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Diversity 2017, 9(4), 48; doi:10.3390/d9040048

Duplex Alu Screening for Degraded DNA of Skeletal Human Remains

Department of Historical Anthropology and Human Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany
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Received: 31 July 2017 / Revised: 18 October 2017 / Accepted: 20 October 2017 / Published: 25 October 2017
(This article belongs to the Special Issue Ancient DNA)
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Abstract

The human-specific Alu elements, belonging to the class of Short INterspersed Elements (SINEs), have been shown to be a powerful tool for population genetic studies. An earlier study in this department showed that it was possible to analyze Alu presence/absence in 3000-year-old skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. We developed duplex Alu screening PCRs with flanking primers for two Alu elements, each combined with a single internal Alu primer. By adding an internal primer, the approximately 400–500 bp presence signals of Alu elements can be detected within a range of less than 200 bp. Thus, our PCR approach is suited for highly fragmented ancient DNA samples, whereas NGS analyses frequently are unable to handle repetitive elements. With this analysis system, we examined remains of 12 individuals from the Lichtenstein cave with different degrees of DNA degradation. The duplex PCRs showed fully informative amplification results for all of the chosen Alu loci in eight of the 12 samples. Our analysis system showed that Alu presence/absence analysis is possible in samples with different degrees of DNA degradation and it reduces the amount of valuable skeletal material needed by a factor of four, as compared with a singleplex approach. View Full-Text
Keywords: Alu; SINE; retroposons; transposable elements; ancient DNA; aDNA; multiplex PCR; Lichtenstein cave Alu; SINE; retroposons; transposable elements; ancient DNA; aDNA; multiplex PCR; Lichtenstein cave
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Haß, F.; Hummel, S.; Piskurek, O. Duplex Alu Screening for Degraded DNA of Skeletal Human Remains. Diversity 2017, 9, 48.

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