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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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Autores principales: Nazir, Shahid, Adnan, Atif, Rehman, Rahat Abdul, Al-Qahtani, Wedad Saeed, Alsaleh, Abrar B., Al-Harthi, Hussam S., Safhi, Fatmah Ahmed, Almheiri, Reem, Lootah, Reem, Alreyami, Afra, Almarri, Imran, Wang, Chuan-Chao, Rakha, Allah, Hadi, Sibte
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9407599/
https://www.ncbi.nlm.nih.gov/pubmed/36011314
http://dx.doi.org/10.3390/genes13081403
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author Nazir, Shahid
Adnan, Atif
Rehman, Rahat Abdul
Al-Qahtani, Wedad Saeed
Alsaleh, Abrar B.
Al-Harthi, Hussam S.
Safhi, Fatmah Ahmed
Almheiri, Reem
Lootah, Reem
Alreyami, Afra
Almarri, Imran
Wang, Chuan-Chao
Rakha, Allah
Hadi, Sibte
author_facet Nazir, Shahid
Adnan, Atif
Rehman, Rahat Abdul
Al-Qahtani, Wedad Saeed
Alsaleh, Abrar B.
Al-Harthi, Hussam S.
Safhi, Fatmah Ahmed
Almheiri, Reem
Lootah, Reem
Alreyami, Afra
Almarri, Imran
Wang, Chuan-Chao
Rakha, Allah
Hadi, Sibte
author_sort Nazir, Shahid
collection PubMed
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(−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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spelling pubmed-94075992022-08-26 Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan Nazir, Shahid Adnan, Atif Rehman, Rahat Abdul Al-Qahtani, Wedad Saeed Alsaleh, Abrar B. Al-Harthi, Hussam S. Safhi, Fatmah Ahmed Almheiri, Reem Lootah, Reem Alreyami, Afra Almarri, Imran Wang, Chuan-Chao Rakha, Allah Hadi, Sibte Genes (Basel) Article 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. MDPI 2022-08-07 /pmc/articles/PMC9407599/ /pubmed/36011314 http://dx.doi.org/10.3390/genes13081403 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Nazir, Shahid
Adnan, Atif
Rehman, Rahat Abdul
Al-Qahtani, Wedad Saeed
Alsaleh, Abrar B.
Al-Harthi, Hussam S.
Safhi, Fatmah Ahmed
Almheiri, Reem
Lootah, Reem
Alreyami, Afra
Almarri, Imran
Wang, Chuan-Chao
Rakha, Allah
Hadi, Sibte
Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan
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 Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9407599/
https://www.ncbi.nlm.nih.gov/pubmed/36011314
http://dx.doi.org/10.3390/genes13081403
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