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Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations

机译：开发单碱基扩展方法以解决撒哈拉以南非洲人群的Y染色体单倍群

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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.
机译：背景技术Y染色体保留其进化记录的能力已使其成为分子人类学的重要工具。然而，在最近几年中，它也被用于法医遗传学，提供有关个体地理起源的信息。有效的筛查方法的发展和对地理分布知识的增强，为这提供了帮助。在这项研究中，我们描述了用于解决61个Y染色体单倍群（主要在非洲的A，B和E单倍群中）的单碱基延伸测定法的发展。结果开发了包含60个Y染色体标记的7种多重分析。这些Y染色体解析到非洲主要单倍体A，B和E的61个末端分支，同时还包括一些偶尔在非洲男性中发现的欧亚单倍体。经过验证后，该检测方法用于筛查来自南部非洲的683名个体，包括东南部班图人（BAN），Khoe-San（KS）和南非白人（SAW）。在这些测定共同解决的61个单倍群中，在683个样品中发现了26个。虽然BAN和KS之间存在单倍群共享，但是这些单倍群的出现频率却存在明显差异。两组都显示出较低的欧亚单倍体同化水平，并且SAW中只有两个人明显具有非洲血统的Y染色体。结论使用这些单碱基延伸测定法筛选可提高单倍型分辨率和样品通量，同时节省时间和DNA。它们的使用以及短串联重复标记的筛选将大大提高分辨率，从而改善个人的地理血统。

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