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Large-scale pedigree analysis highlights rapidly mutating Y-chromosomal short tandem repeats for differentiating patrilineal relatives and predicting their degrees of consanguinity. Hum Genet 2023; 142:145-160. [PMID: 36190543 PMCID: PMC9839801 DOI: 10.1007/s00439-022-02493-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/26/2022] [Indexed: 01/18/2023]
Abstract
Rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) were suggested for differentiating patrilineally related men as relevant in forensic genetics, anthropological genetics, and genetic genealogy. Empirical data are available for closely related males, while differentiation rates for more distant relatives are scarce. Available RM Y-STR mutation rate estimates are typically based on father-son pair data, while pedigree-based studies for efficient analysis requiring less samples are rare. Here, we present a large-scale pedigree analysis in 9379 pairs of men separated by 1-34 meioses on 30 Y-STRs with increased mutation rates including all known RM Y-STRs (RMplex). For comparison, part of the samples were genotyped at 25 standard Y-STRs mostly with moderate mutation rates (Yfiler Plus). For 43 of the 49 Y-STRs analyzed, pedigree-based mutation rates were similar to previous father-son based estimates, while for six markers significant differences were observed. Male relative differentiation rates from the 30 RMplex Y-STRs were 43%, 84%, 96%, 99%, and 100% for relatives separated by one, four, six, nine, and twelve meioses, respectively, which largely exceeded rates obtained by 25 standard Y-STRs. Machine learning based models for predicting the degree of patrilineal consanguinity yielded accurate and reasonably precise predictions when using RM Y-STRs. Fully matching haplotypes resulted in a 95% confidence interval of 1-6 meioses with RMplex compared to 1-25 with Yfiler Plus. Our comprehensive pedigree study demonstrates the value of RM Y-STRs for differentiating male relatives of various types, in many cases achieving individual identification, thereby overcoming the largest limitation of forensic Y-chromosome analysis.
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Nazir S, Adnan A, Rehman RA, Al-Qahtani WS, Alsaleh AB, Al-Harthi HS, Safhi FA, Almheiri R, Lootah R, Alreyami A, Almarri I, Wang CC, Rakha A, Hadi S. Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan. Genes (Basel) 2022; 13:genes13081403. [PMID: 36011314 PMCID: PMC9407599 DOI: 10.3390/genes13081403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/03/2022] [Indexed: 11/30/2022] Open
Abstract
Y chromosome short tandem repeat polymorphisms (Y-STRs) are important in many areas of human genetics. Y chromosomal STRs, being normally utilized in the field of forensics, exhibit low haplotype diversity in consanguineous populations and fail to discriminate among male relatives from the same pedigree. Rapidly mutating Y-STRs (RM Y-STRs) have received much attention in the past decade. These 13 RM Y-STRs have high mutation rates (>10−2) and have considerably higher haplotype diversity and discrimination capacity than conventionally used Y-STRs, showing remarkable power when it comes to differentiation in paternal lineages in endogamous populations. Previously, we analyzed two to four generations of 99 pedigrees with 1568 pairs of men covering one to six meioses from all over Pakistan and 216 male relatives from 18 deep-rooted endogamous Sindhi pedigrees covering one to seven meioses. Here, we present 861 pairs of men from 62 endogamous pedigrees covering one to six meioses from the Punjabi population of Punjab, Pakistan. Mutations were frequently observed at DYF399 and DYF403, while no mutation was observed at DYS526a/b. The rate of differentiation ranged from 29.70% (first meiosis) to 80.95% (fifth meiosis), while overall (first to sixth meiosis) differentiation was 59.46%. Combining previously published data with newly generated data, the overall differentiation rate was 38.79% based on 5176 pairs of men related by 1−20 meioses, while Yfiler differentiation was 9.24% based on 3864 pairs. Using father−son pair data from the present and previous studies, we also provide updated RM Y-STR mutation rates.
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Affiliation(s)
- Shahid Nazir
- Department of Forensic Sciences, University of Health Sciences, Lahore 54600, Pakistan
| | - Atif Adnan
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
- Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi Arabia
- Correspondence: (A.A.); (C.-C.W.); (A.R.); (S.H.)
| | - Rahat Abdul Rehman
- Department of Forensic Sciences, University of Health Sciences, Lahore 54600, Pakistan
| | - Wedad Saeed Al-Qahtani
- Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi Arabia
| | - Abrar B. Alsaleh
- Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi Arabia
| | - Hussam S. Al-Harthi
- Prince Sultan Military Medical City, Makkah Al Mukarramah Road, Al-Sulimaniyah, Riyadh 12233, Saudi Arabia
| | - Fatmah Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Reem Almheiri
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Reem Lootah
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Afra Alreyami
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Imran Almarri
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
- Correspondence: (A.A.); (C.-C.W.); (A.R.); (S.H.)
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore 54600, Pakistan
- Correspondence: (A.A.); (C.-C.W.); (A.R.); (S.H.)
| | - Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi Arabia
- Correspondence: (A.A.); (C.-C.W.); (A.R.); (S.H.)
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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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Ralf A, Zandstra D, Weiler N, van Ijcken WFJ, Sijen T, Kayser M. RMplex: An efficient method for analyzing 30 Y-STRs with high mutation rates. Forensic Sci Int Genet 2021; 55:102595. [PMID: 34543845 DOI: 10.1016/j.fsigen.2021.102595] [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: 05/05/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Y-chromosomal short tandem repeats (Y-STRs) with high mutation rates are recognized as valuable genetic markers for differentiating paternally related men, who typically cannot be separated with standard Y-STRs, and were shown to provide paternal lineage differentiation on a higher resolution level than standard Y-STRs. Both features make Y-STRs with high mutation rates relevant in criminal casework, particularly in sexual assault cases involving highly unbalanced male-female DNA mixtures that often fail autosomal forensic STR profiling for the male donor. Previously, the number of known Y-STRs with mutation rates higher than 10-2 per locus per generation termed rapidly mutating Y-STRs (RM Y-STRs) was limited to 13, which has recently been overcome by the discovery and characterization of 12 additional RM Y-STRs. Here, we present the development and validation of RMplex, an efficient genotyping system for analyzing 30 Y-STRs with high mutation rates, including all currently known RM Y-STRs, using multiplex PCR with capillary electrophoresis (CE) or massively parallel sequencing (MPS), overall targeting a total of 44 male-specific loci. If previously unavailable, repeat number assignations were provided based on newly generated MPS data. Validation tests based on the CE method demonstrated that the results were both repeatable and reproducible, full profiles were achieved with minimal input DNA of 250 pg for RMplex 1 and 100 pg for RMplex 2, and in the presence of inhibitors, or with a surplus of female DNA, the assays performed reasonably well. Application of RMplex to differentiate between paternally related men was exemplified in 32 males belonging to five different paternal pedigrees. Given further successful forensic validation testing, we envision the future application of RMplex in criminal cases where it is suspected, or cannot be excluded, that the crime scene trace originated from a male relatives of the suspect who is highlighted with standard Y-STR matching. Other applications of RMplex are in criminal cases without known suspects to differentiate between male relatives highlighted in familial searching based on standard Y-STR matching.
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Affiliation(s)
- Arwin Ralf
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Dion Zandstra
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Natalie Weiler
- Division of Biological Traces, Netherlands Forensic Institute, The Hague, the Netherlands
| | - Wilfred F J van Ijcken
- Center for Biomics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Titia Sijen
- Division of Biological Traces, Netherlands Forensic Institute, The Hague, the Netherlands; University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
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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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Oldoni F, Podini D. Forensic molecular biomarkers for mixture analysis. Forensic Sci Int Genet 2019; 41:107-119. [DOI: 10.1016/j.fsigen.2019.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/06/2019] [Accepted: 04/17/2019] [Indexed: 01/10/2023]
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