with the ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. Since repeat region (RR) and flanking region (FR) variation can be detected by massively parallel sequencing (MPS), the increase in the number of unique alleles and the average of gene diversity was 78.18% and 3.51% between sequence and length, respectively. A total of 74 novel RR variants were identified at 33 STRs compared with STRSeq and previous studies, and 13 FR variants (rs1770275883, rs2053373277, rs2082557941, rs1925525766, rs1926380862, rs1569322793, rs2051848492, rs2051848696, rs2016239814, rs2053269960, rs2044518192, rs2044536444, and rs2089968964) were first submitted to dbSNP. Also, 99.94% of alleles were concordant between the ForenSeq DNA Signature Prep Kit and commercial CE kits. Discordance resulted from the low performance at D22S1045 and occasionally at DYS392, flanking region deletions at D7S820 and DXS10074, and the strict alignment algorithm at DXS7132. Null alleles at DYS505 and DYS448 and multialleles at DYS387S1a/b, DYS385a/b, DYS448, DYS505, DXS7132, and HPRTB were validated with other MPS and CE kits. Thus, a high-resolution sequence-based (SB) and length-based (LB) allele frequencies dataset from Northern Han Chinese has been established already. As expected, forensic parameters increased significantly on combined power of discrimination (PD) and combined power of exclusion (PE) at A-STRs, mildly on combined PD and combined mean exclusion chance (MEC) at X-STRs, and barely on discrimination capacity (DC) at Y-STRs. Additionally, MiSeq FGx quality metrics and MPS performance were evaluated in this study, which presented the high-quality of the dataset at 20 consecutive runs, such as ≥ 60% bases with a quality score of 20 or higher (%≥ Q20), > 60% of effective reads, > 2000 × of depth of coverage (DoC), ≥ 60% of allele coverage ratio (ACR) or heterozygote balance, ≥ 70% of inter-locus balance, and ≤ 0.4 of the absolute value of observed minus expected heterozygosity (|Hexp - Hobs|). In conclusion, MiSeq FGx can help us generate a high-resolution and high-quality dataset for human identification and population genetic studies.
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Affiliation(s)
- Fei Guo
- School of Forensic Science and Technology, Criminal Investigation Police University of China, Shenyang, Liaoning 110854, PR China.
| | - Ze Liu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China
| | - Guannan Long
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China
| | - Biao Zhang
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China
| | - Xinyu Dong
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, PR China
| | - Dahua Liu
- Department of Forensic Medicine, Jinzhou Medical University, Jinzhou, Liaoning 121001, PR China
| | - Shaobo Yu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China.
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Biogeographic origin and genetic characteristics of the peopling of Jeju Island based on lineage markers. Genes Genomics 2023; 45:307-318. [PMID: 36607592 DOI: 10.1007/s13258-022-01363-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 12/26/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Jeju Island is the largest island of South Korea, located southwest far from the mainland of Korea, and has a unique history and its own cultures that are distinguished from those of the other regions of the Korean mainland. However, the Jeju population has not been deeply investigated to date to understand their genetic structure, which may reflect their historical and geographical background. OBJECTIVE To identify the genetic characteristics and biogeographic origin of people of Jeju Island based on the statistical analysis of genetic data using lineage markers. METHODS 17 Y-STRs data for 615 unrelated males and mitochondrial DNA haplogroup data for 799 unrelated individuals residing on Jeju Island were generated, and analyzed to investigate genetic diversity and genetic characteristics using statistical methods including pairwise Fst or Rst, Analysis of molecular variance (AMOVA) and Multidimensional scaling (MDS). RESULTS For male individuals of Jeju Island, unique genetic characteristics were observed in the analysis of Y-STRs, including low haplotype diversity, strong association with surnames, genetic difference from other regions of Korea, and common genetic variation of the Y-STR loci known to be predominant in Northern populations, such as Mongolians. Statistical analysis of the mitochondrial DNA haplogroups also revealed similar results that showed low haplogroup diversity and high frequency of haplogroup Y prevalent mostly in ethnic populations around the Sea of Okhotsk in Northeastern Asia. All these results suggest that Jeju Island is genetically distinct from other regions of Korea, possibly being a subpopulation in Korea, and related closely to Northern Asian populations. CONCLUSION The findings in the genetic approach could support understanding of the historical background of Jeju Island that is consistent with evidence from other multidisciplinary studies.
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Javed F, Shafique M, McNevin D, Javed MU, Shehzadi A, Shahid AA. Empirical Evidence on Enhanced Mutation Rates of 19 RM-YSTRs for Differentiating Paternal Lineages. Genes (Basel) 2022; 13:genes13060946. [PMID: 35741708 PMCID: PMC9222627 DOI: 10.3390/genes13060946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/13/2022] [Accepted: 05/20/2022] [Indexed: 11/21/2022] Open
Abstract
Rapidly mutating Y-chromosomal short tandem repeats (RM Y STRs) with mutation rates ≥ 10−2 per locus per generation are valuable for differentiating amongst male paternal relatives where standard Y STRs with mutation rates of ≤10−3 per locus per generation may not. Although the 13 RM Y STRs commonly found in commercial assays provide higher levels of paternal lineage differentiation than conventional Y STRs, there are many male paternal relatives that still cannot be differentiated. This can be improved by increasing the number of Y STRs or choosing those with high mutation rates. We present a RM Y STR multiplex comprising 19 loci with high mutation rates and its developmental validation (repeatability, sensitivity and male specificity). The multiplex was found to be robust, reproducible, specific and sensitive enough to generate DNA profiles from samples with inhibitors. It was also able to detect all contributor alleles of mixtures in ratios up to 9:1. We provide preliminary evidence for the ability of the multiplex to discriminate between male paternal relatives by analyzing large numbers of male relative pairs (536) separated by one to seven meioses. A total of 96 mutations were observed in 162 meioses of father–son pairs, and other closely related male pairs were able to be differentiated after 1, 2, 3, 4, 5, 6 and 7 meiosis in 44%, 69%, 68%, 85%, 0%, 100% and 100% of cases, respectively. The multiplex offers a noticeable enhancement in the ability to differentiate paternally related males compared with the 13 RM Y STR set. We envision the future application of our 19 RM Yplex in criminal cases for the exclusion of male relatives possessing matching standard Y STR profiles and in familial searching with unknown suspects. It represents a step towards the complete individualization of closely related males.
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Affiliation(s)
- Faqeeha Javed
- Forensic Research Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan; (F.J.); (A.S.); (A.A.S.)
| | - Muhammad Shafique
- Forensic Research Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan; (F.J.); (A.S.); (A.A.S.)
- Correspondence:
| | - Dennis McNevin
- Centre for Forensic Science, University of Technology Sydney, Sydney 2007, Australia;
| | - Muhammad Usama Javed
- Faculty of Medicine, Allama Iqbal Medical College, University of Health Sciences, Lahore 54700, Pakistan;
| | - Abida Shehzadi
- Forensic Research Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan; (F.J.); (A.S.); (A.A.S.)
| | - Ahmad Ali Shahid
- Forensic Research Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan; (F.J.); (A.S.); (A.A.S.)
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Zhou Y, Song F, Dai H, Wang S, Zhang K, Wei X, Wang X, Luo H. Developmental validation of the Microreader™ RM-Y ID System: a new rapidly mutating Y-STR 17-plex system for forensic application. Int J Legal Med 2021; 136:501-512. [PMID: 34302216 DOI: 10.1007/s00414-021-02632-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/07/2021] [Indexed: 10/20/2022]
Abstract
Y-chromosomal short tandem repeats (Y-STRs) are widely applied to evolutionary, genealogical, and kinship analyses of male linages in forensic studies, but these low to midrange mutated Y-STRs typically fail to separate related males from the same paternal lineage. Recently, rapidly mutating Y-STRs (RM Y-STRs) have been demonstrated to improve the differentiation of male relatives and individuals. The Microreader™ RM-Y ID System is a new RM Y-STR kit that is capable of simultaneously amplifying 17 RM Y-STRs. Herein, to verify the efficiency and accuracy of the Microreader™ RM-Y ID System, developmental validation was conducted, including PCR-based studies, sensitivity, stability, species specificity, mixture, stutter percentage, and precision studies. Full profiles could be obtained when the hematin concentration was 250 μM, humic acid concentration was 1500 ng/μl, and tannic acid concentration was 200 ng/μl. Full profiles of the mixture of males/males could be detected up to a ratio of 19:1, and full profiles of females/males could always be detected even at ratios up to 24,000:1. Moreover, the forensic characteristics of 250 DNA-confirmed father-son pairs were analysed. The results showed that these 17 RM Y-STRs had high power for forensic discrimination (HD = 1) in the Chinese Han population, and the mutation rates were in the range of 4 × 10-3 (95% CI 1.00 × 10-4 to 2.21 × 10-2, DYS464) to 8.8 × 10-2 (95% CI 5.60 × 10-2 to 1.30 × 10-1, DYF399S1), indicating that the kit was effective for RM Y-STR studies and absolute individualisation of interrelated male individuals.
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Affiliation(s)
- Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 3-16 Renmin South Road, Chengdu, 610041, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 3-16 Renmin South Road, Chengdu, 610041, China
| | - Hao Dai
- Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Shuangshuang Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 3-16 Renmin South Road, Chengdu, 610041, China
| | - Ke Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 3-16 Renmin South Road, Chengdu, 610041, China
| | - Xiaowen Wei
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 3-16 Renmin South Road, Chengdu, 610041, China
| | - Xindi Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 3-16 Renmin South Road, Chengdu, 610041, China
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 3-16 Renmin South Road, Chengdu, 610041, China.
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Ravasini F, D'Atanasio E, Bonito M, Bonucci B, Della Rocca C, Berti A, Trombetta B, Cruciani F. Sequence Read Depth Analysis of a Monophyletic Cluster of Y Chromosomes Characterized by Structural Rearrangements in the AZFc Region Resulting in DYS448 Deletion and DYF387S1 Duplication. Front Genet 2021; 12:669405. [PMID: 33936180 PMCID: PMC8085532 DOI: 10.3389/fgene.2021.669405] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/29/2021] [Indexed: 12/26/2022] Open
Abstract
The azoospermia factor c region (AZFc), located in the long arm of the human Y chromosome, is frequently involved in chromosome rearrangements, mainly due to non-allelic homologous recombination events that occur between the nearly identical sequences (amplicon) that comprises it. These rearrangements may have major phenotypic effects like spermatogenic failure or other pathologies linked to male infertility. Moreover, they may also be relevant in forensic genetics, since some of the Y chromosome short tandem repeats (Y-STRs) commonly used in forensic analysis are located in amplicons or in inter-amplicon sequences of the AZFc. In a previous study, we identified four phylogenetically related samples with a null allele at DYS448 and a tetrallelic pattern at DYF387S1, two Y-STRs located in the AZFc. Through NGS read depth analysis, we found that the unusual Y-STR pattern may be due to a 1.6 Mb deletion arising concurrently or after a 3.5 Mb duplication event. The observed large genomic rearrangement results in copy number reduction for the RBMY gene family as well as duplication of other AZFc genes. Based on the diversity of 16 additional Y-STRs, we estimated that the duplication/deletion event occurred at least twenty generations ago, suggesting that it has not been affected by negative selection.
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Affiliation(s)
- Francesco Ravasini
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Eugenia D'Atanasio
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Maria Bonito
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Biancamaria Bonucci
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Chiara Della Rocca
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Andrea Berti
- Sezione di Biologia, Reparto CC Investigazioni Scientifiche di Roma, Rome, Italy
| | - Beniamino Trombetta
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Fulvio Cruciani
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy.,Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy
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Zeyad T, Adam A, Alghafri R, Iratni R. Study of 27 Y-STR markers in United Arab Emirates population. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2020. [DOI: 10.1016/j.fsir.2020.100057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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8
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Villaescusa P, Seidel M, Nothnagel M, Pinotti T, González-Andrade F, Alvarez-Gila O, M de Pancorbo M, Roewer L. A Y-chromosomal survey of Ecuador's multi-ethnic population reveals new insights into the tri-partite population structure and supports an early Holocene age of the rare Native American founder lineage C3-MPB373. Forensic Sci Int Genet 2020; 51:102427. [PMID: 33254102 DOI: 10.1016/j.fsigen.2020.102427] [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: 05/14/2020] [Revised: 11/03/2020] [Accepted: 11/10/2020] [Indexed: 10/23/2022]
Abstract
Ecuador is a multiethnic and pluricultural country with a complex history defined by migration and admixture processes. The present study aims to increase our knowledge on the Ecuadorian Native Amerindian groups and the unique South American Y-chromosome haplogroup C3-MPB373 through the analysis of up to 23 Y-chromosome STRs (Y-STRs) and several Y-SNPs in a sample of 527 Ecuadorians from 7 distinct populations and geographic areas, including Kichwa and non-Kichwa Native Amerindians, Mestizos and Afro-Ecuadorians. Our results reveal the presence of C3-MPB373 both in the Amazonian lowland Kichwa with frequencies up to 28 % and, for the first time, in notable proportions in Kichwa populations from the Ecuadorian highlands. The substantially higher frequencies of C3-MPB373 in the Amazonian lowlands found in Kichwa and Waorani individuals suggest a founder effect in that area. Notably, estimates for the time to the most recent common ancestor (TMRCA) in the range of 7.2-9.0 kya point to an ancient origin of the haplogroup and suggest an early Holocene expansion of C3-MPB373 into South America. Finally, the pairwise genetic distances (RST) separate the Kichwa Salasaka from all the other Native Amerindian and Ecuadorian groups, indicating a so far hidden diversity among the Kichwa-speaking populations and suggesting a more southern origin of this population. In sum, our study provides a more in-depth knowledge of the male genetic structure of the multiethnic Ecuadorian population, as well as a valuable reference dataset for forensic use.
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Affiliation(s)
- Patricia Villaescusa
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain.
| | - Maria Seidel
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Nothnagel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Cologne, Germany; University Hospital Cologne, Cologne, Germany
| | - Thomaz Pinotti
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Oscar Alvarez-Gila
- Department of Medieval, Early Modern and American History, Faculty of Letters, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
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Nan H, Wu W, Hao H, Ren W, Lu D. Deletions and duplications of 42 Y chromosomal short tandem repeats in Chinese Han population. Int J Legal Med 2020; 135:153-159. [PMID: 32483669 DOI: 10.1007/s00414-020-02320-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/20/2020] [Indexed: 11/30/2022]
Abstract
Genotypes of 42 Y chromosome STR (Y-STR) loci were analyzed for a sample of 1420 unrelated males and 1160 father-son pairs from a Chinese Han population. Deletions of Y-STR loci were detected at DYS389I, DYS389II, DYS437, DYS446, DYS447, DYS448, and DYS557 loci. The most common deletion occurred at DYS448 and DYS557 with a frequency of 0.0056 and 0.0035, respectively. On the other hand, duplications of alleles were observed at DYF387S1a/b, DYS385a/b, DYS460, DYS527a/b, DYS459a/b, and DYS557 loci. The DYF387S1a/b, DYS527a/b, and DYS385a/b showed the highest duplicated frequencies of 0.0148, 0.0134, and 0.0099, respectively. The Y-STRs located on palindromes significantly exhibited more deletions or duplications than those non-palindromic loci. Also, duplications were more frequent than deletions. Hence, deletions or duplications of Y-STRs related to their positions on the Y chromosome. All the 52 deleted or duplicated events occurred in the two-generation families inherited stably. Furthermore, the deletions may show the Chinese Han population specificity, but the duplications may not have a similar phenomenon. Our results will be helpful to correct interpretation of the genetic profile of Y-STR loci in forensic casework.
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Affiliation(s)
- Hailun Nan
- Faculty of Forensic Medicine, Zhongshan Medical School of Sun Yat-Sen University, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center of Sun Yat-Sen University, 74# Zhongshan 2nd Road, Guangzhou, 510080, People's Republic of China
| | - Weiwei Wu
- Institute of Forensic Science of Zhejiang Provincial Public Security Bureau, Zhejiang Key Laboratory of Forensic Science and Technology, 66# Minsheng Road, Hangzhou, 310009, People's Republic of China
| | - Honglei Hao
- Institute of Forensic Science of Zhejiang Provincial Public Security Bureau, Zhejiang Key Laboratory of Forensic Science and Technology, 66# Minsheng Road, Hangzhou, 310009, People's Republic of China
| | - Wenran Ren
- Institute of Forensic Science of Zhejiang Provincial Public Security Bureau, Zhejiang Key Laboratory of Forensic Science and Technology, 66# Minsheng Road, Hangzhou, 310009, People's Republic of China
| | - Dejian Lu
- Faculty of Forensic Medicine, Zhongshan Medical School of Sun Yat-Sen University, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center of Sun Yat-Sen University, 74# Zhongshan 2nd Road, Guangzhou, 510080, People's Republic of China.
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10
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Xie S, Zhang Y, Yang Y. Is the primary AZFc duplication a potential risk for male infertility?: A systematic review and meta-analysis. Andrology 2020; 8:996-1004. [PMID: 32298532 DOI: 10.1111/andr.12800] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/14/2020] [Accepted: 04/08/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND Numerous studies have been performed to investigate the association between the primary AZFc duplication and male infertility risk; however, the sample sizes have been small and the results have been controversial. A meta-analysis was performed to assess these associations. METHODS A systematic search was conducted to identify all relevant studies from the PubMed, Web of Science, Medline, CNKI, and Wanfang databases up to October 22, 2019. The odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess the strength of associations. All of the statistical analyses were conducted by using RevMan 5.3. RESULTS Eleven studies were identified that involved 3140 infertile men and 2280 fertile men. Overall, there was a statistically significant association between the primary AZFc duplication and male infertility (OR = 1.66, 95% CI = 1.29-2.14, P < .0001). In the subgroup analysis by ethnic group, a statistically significant association between the primary AZFc duplication and male infertility was observed in Asian men (OR = 2.26, 95% CI = 1.64-3.12, P < .00001), but not in European men (OR = 0.90, 95% CI = 0.59-1.38, P = .64). For subtypes of the primary AZFc duplication, a statistically significant association was observed between the gr/gr duplication-only (OR = 2.71, 95% CI = 1.38-5.32, P = .004) and infertility in Asian men. Asian men with the primary AZFc duplication resulting in more than four DAZ genes were found to be at an increased risk for infertility (OR = 2.70, 95% CI = 1.49-4.89, P = .001). CONCLUSION Our meta-analysis provides an unprecedented illustration of how the association between the primary AZFc duplication and male infertility may be dependent on ethnicity or geographic location. Furthermore, gr/gr duplication or increased DAZ copy number can be detrimental to spermatogenesis in Asian men.
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Affiliation(s)
- Shengyu Xie
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Yangwei Zhang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Yuan Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
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Lang M, Liu H, Song F, Qiao X, Ye Y, Ren H, Li J, Huang J, Xie M, Chen S, Song M, Zhang Y, Qian X, Yuan T, Wang Z, Liu Y, Wang M, Liu Y, Liu J, Hou Y. Forensic characteristics and genetic analysis of both 27 Y-STRs and 143 Y-SNPs in Eastern Han Chinese population. Forensic Sci Int Genet 2019; 42:e13-e20. [PMID: 31353318 DOI: 10.1016/j.fsigen.2019.07.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 07/20/2019] [Accepted: 07/20/2019] [Indexed: 12/11/2022]
Abstract
Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) frequency distributions provide resources for assessment of male population stratification among world-wide populations. Currently, the Y-STR Haplotype Reference Database (YHRD) contains numerous Y-chromosome haplotype profiles from various populations and countries around the world. However, for many of the recently discovered and already phylogenetically mapped Y-SNPs, the population data are scarce. Herein, the typing of 27 Y-STRs (Yfiler Plus) and 143 Y-SNPs (self-designed Y-SNP panel) was performed on 1269 unrelated males from 11 Han Chinese populations. Haplogroup O-M175 was the most predominant haplogroup in our Han Chinese data, ranging from 67.34% (Henan Han) to 93.16% (Guangdong Han). The highest haplogroup diversity (0.967056) was observed in Heilongjiang Han, with a discrimination capacity (DC) value of 0.3723. The number of alleles at single-copy loci varied from 2 for DYS391 (Guangdong Han) to 16 for DYS518 (Henan Han). For the majority of the populations (8/11), both the haplotype diversity and DC values are 1.0000. Furthermore, genetic differentiations were observed between Northern and Southern Han Chinese. These genetic differences were mainly reflected in haplogroup distribution and frequency, and they were confirmed by statistical analysis.
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Affiliation(s)
- Min Lang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Hai Liu
- The Institute of Forensic Science and Technology, Henan Provincial Public Security Bureau, Zhengzhou 450003, China
| | - Feng Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xianhua Qiao
- The Institute of Forensic Science and Technology, Henan Provincial Public Security Bureau, Zhengzhou 450003, China
| | - Yi Ye
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - He Ren
- Beijing Police College, Beijing 102202, China
| | - Jienan Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jian Huang
- Department of Forensic genetics, Brain Hospital of Hunan Province, Hunan University of Chinese Medicine, Changsha 410007, China
| | - Mingkun Xie
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shengjie Chen
- Criminal Detection Unit of Qingxiu District Public Security Sub-bureau in Nanning, Nanning 530000, China
| | - Mengyuan Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Youfang Zhang
- Department of Forensic Science, Zhejiang Police College, Hangzhou 310053, China
| | - Xiaoqin Qian
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Taoxiu Yuan
- Forensic Science Institute of Zhejiang Di'an Diagnosis Technology Co., Ltd, Hangzhou 310012, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yuming Liu
- Forensic Science Center Zhongding Guangdong, Zhanjiang 524000, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yacheng Liu
- Beijing Tongda Shoucheng Institute of Forensic Science, Beijing 100085, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Nan H, Wu WW, Hao H, Lu D. Profile interpretation of extremely long alleles at DYF387S1 and DYS447 migrated into allele range of adjacent loci. JOURNAL OF FORENSIC SCIENCE AND MEDICINE 2019. [DOI: 10.4103/jfsm.jfsm_10_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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13
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Forensic genetic value of a 27 Y-STR loci multiplex (Yfiler® Plus kit) in an Italian population sample. Forensic Sci Int Genet 2016; 21:e1-5. [DOI: 10.1016/j.fsigen.2015.11.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/11/2015] [Accepted: 11/18/2015] [Indexed: 11/19/2022]
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