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Ancient DNA pp 141–147Cite as

Targeted PCR Amplification and Multiplex Sequencing of Ancient DNA for SNP Analysis

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1963))

Abstract

The analysis of single-nucleotide polymorphisms (SNPs) has proven to be advantageous for addressing variation within samples of highly degraded or low-quality DNA samples. This is because only short fragments need to be amplified to analyze SNPs, and this can be achieved by multiplex PCR. Here, we present a sensitive method for the targeted sequencing of SNP loci that requires only small amounts of template DNA. The approach combines multiplex amplification of very short fragments covering SNP positions followed by sample barcoding and next-generation sequencing. This method allows generation of data from large sample sets of poorly preserved specimens, such as fossil remains, forensic samples, and museum specimens. The approach is cost-effective, rapid, and applicable to forensics, population genetics, and phylogenetic research questions.

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Acknowledgments

Thanks to Johanna Paijmans for the opportunity to contribute to this special edition and to the Deutsche Forschungsgemeinschaft (DFG) for financial support.

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Authors and Affiliations

  1. Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland

    Saskia Wutke

  2. Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany

    Arne Ludwig

Authors
  1. Saskia Wutke
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  2. Arne Ludwig
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Corresponding author

Correspondence to Arne Ludwig .

Editor information

Editors and Affiliations

  1. Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA

    Beth Shapiro

  2. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Axel Barlow

  3. Tromsø University Museum, UiT—The Arctic University of Norway, Tromsø, Norway

    Peter D. Heintzman

  4. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Michael Hofreiter

  5. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Johanna L. A. Paijmans

  6. Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil

    André E. R. Soares

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Wutke, S., Ludwig, A. (2019). Targeted PCR Amplification and Multiplex Sequencing of Ancient DNA for SNP Analysis. In: Shapiro, B., Barlow, A., Heintzman, P., Hofreiter, M., Paijmans, J., Soares, A. (eds) Ancient DNA. Methods in Molecular Biology, vol 1963. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9176-1_15

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  • DOI: https://doi.org/10.1007/978-1-4939-9176-1_15

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9175-4

  • Online ISBN: 978-1-4939-9176-1

  • eBook Packages: Springer Protocols

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