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

Kirsten A. Ziesemer, Jazmín Ramos-Madrigal, Allison E. Mann, Bernd W. Brandt, Krithivasan Sankaranarayanan, Andrew T. Ozga, Menno Hoogland, Courtney A. Hofman, Domingo C. Salazar-García, Bruno Frohlich, George R. Milner, Anne C. Stone, Mark Aldenderfer, Cecil M. Lewis, Corinne L. Hofman, Christina Warinner, Hannes Schroeder

Research output: Contribution to journalArticle

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 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.

Original languageEnglish (US)
Pages (from-to)496-509
Number of pages14
JournalAmerican Journal of Physical Anthropology
Volume168
Issue number3
DOIs
StatePublished - Mar 2019

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Dental Calculus
Human Genome
Dentin
Calculi
DNA
reconstruction
Dental Libraries
Libraries
efficiency
Genome
Mitochondrial Genome
Microbiota

All Science Journal Classification (ASJC) codes

  • Anatomy
  • Anthropology

Cite this

Ziesemer, K. A., Ramos-Madrigal, J., Mann, A. E., Brandt, B. W., Sankaranarayanan, K., Ozga, A. T., ... Schroeder, H. (2019). The efficacy of whole human genome capture on ancient dental calculus and dentin. American Journal of Physical Anthropology, 168(3), 496-509. https://doi.org/10.1002/ajpa.23763
Ziesemer, Kirsten A. ; Ramos-Madrigal, Jazmín ; Mann, Allison E. ; Brandt, Bernd W. ; Sankaranarayanan, Krithivasan ; Ozga, Andrew T. ; Hoogland, Menno ; Hofman, Courtney A. ; Salazar-García, Domingo C. ; Frohlich, Bruno ; Milner, George R. ; Stone, Anne C. ; Aldenderfer, Mark ; Lewis, Cecil M. ; Hofman, Corinne L. ; Warinner, Christina ; Schroeder, Hannes. / The efficacy of whole human genome capture on ancient dental calculus and dentin. In: American Journal of Physical Anthropology. 2019 ; Vol. 168, No. 3. pp. 496-509.
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Ziesemer, KA, Ramos-Madrigal, J, Mann, AE, Brandt, BW, Sankaranarayanan, K, Ozga, AT, Hoogland, M, Hofman, CA, Salazar-García, DC, Frohlich, B, Milner, GR, Stone, AC, Aldenderfer, M, Lewis, CM, Hofman, CL, Warinner, C & Schroeder, H 2019, 'The efficacy of whole human genome capture on ancient dental calculus and dentin', American Journal of Physical Anthropology, vol. 168, no. 3, pp. 496-509. https://doi.org/10.1002/ajpa.23763

The efficacy of whole human genome capture on ancient dental calculus and dentin. / Ziesemer, Kirsten A.; Ramos-Madrigal, Jazmín; Mann, Allison E.; Brandt, Bernd W.; Sankaranarayanan, Krithivasan; Ozga, Andrew T.; Hoogland, Menno; Hofman, Courtney A.; Salazar-García, Domingo C.; Frohlich, Bruno; Milner, George R.; Stone, Anne C.; Aldenderfer, Mark; Lewis, Cecil M.; Hofman, Corinne L.; Warinner, Christina; Schroeder, Hannes.

In: American Journal of Physical Anthropology, Vol. 168, No. 3, 03.2019, p. 496-509.

Research output: Contribution to journalArticle

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AU - Brandt, Bernd W.

AU - Sankaranarayanan, Krithivasan

AU - Ozga, Andrew T.

AU - Hoogland, Menno

AU - Hofman, Courtney A.

AU - Salazar-García, Domingo C.

AU - Frohlich, Bruno

AU - Milner, George R.

AU - Stone, Anne C.

AU - Aldenderfer, Mark

AU - Lewis, Cecil M.

AU - Hofman, Corinne L.

AU - Warinner, Christina

AU - Schroeder, Hannes

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N2 - 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.

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Ziesemer KA, Ramos-Madrigal J, Mann AE, Brandt BW, Sankaranarayanan K, Ozga AT et al. The efficacy of whole human genome capture on ancient dental calculus and dentin. American Journal of Physical Anthropology. 2019 Mar;168(3):496-509. https://doi.org/10.1002/ajpa.23763