Ancient DNA pp 177-188 | Cite as

Target Enrichment via DNA Hybridization Capture

  • Susanne HornEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 840)


Recent advances in high-throughput DNA sequencing technologies have allowed entire nuclear genomes to be shotgun sequenced from ancient DNA (aDNA) extracts. Nonetheless, targeted analyses of specific genomic loci will remain an important tool for future aDNA studies. DNA capture via hybridization allows the efficient exploitation of current high-throughput sequencing for population genetic analyses using aDNA samples. Specifically, hybridization capture allows larger data sets to be generated for multiple target loci as well as for multiple samples in parallel. “Bait” molecules are used to select target regions from DNA libraries for sequencing. Here we present a brief overview of the currently available hybridization capture protocols using either an in-solution or a solid-phase (immobilized) approach. While it is possible to purchase ready-made kits for this purpose, I present a protocol that allows users to generate their own custom bait to be used for hybridization capture.

Key words

ancient DNA target enrichment hybridization DNA capture bait high-throughput sequencing 



I would like to thank the Volkswagen foundation and the Max Planck society for funding and M Stiller for helpful comments on this manuscript.


  1. 1.
    Rasmussen M et al (2010) Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463(7282):757–762PubMedCrossRefGoogle Scholar
  2. 2.
    Green RE et al (2010) A draft sequence of the Neandertal genome. Science 328(5979):710–722PubMedCrossRefGoogle Scholar
  3. 3.
    Reich D et al (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468(7327):1053–1060PubMedCrossRefGoogle Scholar
  4. 4.
    John JS, Quinn TW (2008) Rapid capture of DNA targets. Biotechniques 44(2):259–264CrossRefGoogle Scholar
  5. 5.
    Gnirke A et al (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27(2):182–189PubMedCrossRefGoogle Scholar
  6. 6.
    Hodges E et al (2007) Genome-wide in situ exon capture for selective resequencing. Nat Genet 39(12):1522–1527PubMedCrossRefGoogle Scholar
  7. 7.
    Burbano HA et al (2010) Targeted investigation of the Neandertal genome by array-based sequence capture. Science 328(5979):723–725PubMedCrossRefGoogle Scholar
  8. 8.
    Stiller M et al (2006) Inaugural article: patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA. Proc Natl Acad Sci U S A 103(37):13578–13584PubMedCrossRefGoogle Scholar
  9. 9.
    Briggs AW et al (2007) Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci 104(37):14616–14621PubMedCrossRefGoogle Scholar
  10. 10.
    Briggs AW et al (2009) Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science 325(5938):318–321PubMedCrossRefGoogle Scholar
  11. 11.
    Meyer M, Kircher M (2010) Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc 2010(6):pdb.prot5448. doi: 10.1101/pdb.prot5448 PubMedCrossRefGoogle Scholar
  12. 12.
    Teer JK et al (2010) Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Res 20(10):1420–1431PubMedCrossRefGoogle Scholar
  13. 13.
    Blow N (2009) Genomics: catch me if you can. Nat Methods 6(7):539–544CrossRefGoogle Scholar
  14. 14.
    Maricic T, Whitten M, Pääbo S (2010) Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS One 5(11):e14004PubMedCrossRefGoogle Scholar
  15. 15.
    Noonan JP et al (2006) Sequencing and analysis of Neanderthal genomic DNA. Science 314:1113–1118PubMedCrossRefGoogle Scholar
  16. 16.
  17. 17.
  18. 18.
    Meyer M, Stenzel U, Hofreiter M (2008) Parallel tagged sequencing on the 454 platform. Nat Protoc 3(2):267–278PubMedCrossRefGoogle Scholar
  19. 19.
    Paul N, Yee J (2010) PCR incorporation of modified dNTPs: the substrate properties of biotinylated dNTPs. Biotechniques 48(4):333–334CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Max Planck Institute for Evolutionary AnthropologyGermany and German Cancer Research Center (DKFZ)HeidelbergGermany

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