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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

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.citation	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.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.subject	Prehistòria
dc.title	The efficacy of whole human genome capture on ancient dental calculus and dentin
dc.type	journal article	es_ES
dc.date.updated	2019-02-27T11:07:48Z
dc.identifier.idgrec	130225
dc.rights.accessRights	open access	es_ES