Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations
Thijessen Naidoo et al.
Background: The ability of the Y chromosome to retain a record of its evolution has seen it become an essentialtool of molecular anthropology. In the last few years, however, it has also found use in forensic genetics, providinginformation on the geographic origin of individuals. This has been aided by the development of efficient screeningmethods and an increased knowledge of geographic distribution. In this study, we describe the development ofsingle base extension assays used to resolve 61 Y chromosome haplogroups, mainly within haplogroups A, B andE, found in Africa.
Results: Seven multiplex assays, which incorporated 60 Y chromosome markers, were developed. These resolved Ychromosomes to 61 terminal branches of the major African haplogroups A, B and E, while also including a fewEurasian haplogroups found occasionally in African males. Following its validation, the assays were used to screen683 individuals from Southern Africa, including south eastern Bantu speakers (BAN), Khoe-San (KS) and SouthAfrican Whites (SAW). Of the 61 haplogroups that the assays collectively resolved, 26 were found in the 683samples. While haplogroup sharing was common between the BAN and KS, the frequencies of these haplogroupsvaried 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 andsampling throughput, while saving time and DNA. Their use, together with the screening of short tandem repeatmarkers would considerably improve resolution, thus refining the geographic ancestry of individuals.