Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan
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 pedi...
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| Format: | Article |
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MDPI AG
2022-08-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/8/1403 |
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| author | Shahid Nazir Atif Adnan Rahat Abdul Rehman Wedad Saeed Al-Qahtani Abrar B. Alsaleh Hussam S. Al-Harthi Fatmah Ahmed Safhi Reem Almheiri Reem Lootah Afra Alreyami Imran Almarri Chuan-Chao Wang Allah Rakha Sibte Hadi |
| author_facet | Shahid Nazir Atif Adnan Rahat Abdul Rehman Wedad Saeed Al-Qahtani Abrar B. Alsaleh Hussam S. Al-Harthi Fatmah Ahmed Safhi Reem Almheiri Reem Lootah Afra Alreyami Imran Almarri Chuan-Chao Wang Allah Rakha Sibte Hadi |
| author_sort | Shahid Nazir |
| collection | DOAJ |
| description | 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<sup>−2</sup>) 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. |
| first_indexed | 2024-03-09T04:23:36Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T04:23:36Z |
| publishDate | 2022-08-01 |
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| series | Genes |
| spelling | doaj.art-1a6d59b023704874ad6ea4b7527545332023-12-03T13:43:01ZengMDPI AGGenes2073-44252022-08-01138140310.3390/genes13081403Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from PakistanShahid Nazir0Atif Adnan1Rahat Abdul Rehman2Wedad Saeed Al-Qahtani3Abrar B. Alsaleh4Hussam S. Al-Harthi5Fatmah Ahmed Safhi6Reem Almheiri7Reem Lootah8Afra Alreyami9Imran Almarri10Chuan-Chao Wang11Allah Rakha12Sibte Hadi13Department of Forensic Sciences, University of Health Sciences, Lahore 54600, PakistanDepartment of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, ChinaDepartment of Forensic Sciences, University of Health Sciences, Lahore 54600, PakistanDepartment of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi ArabiaDepartment of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi ArabiaPrince Sultan Military Medical City, Makkah Al Mukarramah Road, Al-Sulimaniyah, Riyadh 12233, Saudi ArabiaDepartment of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi ArabiaGeneral Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab EmiratesGeneral Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab EmiratesGeneral Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab EmiratesGeneral Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab EmiratesDepartment of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, ChinaDepartment of Forensic Sciences, University of Health Sciences, Lahore 54600, PakistanDepartment of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi ArabiaY 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<sup>−2</sup>) 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.https://www.mdpi.com/2073-4425/13/8/1403endogamousPunjabPakistandeep-rooted pedigreesRM Y-STRsmutation rates |
| spellingShingle | Shahid Nazir Atif Adnan Rahat Abdul Rehman Wedad Saeed Al-Qahtani Abrar B. Alsaleh Hussam S. Al-Harthi Fatmah Ahmed Safhi Reem Almheiri Reem Lootah Afra Alreyami Imran Almarri Chuan-Chao Wang Allah Rakha Sibte Hadi Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan Genes endogamous Punjab Pakistan deep-rooted pedigrees RM Y-STRs mutation rates |
| title | Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan |
| title_full | Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan |
| title_fullStr | Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan |
| title_full_unstemmed | Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan |
| title_short | Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan |
| title_sort | mutation rate analysis of rm y strs in deep rooted multi generational punjabi pedigrees from pakistan |
| topic | endogamous Punjab Pakistan deep-rooted pedigrees RM Y-STRs mutation rates |
| url | https://www.mdpi.com/2073-4425/13/8/1403 |
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