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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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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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Turrina S, De Leo D. Resizing reaction volumes for the ForenSeq™ DNA Signature Prep kit library preparation. MEDICINE, SCIENCE, AND THE LAW 2021; 61:92-95. [PMID: 33591883 DOI: 10.1177/0025802420923163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The introduction of next generation sequencing (NGS; also known as massively parallel sequencing) technology in the field of forensic genetics has been welcomed by the scientific community, above all because it complements the weaknesses of capillary electrophoresis (CE) in the analysis of genetic markers, such as single nucleotide polymorphism (SNP) typing. However, one of the main obstacles to its adoption does not seem to be the cost of the instrumentation, but rather the cost of the NGS library preparation kits. With the aim of reducing the cost of library preparation without compromising the quality of the results, we tried to scale down reaction volumes for the first two polymerase chain reactions in the amplification and enrichment phases of the targeted loci of library preparation using the ForenSeq™ DNA Signature Prep kit. We used 1 µL templated DNA input to a concentration of 1 ng/µL, instead of the 5 µL at 0.2 ng/µL recommended by the manufacturer. Our findings indicate that reduction of the library preparation volume using the ForenSeq™ DNA Signature Prep kit did not interfere with the quality and reproducibility of the DNA profiles obtained and can help lower the overall cost of NGS.
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Affiliation(s)
- Stefania Turrina
- Department of Diagnostics and Public Health, Unit of Forensic Medicine - Forensic Genetics Laboratory, University of Verona, Italy
| | - Domenico De Leo
- Department of Diagnostics and Public Health, Unit of Forensic Medicine - Forensic Genetics Laboratory, University of Verona, Italy
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Liu Y, Jin X, Guo Y, Zhang X, Zhu W, Zhang W, Mei T. Haplotypic diversity and population genetic study of a population in Kashi region by 27 Y-chromosomal short tandem repeat loci. Mol Genet Genomic Med 2020; 8:e1338. [PMID: 32537948 PMCID: PMC7434754 DOI: 10.1002/mgg3.1338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/11/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Y-chromosomal short tandem repeats (Y-STRs) have been certified to be the serviceable markers for some paternity cases in the last few years. METHODS We presented the gene diversity, haplotypic diversity, and forensic statistical parameters of 340 unrelated Uighur males from Kashi region based on the 27 Y-STRs. Genomic DNA was extracted from bloodstain samples using the Chelex-100 method and amplified by Yfiler® Plus PCR Amplification kit. RESULTS Gene diversity values on the 27 Y-STRs ranged from 0.4749 (at DYS437 locus) to 0.9416 (at DYS385a,b loci). According to forensic parameters of the 27 Y-STR loci, 295 disparate haplotypes were acquired, 258 of which were unique. The haplotypic diversities and discrimination capacities at Yfiler plus 27 loci, Yfiler 17 loci, extended 11 loci, and minimal 9 loci were 0.9990 and 0.8676; 0.9961 and 0.6912; 0.9952 and 0.5941; and 0.9919 and 0.5676, respectively. Multidimensional scaling plot and neighbor-joining tree between the studied Uighur group and 17 reference populations were conducted, and the obtained results indicated the Kashi Uighur group had the closer genetic relationships with Uighur groups living in different regions. CONCLUSION To sum up, the present study may provide valuable population data and background information of Kashi Uighur group.
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Affiliation(s)
- Yaoshun Liu
- Ankang Hospital of Traditional Chinese MedicineAnkangChina
| | - Xiaoyue Jin
- Ankang Hospital of Traditional Chinese MedicineAnkangChina
| | - Yuxi Guo
- Ankang Hospital of Traditional Chinese MedicineAnkangChina
| | - Xingrui Zhang
- Ankang Hospital of Traditional Chinese MedicineAnkangChina
| | - Wu Zhu
- Ankang Hospital of Traditional Chinese MedicineAnkangChina
| | - Wenli Zhang
- Department of Clinical LaboratoryChildren’s HospitalUrumqiChina
| | - Ting Mei
- Department of Clinical LaboratoryChildren’s HospitalUrumqiChina
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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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Zupanič Pajnič I, Obal M, Zupanc T. Identifying victims of the largest Second World War family massacre in Slovenia. Forensic Sci Int 2020; 306:110056. [DOI: 10.1016/j.forsciint.2019.110056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 01/25/2023]
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7
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Murphy C, Kenna J, Flanagan L, Lee Gorman M, Boland C, Ryan J. A Study of the Background Levels of Male DNA on Underpants Worn by Females. J Forensic Sci 2019; 65:399-405. [PMID: 31566745 DOI: 10.1111/1556-4029.14198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/01/2019] [Accepted: 08/31/2019] [Indexed: 11/27/2022]
Abstract
This study is the first to examine the background level of male DNA on underpants worn by females in the absence of sexual contact. Here, we examined 103 samples from the inside front of underpants from 85 female volunteers. Samples were examined for the presence of male DNA using NGM SElect and PowerPlex Y23 kits. Only five samples gave a "complete" Y-STR profile, even though 83.5% of our volunteers cohabited with a male. In all cases where a partner reference sample was available, the Y-STR profile matched the cohabiting partner. We have demonstrated that a Y-STR profile is not expected on the inside front of underpants worn by females after social contact alone. The results of this study are informative for evaluating the significance of a Y-STR profile on underpants in cases of alleged sexual assault.
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Affiliation(s)
- Charlotte Murphy
- Department of Justice, Forensic Science Ireland, Garda HQ Phoenix Park, Dublin 8, Ireland
| | - June Kenna
- Department of Justice, Forensic Science Ireland, Garda HQ Phoenix Park, Dublin 8, Ireland
| | - Lorna Flanagan
- Department of Justice, Forensic Science Ireland, Garda HQ Phoenix Park, Dublin 8, Ireland
| | - Marce Lee Gorman
- Department of Justice, Forensic Science Ireland, Garda HQ Phoenix Park, Dublin 8, Ireland
| | - Clara Boland
- Department of Justice, Forensic Science Ireland, Garda HQ Phoenix Park, Dublin 8, Ireland
| | - Jennifer Ryan
- Department of Justice, Forensic Science Ireland, Garda HQ Phoenix Park, Dublin 8, Ireland
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8
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Abdeli A, Benhassine T. Paternal lineage of the Berbers from Aurès in Algeria: estimate of their genetic variation. Ann Hum Biol 2019; 46:160-168. [PMID: 30939942 DOI: 10.1080/03014460.2019.1602166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Background: Aurès is a vast territory in the east of Algeria, characterised by its traditional Berber settlement which has preserved its language and its rich history; its name goes back to antiquity and before the Roman conquest it was part of the territory of ancient Numidia. The Chaoui people in this region are one of Algeria's largest Berber groups. Aim: The aims were to investigate the level of genetic diversity of the Berbers of Aurès through the analysis of the paternal gene pool and to estimate the percentage of genetic variation among different geographical regions and linguistic groups from Algeria. Subjects and methods: Twenty-three Y-STRs were genotyped in a sample of 218 unrelated males of the Berbers of Aurès. Algorithms were used to estimate the Y-chromosome haplogroups. Genetic distance, non-metric MDS and AMOVA were used to analyse the genetic relationships between sample groups. Results: The paternal lineage of this sample of the Aurès region did not exhibit strong signals of differentiation with other samples from North-central, Northwest, and South Algeria. However, significant differences were found within this sample, demonstrating a high degree of heterogeneity. Conclusion: The results demonstrate that Aurès people are isolated and closed, but nevertheless have quite different genetic profiles.
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Affiliation(s)
- Amine Abdeli
- a Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques , Université des Sciences et de la Technologie Houari Boumediene , Algiers , Algeria.,b Institut National de Criminalistique et de Criminologie de la Gendarmerie Nationale , Algiers , Algeria
| | - Traki Benhassine
- a Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques , Université des Sciences et de la Technologie Houari Boumediene , Algiers , Algeria
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Genetic diversities and phylogenetic analyses of three Chinese main ethnic groups in southwest China: A Y-Chromosomal STR study. Sci Rep 2018; 8:15339. [PMID: 30337624 PMCID: PMC6193932 DOI: 10.1038/s41598-018-33751-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 10/05/2018] [Indexed: 01/25/2023] Open
Abstract
Short tandem repeats (STRs) located on the Y chromosome with the properties of male-specific inheritance and haploidy are widely used in forensics to analyze paternal genealogies and match male trace donors to evidence. Besides, Y-chromosomal haplotypes play an important role in providing breathtaking insights into population genetic history. However, the genetic diversity and forensic characteristics of Y-STRs in Guizhou main ethnic groups (Hans, Miaos and Bouyeis) remain uncharacterized. Here, we obtained Y-chromosomal 23-marker haplotypes in three Guizhou populations and submitted the first batch of Y-STR haplotype data to the YHRD. The HD in the aforementioned three populations are 0.99990, 0.99983, and 0.99979, respectively, and DC values are 0.9902, 0.9908, and 0.97959, respectively. Subsequently, genetic differentiation between our newly studied populations and reference groups along ethnic/administrative divisions, as well as national/continental boundaries were investigated via AMOVA, MDS, and phylogenetic relationship reconstruction. Significant genetic differentiations from our subjects and other groups are identified in ethnically, linguistically and geographically diverse populations, including most prominently Tibetans and Uyghurs among 30 mainland Chinese populations, Taiwanese groups and others among 58 Asian populations, as well as African groups and others among 89 worldwide populations. Qiannan Bouyei has a close genetic relationship with Guangxi Zhuang, and Zunyi Han and Qiandongnan Miao have close genetic affinity with Hunan Han and Guizhou Shui, respectively. Collectively, this new-generation Y-STR amplification system can be used as a supplementary tool in forensic identification and male parentage testing and even pedigree search.
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Ferreira-Silva B, Fonseca-Cardoso M, Porto MJ, Magalhães T, Cainé L. A Comparison Among Three Multiplex Y-STR Profiling Kits for Sexual Assault Cases. J Forensic Sci 2018; 63:1836-1840. [PMID: 29464703 DOI: 10.1111/1556-4029.13757] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/20/2017] [Accepted: 01/23/2018] [Indexed: 11/30/2022]
Abstract
Biological evidence of sexual assault is one of the most difficult sample types to analyze in forensic laboratories. Y-STR markers are thus a valuable tool for analyzing these samples. The aim of this project was to compare three Y-STR commercial kits by analyzing their amplification performance on casework samples. Overall, 247 trace samples were analyzed with a Yfiler® Plus PCR Amplification Kit (Applied Biosystems), PowerPlex® Y23 (Promega® ) System and AmpFLSTR® Yfiler™ PCR Amplification Kit (Applied Biosystems). Comparing the amplification performance of the three kits, the first two were significantly more sensitive than the latter (p < 0.001). For samples, with a male DNA quantity less than 0.5 ng, the PowerPlex Y23® kit was the most sensitive and best performing kit, followed by the Yfiler® Plus kit (p = 0.009). In conclusion, the Yfiler® Plus and PowerPlex Y-23® kits are viable alternatives to older kits for samples with low amounts of male DNA.
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Affiliation(s)
- Benedita Ferreira-Silva
- Department of Public Health, Forensic Sciences and Medical Education, Faculty of Medicine, University of Porto, Porto, Portugal.,National Institute of Legal Medicine and Forensic Sciences, Porto, Portugal
| | - Margarida Fonseca-Cardoso
- Abel Salazar Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal.,CIIMAR, Matosinhos, Portugal
| | - Maria João Porto
- National Institute of Legal Medicine and Forensic Sciences, Porto, Portugal
| | - Teresa Magalhães
- Department of Public Health, Forensic Sciences and Medical Education, Faculty of Medicine, University of Porto, Porto, Portugal.,Institute of Research and Advanced Training in Health Sciences and Technologies (IINFACTS), Department of Sciences, University Institute of Health Sciences (IUCS-CESPU), Gandra, Portugal
| | - Laura Cainé
- Department of Public Health, Forensic Sciences and Medical Education, Faculty of Medicine, University of Porto, Porto, Portugal.,National Institute of Legal Medicine and Forensic Sciences, Porto, Portugal
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11
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Wu W, Ren W, Hao H, Nan H, He X, Liu Q, Lu D. Mutation rates at 42 Y chromosomal short tandem repeats in Chinese Han population in Eastern China. Int J Legal Med 2018; 132:1317-1319. [DOI: 10.1007/s00414-018-1784-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 01/17/2018] [Indexed: 10/18/2022]
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12
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Toward a consensus on SNP and STR mutation rates on the human Y-chromosome. Hum Genet 2017; 136:575-590. [PMID: 28455625 DOI: 10.1007/s00439-017-1805-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/20/2017] [Indexed: 10/19/2022]
Abstract
The mutation rate on the Y-chromosome matters for estimating the time-to-the-most-recent-common-ancestor (TMRCA, i.e. haplogroup age) in population genetics, as well as for forensic, medical, and genealogical studies. Large-scale sequencing efforts have produced several independent estimates of Y-SNP mutation rates. Genealogical, or pedigree, rates tend to be slightly faster than evolutionary rates obtained from ancient DNA or calibrations using dated (pre)historical events. It is, therefore, suggested to report TMRCAs using an envelope defined by the average aDNA-based rate and the average pedigree-based rate. The current estimate of the "envelope rate" is 0.75-0.89 substitutions per billion base pairs per year. The available Y-SNP mutation rates can be applied to high-coverage data from the entire X-degenerate region, but other datasets may demand recalibrated rates. While a consensus on Y-SNP rates is approaching, the debate on Y-STR rates has continued for two decades, because multiple genealogical rates were consistent with each other but three times faster than the single evolutionary estimate. Applying Y-SNP and Y-STR rates to the same haplogroups recently helped to clarify the issue. Genealogical and evolutionary STR rates typically provide lower and upper bounds of the "true" (SNP-based) age. The genealogical rate often-but not always-works well for haplogroups less than 7000 years old. The evolutionary rate, although calibrated using recent events, inflates ages of young haplogroups and deflates the age of the entire Y-chromosomal tree, but often provides reasonable estimates for intermediate ages (old haplogroups). Future rate estimates and accumulating case studies should further clarify the Y-SNP rates.
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13
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Núñez C, Baeta M, Ibarbia N, Ortueta U, Jiménez-Moreno S, Blazquez-Caeiro JL, Builes JJ, Herrera RJ, Martínez-Jarreta B, de Pancorbo MM. 17 to 23: A novel complementary mini Y-STR panel to extend the Y-STR databases from 17 to 23 markers for forensic purposes. Electrophoresis 2017; 38:1016-1021. [PMID: 27987217 DOI: 10.1002/elps.201600313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 11/19/2016] [Accepted: 12/10/2016] [Indexed: 11/08/2022]
Abstract
A Y-STR multiplex system has been developed with the purpose of complementing the widely used 17 Y-STR haplotyping (AmpFlSTR Y Filer® PCR Amplification kit) routinely employed in forensic and population genetic studies. This new multiplex system includes six additional STR loci (DYS576, DYS481, DYS549, DYS533, DYS570, and DYS643) to reach the 23 Y-STR of the PowerPlex® Y23 System. In addition, this kit includes the DYS456 and DYS385 loci for traceability purposes. Male samples from 625 individuals from ten worldwide populations were genotyped, including three sample sets from populations previously published with the 17 Y-STR system to expand their current data. Validation studies demonstrated good performance of the panel set in terms of concordance, sensitivity, and stability in the presence of inhibitors and artificially degraded DNA. The results obtained for haplotype diversity and discrimination capacity with this multiplex system were considerably high, providing further evidences of the suitability of this novel Y-STR system for forensic purposes. Thus, the use of this multiplex for samples previously genotyped with 17 Y-STRs will be an efficient and low-cost alternative to complete the set of 23 Y-STRs and improve allele databases for population and forensic purposes.
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Affiliation(s)
- Carolina Núñez
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Avda. Miguel de Unamuno, Vitoria-Gasteiz, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Avda. Miguel de Unamuno, Vitoria-Gasteiz, Spain
| | - Nerea Ibarbia
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Avda. Miguel de Unamuno, Vitoria-Gasteiz, Spain
| | - Urko Ortueta
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Avda. Miguel de Unamuno, Vitoria-Gasteiz, Spain
| | - Susana Jiménez-Moreno
- Área Medicina Legal y Forense, Department of Patología y Cirugía, Universidad Miguel Hernández de Elche, Elche, Alicante, Spain
| | | | - Juan José Builes
- Laboratorios Genes Ltd., Medellín, Colombia.,Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO, USA
| | | | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Avda. Miguel de Unamuno, Vitoria-Gasteiz, Spain
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14
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Mei T, Zhang LP, Liu YS, Chen JG, Meng HT, Yan JW, Zhu BF. 24 Y-chromosomal STR haplotypic structure for Chinese Kazak ethnic group and its genetic relationships with other groups. Int J Legal Med 2016; 130:1199-201. [PMID: 27085524 DOI: 10.1007/s00414-016-1331-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 02/03/2016] [Indexed: 11/25/2022]
Abstract
The Kazak ethnic minority is a large ethnic group in the Xinjiang Uygur Autonomous Region of China and is valuable resource for the study of ethnogeny. In the present study, 24 Y-chromosomal short tandem repeat (Y-STR) loci were analyzed in 201 unrelated Kazak male individuals from Ili Kazak Autonomous Prefecture, Xinjiang, China. The gene diversity of the 24 Y-STR loci in the studied Kazak group ranged from 0.0050 to 0.9104. According to haplotypic analysis of the 24 Y-STR loci, 113 different haplotypes were obtained, 96 of which were unique. The haplotype diversity and discrimination capacity in Kazak group were 0.9578 and 0.5622 at 24 STR loci, respectively. The haplotype diversity and discrimination capacity at Y-filer 17 loci, extended 11 loci, and minimal 9 loci were reduced to 0.9274 and 0.4279, 0.8459 and 0.3284, and 0.8354 and 0.2985, respectively, which could indicate that the more loci were detected, the higher forensic efficacy was obtained. We evaluated the application value of the 24 loci in forensic sciences and analyzed interpopulation differentiations by making comparisons between the Kazak1 (represent our samples from Ili Kazak Autonomous Prefecture) group and other 14 groups. The results of pairwise genetic distances, multidimensional scaling plot, and neighbor-joining tree at the same set of 17 Y-filer loci indicated that the Kazak1 group had the closer genetic relationships with Kazak2 (represent samples from the whole territory of Xinjiang Uygur Autonomous Region), Mongolian, and Uygur ethnic groups. The present results may provide useful information for paternal lineages in forensic cases and can also increase our understanding of the genetic relationships between Kazak1 and other groups.
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Affiliation(s)
- Ting Mei
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China.,Research Center of Stomatology, Stomatological Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China.,Department of Biochemistry, Preclinical Medicine College, Xinjiang Medical University, Urumqi, 830011, People's Republic of China
| | - Li-Ping Zhang
- Department of Biochemistry, Preclinical Medicine College, Xinjiang Medical University, Urumqi, 830011, People's Republic of China
| | - Yao-Shun Liu
- Department of Biochemistry, Preclinical Medicine College, Xinjiang Medical University, Urumqi, 830011, People's Republic of China
| | - Jian-Gang Chen
- Department of Biochemistry, Preclinical Medicine College, Xinjiang Medical University, Urumqi, 830011, People's Republic of China
| | - Hao-Tian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China.,Research Center of Stomatology, Stomatological Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China
| | - Jiang-Wei Yan
- Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Bo-Feng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China. .,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China. .,Research Center of Stomatology, Stomatological Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China.
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