The 81st Annual Meeting of the American Association of Physical Anthropologists (2012)


*PRESENTATION WITHDRAWN* Designing a hierarchical probe assay to identify native specific Y haplogroups in admixed populations

TORREY D. PARRISH1, ANNE E. JUSTICE2,4, STEPHEN M. JOHNSON2, KRISTIE G. BEATY2, CHRISTINE PHILLIPS-KRAWCZAK3, PATRICK WILLIAMS1 and MICHAEL H. CRAWFORD2.

1Molecular Biology Laboratory, Evogen, Inc, 2Department of Anthropology, Lab of Biological Anthropology, University of Kansas, 3Genetics Program, Department of Molecular Biosciences, Universityof Kansas, 4Department of Epidemiolgy, University of North Carolina

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Major Y chromosome haplogroups are identified using both STRs and SNPs. However, STRs and haplogroup predictors are unreliable for identifying major Y haplogroups, especially those common in the Americas. Y chromosome SNPs identified by the YCC are a much more consistent means of identifying Y chromosome haplogroups. Identifying these SNPs usually requires costly and/or time consuming methods, such as sequencing, SBE, or RFLP. The cost and time are inflated when dealing with populations which have undergone significant admixture, such as those found in the Americas. Efficient and reliable techniques for Y haplogroup identification are needed, and ones for which cost is not prohibitive for smaller anthropological laboratories. Amethod is described here using a new probe technology, Hybeacons® (Evogen, Inc.), which addresses these needs. In order to save time and cost, a hierarchical multiplex was designed to first identify major global haplogroup/macrohaplogroup in three separate reactions (A, B, C, D/E, F; G, H, I/J, K; and L, M, N/O, Q, and R), then two singleplex reactions are performed to identify Native American specific SNPs (Q1a3a-M3 and C3b-P39). The multiplexes were authenticated on admixed populations from Europe, Africa, Asia, the Caribbean, and North, Central, and South America. The results were consistent with those obtained from independent sequencing of a subset of samples from each marker. The SNP multiplex provides a low-cost and rapid method for the typing of Y chromosome haplogroups important for any field whose data are dependent on identifying ancestry of male participants.

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