in

Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA

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  • 1.

    Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 2.

    Gansauge, M. T. & Meyer, M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc. 8, 737–748 (2013).

    PubMed  Google Scholar 

  • 3.

    Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014).

    PubMed  Google Scholar 

  • 4.

    Prüfer, K. et al. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 358, 655–658 (2017).

    PubMed  PubMed Central  Google Scholar 

  • 5.

    Mafessoni, F. et al. A high-coverage Neandertal genome from Chagyrskaya Cave. Preprint at https://www.biorxiv.org/content/10.1101/2020.03.12.988956v1 (2020).

  • 6.

    Fu, Q. et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445–449 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 7.

    Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013).

    CAS  PubMed  Google Scholar 

  • 8.

    Meyer, M. et al. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505, 403–406 (2014).

    CAS  PubMed  Google Scholar 

  • 9.

    Meyer, M. et al. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature 531, 504–507 (2016).

    CAS  PubMed  Google Scholar 

  • 10.

    Slon, V. et al. Neandertal and Denisovan DNA from Pleistocene sediments. Science 356, 605–608 (2017).

    CAS  PubMed  Google Scholar 

  • 11.

    Korlević, P. et al. Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. Biotechniques 59, 87–93 (2015).

    PubMed  Google Scholar 

  • 12.

    Gansauge, M. T. et al. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Res. 45, e79 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 13.

    Gansauge, M. T. & Meyer, M. A method for single-stranded ancient DNA library preparation. Methods Mol. Biol. 1963, 75–83 (2019).

  • 14.

    Glocke, I. & Meyer, M. Extending the spectrum of DNA sequences retrieved from ancient bones and teeth. Genome Res. 27, 1230–1237 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 15.

    de Filippo, C., Meyer, M. & Prüfer, K. Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences. BMC Biol. 16, 121 (2018).

    PubMed  PubMed Central  Google Scholar 

  • 16.

    Bennett, E. A. et al. Library construction for ancient genomics: single strand or double strand? Biotechniques 56, 289–290 (2014).

    CAS  PubMed  Google Scholar 

  • 17.

    Wales, N. et al. New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA. Biotechniques 59, 368–371 (2015).

    CAS  PubMed  Google Scholar 

  • 18.

    Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, pdb prot5448 (2010).

  • 19.

    Caroe, C. et al. Single-tube library preparation for degraded DNA. Methods Ecol. Evol. 9, 410–419 (2018).

    Google Scholar 

  • 20.

    Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA 104, 14616–14621 (2007).

    CAS  PubMed  Google Scholar 

  • 21.

    Skoglund, P. et al. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proc. Natl Acad. Sci. USA 111, 2229–2234 (2014).

    CAS  PubMed  Google Scholar 

  • 22.

    Gansauge, M. T. & Meyer, M. Selective enrichment of damaged DNA molecules for ancient genome sequencing. Genome Res. 24, 1543–1549 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 23.

    Bokelmann, L. et al. A genetic analysis of the Gibraltar Neanderthals. Proc. Natl Acad. Sci. USA 116, 15610–15615 (2019).

    CAS  PubMed  Google Scholar 

  • 24.

    Stiller, M. et al. Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) cancer DNA. Oncotarget 7, 59115–59128 (2016).

    PubMed  PubMed Central  Google Scholar 

  • 25.

    Snyder, M. W., Kircher, M., Hill, A. J., Daza, R. M. & Shendure, J. Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell 164, 57–68 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 26.

    Burnham, P. et al. Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma. Sci. Rep. 6, 27859 (2016).

  • 27.

    Turchinovich, A. et al. Capture and Amplification by Tailing and Switching (CATS). An ultrasensitive ligation-independent method for generation of DNA libraries for deep sequencing from picogram amounts of DNA and RNA. RNA Biol. 11, 817–828 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 28.

    Karlsson, K. et al. Amplification-free sequencing of cell-free DNA for prenatal non-invasive diagnosis of chromosomal aberrations. Genomics 105, 150–158 (2015).

    CAS  PubMed  Google Scholar 

  • 29.

    Raine, A., Manlig, E., Wahlberg, P., Syvanen, A. C. & Nordlund, J. SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing. Nucleic Acids Res. 45, e36 (2017).

    PubMed  Google Scholar 

  • 30.

    Wu, J., Dai, W., Wu, L. & Wang, J. SALP, a new single-stranded DNA library preparation method especially useful for the high-throughput characterization of chromatin openness states. BMC Genomics 19, 143 (2018).

    PubMed  PubMed Central  Google Scholar 

  • 31.

    Ding, J., Taylor, M. S., Jackson, A. P. & Reijns, M. A. Genome-wide mapping of embedded ribonucleotides and other noncanonical nucleotides using emRiboSeq and EndoSeq. Nat. Protoc. 10, 1433–1444 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 32.

    Petryk, N. et al. Replication landscape of the human genome. Nat. Commun. 7, 10208 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 33.

    Tin, M. M., Economo, E. P. & Mikheyev, A. S. Sequencing degraded DNA from non-destructively sampled museum specimens for RAD-tagging and low-coverage shotgun phylogenetics. PLoS ONE 9, e96793 (2014).

    PubMed  PubMed Central  Google Scholar 

  • 34.

    Troll, C. J. et al. A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos. BMC Genomics 20, 1023 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 35.

    Knapp, M., Clarke, A. C., Horsburgh, K. A. & Matisoo-Smith, E. A. Setting the stage – building and working in an ancient DNA laboratory. Ann. Anat. 194, 3–6 (2012).

    CAS  PubMed  Google Scholar 

  • 36.

    Kampmann, M. L., Borsting, C. & Morling, N. Decrease DNA contamination in the laboratories. Forensic Sci. Int. Genet. 6, E577–E578 (2017).

    Google Scholar 

  • 37.

    Rohland, N., Glocke, I., Aximu-Petri, A. & Meyer, M. Extraction of highly degraded DNA from ancient bones, teeth and sediments for high-throughput sequencing. Nat. Protoc. 13, 2447–2461 (2018).

    CAS  PubMed  Google Scholar 

  • 38.

    Prüfer, K. snpAD: an ancient DNA genotype caller. Bioinformatics 34, 4165–4171 (2018).

    PubMed  PubMed Central  Google Scholar 

  • 39.

    Varshney, U. & van de Sande, J. H. Specificities and kinetics of uracil excision from uracil-containing DNA oligomers by Escherichia coli uracil DNA glycosylase. Biochemistry 30, 4055–4061 (1991).

    CAS  PubMed  Google Scholar 

  • 40.

    Burbano, H. A. et al. Targeted investigation of the Neandertal genome by array-based sequence capture. Science 328, 723–725 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 41.

    Fu, Q. et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl Acad. Sci. USA 110, 2223–2227 (2013).

    CAS  PubMed  Google Scholar 

  • 42.

    Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 43.

    Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res 40, e3 (2012).

    CAS  PubMed  Google Scholar 

  • 44.

    Dabney, J. & Meyer, M. Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. Biotechniques 52, 87–94 (2012).

    CAS  PubMed  Google Scholar 

  • 45.

    Thompson, J. R., Marcelino, L. A. & Polz, M. F. Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by ‘reconditioning PCR’. Nucleic Acids Res. 30, 2083–2088 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 46.

    Renaud, G., Stenzel, U. & Kelso, J. leeHom: adaptor trimming and merging for Illumina sequencing reads. Nucleic Acids Res. 42, e141 (2014).

    PubMed  PubMed Central  Google Scholar 

  • 47.

    Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 


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