The efficacy of whole human genome capture on ancient dental calculus and dentin
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The efficacy of whole human genome capture on ancient dental calculus and dentin

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The efficacy of whole human genome capture on ancient dental calculus and dentin

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dc.contributor.author Ziesemer, Kirsten A.
dc.contributor.author Ramos-Madrigal, azmín
dc.contributor.author Mann, Allison E.
dc.contributor.author Brandt, Bernd W.
dc.contributor.author Sankaranarayanan, Krithivasan
dc.contributor.author Ozga, Andrew T.
dc.contributor.author Hoogland, Menno
dc.contributor.author Salazar García, Domingo Carlos
dc.contributor.author Frohlich, Bruno
dc.contributor.author Milner, George R.
dc.contributor.author Stone, Anne C.
dc.contributor.author Aldenderfer, Mark
dc.contributor.author Lewis, Cecil M.
dc.contributor.author Hofman, Corinne
dc.contributor.author Warinner, Christina
dc.contributor.author Schroeder, Hannes
dc.contributor.author Hofman, Courtney A.
dc.date.accessioned 2019-02-27T11:07:48Z
dc.date.available 2019-02-27T11:07:48Z
dc.date.issued 2019
dc.identifier.uri http://hdl.handle.net/10550/69204
dc.description.abstract Objectives: Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques. Materials and methods: Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in-solution hybridization capture and high-throughput sequencing. Results: Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to fourfold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on-target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum-level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off-target sequences in human genome-enriched calculus libraries may still be useful for oral microbiome reconstruction. Discussion: While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples.
dc.language.iso eng
dc.relation.ispartof American Journal of Physical Anthropology, 2019, vol. 168, p. 496-509
dc.rights.uri info:eu-repo/semantics/openAccess
dc.source Ziesemer, Kirsten A. Ramos-Madrigal, azmín Mann, Allison E. Brandt, Bernd W. Sankaranarayanan, Krithivasan Ozga, Andrew T. Hoogland, Menno Salazar García, Domingo Carlos Frohlich, Bruno Milner, George R. Stone, Anne C. Aldenderfer, Mark Lewis, Cecil M. Hofman, Corinne Warinner, Christina Schroeder, Hannes Hofman, Courtney A. 2019 The efficacy of whole human genome capture on ancient dental calculus and dentin American Journal of Physical Anthropology 168 496 509
dc.subject Prehistòria
dc.title The efficacy of whole human genome capture on ancient dental calculus and dentin
dc.type info:eu-repo/semantics/article
dc.date.updated 2019-02-27T11:07:48Z
dc.identifier.idgrec 130225

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