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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
medicine
The efficacy of whole human genome capture on ancient dental calculus and dentin
American Journal of Physical Anthropology, Volume 168, No. 3, Year 2019
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Description
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 four-fold 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. © 2018 The Authors. American Journal of Physical Anthropology published by Wiley Periodicals, Inc.
Authors & Co-Authors
Ziesemer, Kirsten A.
Netherlands, Leiden
Universiteit Leiden
Ramos-Madrigal, Jazmín
Denmark, Copenhagen
Københavns Universitet
Mann, Allison E.
United States, Norman
The University of Oklahoma
Brandt, Bernd Willem
Netherlands, Amsterdam
Academisch Centrum Tandheelkunde Amsterdam
Sankaranarayanan, Krithivasan
United States, Norman
The University of Oklahoma
Ozga, Andrew T.
United States, Tempe
Arizona State University
Hoogland, Menno L.P.
Netherlands, Leiden
Universiteit Leiden
Hofman, Courtney A.
United States, Norman
The University of Oklahoma
Salazar-García, Domingo C.
Germany, Jena
Max-planck-institut Für Menschheitsgeschichte
Spain, Bilbao
Ikerbasque, Basque Foundation for Science
Frohlich, Bruno
Unknown Affiliation
Stone, Anne C.
United States, Tempe
Arizona State University
Aldenderfer, Mark Steven
United States, Merced
Uc Merced
Lewis, Cecil M.
United States, Norman
The University of Oklahoma
Hofman, Corinne L.
Netherlands, Leiden
Universiteit Leiden
Warinner, Christina G.
United States, Norman
The University of Oklahoma
Germany, Jena
Max-planck-institut Für Menschheitsgeschichte
Schroeder, Hannes
Netherlands, Leiden
Universiteit Leiden
Denmark, Copenhagen
Københavns Universitet
Statistics
Citations: 20
Authors: 16
Affiliations: 9
Identifiers
Doi:
10.1002/ajpa.23763
ISSN:
00029483
Research Areas
Genetics And Genomics
Health System And Policy