Ancient DNA pp 141-147 | Cite as

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

  • Saskia Wutke
  • Arne LudwigEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1963)


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.

Key words

Ancient DNA Single-nucleotide polymorphism Multiplex PCR Next-generation sequencing Library preparation 



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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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
  2. 2.Department of Evolutionary GeneticsLeibniz Institute for Zoo and Wildlife Research (IZW)BerlinGermany

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