CoChat
Sign Up
Cited by 276

The DOI matches its Crossref record; 16 of the 16 references it cites were found in a registry or an index.

Improving access to endogenous DNA in ancient bones and teeth

Damgaard, Peter B., Margaryan, Ashot, Schroeder, Hannes, Orlando, Ludovic, Willerslev, Eske, Allentoft, Morten E.·2015·Scientific Reports
DOI 10.1038/srep11184PMC PMC4472031

Published version of a preprint

Open this paper in CoChat — free account

Abstract

Poor DNA preservation is the most limiting factor in ancient genomic research. In the majority of ancient bones and teeth, endogenous DNA molecules represent a minor fraction of the whole DNA extract, rendering shot-gun sequencing inefficient for obtaining genomic data. Based on ancient human bone samples from temperate and tropical environments, we show that an EDTA-based enzymatic ‘pre-digestion’ of powdered bone increases the proportion of endogenous DNA several fold. By performing the pre-digestion step between 30 min and 6 hours on five bones, we observe an asymptotic increase in endogenous DNA content, with a 2.7-fold average increase reached at 1 hour. We repeat the experiment using a brief pre-digestion (15 or 30 mins) on 21 ancient bones and teeth from a variety of archaeological contexts and observe an improvement in 16 of these. We here advocate the implementation of a brief pre-digestion step as a standard procedure in ancient DNA extractions. Finally, we demonstrate on 14 ancient teeth that by targeting the outer layer of the roots we obtain up to 14 times more endogenous DNA than when using the inner dentine. Our presented methods are likely to increase the proportion of ancient samples that are suitable for genome-scale characterization.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/srep11184

Cites

16 of 16 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The discovery that particular bone types exhibit better molecular preservation has facilitated collection of ancient DNA time-series data at population and genome-wide scales.

    “The discovery that particular bone types exhibit better molecular preservation 52,53 has also facilitated the collection of aDNA time-series data at both population and genome-wide scales.”

    From Ancient DNA analysis (2021) · cites this paper as [53]

    The Results section (page unavailable) finds more endogenous DNA in the outer root surface than in the dentine core of 11 of 14 ancient teeth. The Abstract says this targeting method is likely to make more samples suitable for genome-scale characterization. The paper compares parts of teeth rather than particular bone types, and it does not report that the finding facilitated collection of population-scale aDNA time-series data. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 32

  1. Der Sarkissian, C. et al. Ancient genomics. Philos. Trans. R. Soc. B Biol. Sci. 370, 20130387 (2015). · DOI
  2. Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010).
  3. Krause, J. et al. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464, 894–897 (2010). · DOI
  4. Raghavan, M. et al. The genetic prehistory of the New World Arctic. Science 345, 1255832 (2014). · DOI · Paper page
  5. Orlando, Ludovic et al. “Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.” Nature 499, 74–78 (2013). · DOI · Paper page
  6. Olalde, I. et al. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature 507, 225–228 (2014). · DOI · Paper page
  7. Skoglund, P. et al. Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers. Science 344, 747–750 (2014). · DOI
  8. Carpenter, M. L. et al. Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. Am. J. Hum. Genet. 93, 852–864 (2013). · DOI
  9. Rizzi, E., Lari, M., Gigli, E., De Bellis, G. & Caramelli, D. Ancient DNA studies: new perspectives on old samples. Genet Sel Evol 44, 21 (2012). · DOI
  10. Poinar, H. N. et al. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311, 392–394 (2006). · DOI
  11. Sarkissian, C. et al. Shotgun microbial profiling of fossil remains. Mol. Ecol. 23, 1780–1798 (2014). · DOI
  12. Campos, P. F. et al. DNA in ancient bone–Where is it located and how should we extract it? Ann. Anat.-Anat. Anz. 194, 7–16 (2012). · DOI
  13. Schwarz, Carsten, et al. “New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains.” Nucleic Acids Research 37, 3215–3229 (2009). · DOI
  14. Jans, Miranda ME. “Microbial bioerosion of bone–a review.” In Current developments in bioerosion, pp. 397–413. Springer Berlin Heidelberg, 2008 · DOI
  15. Ginolhac, A. et al. Improving the performance of true single molecule sequencing for ancient DNA. BMC Genomics 13, 177 (2012). · DOI
  16. Orlando, L. et al. True single-molecule DNA sequencing of a pleistocene horse bone. Genome Res. 21, 1705–1719 (2011). · DOI
  17. Adler, C. J., Haak, W., Donlon, D. & Cooper, A. Survival and recovery of DNA from ancient teeth and bones. J. Archaeol. Sci. 38, 956–964 (2011). · DOI
  18. Higgins, D. & Austin, J. J. Teeth as a source of DNA for forensic identification of human remains: a review. Sci. Justice 53, 433–441 (2013). · DOI
  19. Higgins, D., Kaidonis, J., Townsend, G., Hughes, T. & Austin, J. J. Targeted sampling of cementum for recovery of nuclear DNA from human teeth and the impact of common decontamination measures. Investig. Genet. 4, 18 (2013). · DOI
  20. Trivedi, R., Chattopadhyay, P. & Kashyap, V. K. A new improved method for extraction of DNA from teeth for the analysis of hypervariable loci. Am. J. Forensic Med. Pathol. 23, 191–196 (2002). · DOI
  21. Gilbert, M. T. P., Bandelt, H.-J., Hofreiter, M. & Barnes, I. Assessing ancient DNA studies. Trends Ecol. Evol. 20, 541–544 (2005). · DOI · Paper page
  22. Willerslev, E. & Cooper, A. Review paper. ancient dna. Proc. R. Soc. B Biol. Sci. 272, 3–16 (2005). · DOI · Paper page
  23. Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl. Acad. Sci. 104, 14616–14621 (2007). · DOI · Paper page
  24. Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 6, (2010). · DOI
  25. Lindgreen, S. AdapterRemoval: easy cleaning of next-generation sequencing reads. BMC Res. Notes 5, 337 (2012).
  26. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009). · DOI · Paper page
  27. Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009). · DOI · Paper page
  28. Deagle, B. E., Eveson, J. P. & Jarman, S. N. Quantification of damage in DNA recovered from highly degraded samples–a case study on DNA in faeces. Front. Zool. 3, 11 (2006). · DOI
  29. Allentoft, M. E. et al. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc. R. Soc. B Biol. Sci. 279, 4724–4733 (2012). · DOI · Paper page
  30. Maricic, T., Whitten, M. & Pääbo, S. Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PloS One 5, DOI: 10.1371/journal.pone.0014004 (2010). · DOI
  31. Gansauge, M.-T. & Meyer, M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc. 8, 737–748 (2013). · DOI · Paper page
  32. Gansauge, M.-T. & Meyer, M. Selective enrichment of damaged DNA molecules for ancient genome sequencing. Genome Res. 24, 1543–1549 (2014). · DOI · Paper page

Cited by

Sorted by citations

Metadata

Authors
Damgaard, P. B., Margaryan, A., Schroeder, H., Orlando, L., Willerslev, E., & Allentoft, M. E.
Venue
Scientific Reports
Publisher
Springer Science and Business Media LLC
Published
2015-06-17
Volume
5
Issue
1
ISSN
2045-2322
DOI
10.1038/srep11184
PMC
PMC4472031
Cited by
276
References
16
Language
en
Licence

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review