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Ancient DNA pp 129-139 | Cite as

Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA

  • Johanna L. A. Paijmans
  • Gloria González Fortes
  • Daniel W. Förster
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1963)

Abstract

Genetic studies that include ancient samples are often hampered by the low amount of endogenous DNA that ancient samples often contain, relative to co-extracted “contaminant” DNA from other organisms. One approach to mitigate this challenge is to perform hybridization-based capture of target genomic regions using DNA or RNA baits. Such baits are designed to have high sequence similarity to the target genomic regions and can reduce the off-target fraction in DNA sequencing libraries. Here, we present a protocol to use Agilent SureSelect microarrays to enrich ancient DNA libraries for small-to-medium-sized target loci, such as mitochondrial genomes, from ancient DNA extracts. The protocol that we present builds on previously published work by introducing improvements that improve recovery of short DNA fragments while minimizing the cost and duration of the experiment.

Key words

Ancient DNA Next-generation sequencing Target enrichment Microarray capture Hybridization capture 

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Copyright information

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

Authors and Affiliations

  • Johanna L. A. Paijmans
    • 1
  • Gloria González Fortes
    • 2
  • Daniel W. Förster
    • 3
  1. 1.Institute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
  2. 2.Department of Life Sciences and BiotechnologyUniversity of FerraraFerraraItaly
  3. 3.Department of Evolutionary GeneticsLeibniz-Institute for Zoo and Wildlife Research (IZW)BerlinGermany

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