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Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations
BACKGROUND: The ability of the Y chromosome to retain a record of its evolution has seen it become an essential tool of molecular anthropology. In the last few years, however, it has also found use in forensic genetics, providing information on the geographic origin of individuals. This has been aid...
Autores principales: | , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988483/ https://www.ncbi.nlm.nih.gov/pubmed/21092339 http://dx.doi.org/10.1186/2041-2223-1-6 |
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author | Naidoo, Thijessen Schlebusch, Carina M Makkan, Heeran Patel, Pareen Mahabeer, Rajeshree Erasmus, Johannes C Soodyall, Himla |
author_facet | Naidoo, Thijessen Schlebusch, Carina M Makkan, Heeran Patel, Pareen Mahabeer, Rajeshree Erasmus, Johannes C Soodyall, Himla |
author_sort | Naidoo, Thijessen |
collection | PubMed |
description | BACKGROUND: The ability of the Y chromosome to retain a record of its evolution has seen it become an essential tool of molecular anthropology. In the last few years, however, it has also found use in forensic genetics, providing information on the geographic origin of individuals. This has been aided by the development of efficient screening methods and an increased knowledge of geographic distribution. In this study, we describe the development of single base extension assays used to resolve 61 Y chromosome haplogroups, mainly within haplogroups A, B and E, found in Africa. RESULTS: Seven multiplex assays, which incorporated 60 Y chromosome markers, were developed. These resolved Y chromosomes to 61 terminal branches of the major African haplogroups A, B and E, while also including a few Eurasian haplogroups found occasionally in African males. Following its validation, the assays were used to screen 683 individuals from Southern Africa, including south eastern Bantu speakers (BAN), Khoe-San (KS) and South African Whites (SAW). Of the 61 haplogroups that the assays collectively resolved, 26 were found in the 683 samples. While haplogroup sharing was common between the BAN and KS, the frequencies of these haplogroups varied appreciably. Both groups showed low levels of assimilation of Eurasian haplogroups and only two individuals in the SAW clearly had Y chromosomes of African ancestry. CONCLUSIONS: The use of these single base extension assays in screening increased haplogroup resolution and sampling throughput, while saving time and DNA. Their use, together with the screening of short tandem repeat markers would considerably improve resolution, thus refining the geographic ancestry of individuals. |
format | Text |
id | pubmed-2988483 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-29884832010-11-22 Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations Naidoo, Thijessen Schlebusch, Carina M Makkan, Heeran Patel, Pareen Mahabeer, Rajeshree Erasmus, Johannes C Soodyall, Himla Investig Genet Methodology BACKGROUND: The ability of the Y chromosome to retain a record of its evolution has seen it become an essential tool of molecular anthropology. In the last few years, however, it has also found use in forensic genetics, providing information on the geographic origin of individuals. This has been aided by the development of efficient screening methods and an increased knowledge of geographic distribution. In this study, we describe the development of single base extension assays used to resolve 61 Y chromosome haplogroups, mainly within haplogroups A, B and E, found in Africa. RESULTS: Seven multiplex assays, which incorporated 60 Y chromosome markers, were developed. These resolved Y chromosomes to 61 terminal branches of the major African haplogroups A, B and E, while also including a few Eurasian haplogroups found occasionally in African males. Following its validation, the assays were used to screen 683 individuals from Southern Africa, including south eastern Bantu speakers (BAN), Khoe-San (KS) and South African Whites (SAW). Of the 61 haplogroups that the assays collectively resolved, 26 were found in the 683 samples. While haplogroup sharing was common between the BAN and KS, the frequencies of these haplogroups varied appreciably. Both groups showed low levels of assimilation of Eurasian haplogroups and only two individuals in the SAW clearly had Y chromosomes of African ancestry. CONCLUSIONS: The use of these single base extension assays in screening increased haplogroup resolution and sampling throughput, while saving time and DNA. Their use, together with the screening of short tandem repeat markers would considerably improve resolution, thus refining the geographic ancestry of individuals. BioMed Central 2010-09-01 /pmc/articles/PMC2988483/ /pubmed/21092339 http://dx.doi.org/10.1186/2041-2223-1-6 Text en Copyright ©2010 Naidoo et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Naidoo, Thijessen Schlebusch, Carina M Makkan, Heeran Patel, Pareen Mahabeer, Rajeshree Erasmus, Johannes C Soodyall, Himla Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations |
title | Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations |
title_full | Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations |
title_fullStr | Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations |
title_full_unstemmed | Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations |
title_short | Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations |
title_sort | development of a single base extension method to resolve y chromosome haplogroups in sub-saharan african populations |
topic | Methodology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988483/ https://www.ncbi.nlm.nih.gov/pubmed/21092339 http://dx.doi.org/10.1186/2041-2223-1-6 |
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