Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

Maria del Carmen Avila Arcos; Enrico Cappellini; J. Alberto Romero-Navarro; Nathan Wales; José Victor Moreno Mayar; Morten Rasmussen; Sarah Louise Fordyce; Rafael Montiel; Jean-Philippe Vielle-Calzada; Eske Willerslev; Tom Gilbert

doi:10.1038/srep00074

Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

Maria del Carmen Avila Arcos, Enrico Cappellini, J. Alberto Romero-Navarro, Nathan Wales, José Victor Moreno Mayar, Morten Rasmussen, Sarah Louise Fordyce, Rafael Montiel, Jean-Philippe Vielle-Calzada, Eske Willerslev, Tom Gilbert

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Abstract

The development of second-generation sequencing technologies has greatly benefitted the field of ancient DNA (aDNA). Its application can be further exploited by the use of targeted capture-enrichment methods to overcome restrictions posed by low endogenous and contaminating DNA in ancient samples. We tested the performance of Agilent's SureSelect and Mycroarray's MySelect in-solution capture systems on Illumina sequencing libraries built from ancient maize to identify key factors influencing aDNA capture experiments. High levels of clonality as well as the presence of multiple-copy sequences in the capture targets led to biases in the data regardless of the capture method. Neither method consistently outperformed the other in terms of average target enrichment, and no obvious difference was observed either when two tiling designs were compared. In addition to demonstrating the plausibility of capturing aDNA from ancient plant material, our results also enable us to provide useful recommendations for those planning targeted-sequencing on aDNA.

Original language	English
Article number	74
Journal	Scientific Reports
Volume	1
Number of pages	5
ISSN	2045-2322
DOIs	https://doi.org/10.1038/srep00074
Publication status	Published - 2011

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Avila Arcos, M. D. C., Cappellini, E., Romero-Navarro, J. A., Wales, N., Moreno Mayar, J. V., Rasmussen, M., Fordyce, S. L., Montiel, R., Vielle-Calzada, J.-P., Willerslev, E., & Gilbert, T. (2011). Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA. Scientific Reports, 1, Article 74. https://doi.org/10.1038/srep00074

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title = "Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA",

abstract = "The development of second-generation sequencing technologies has greatly benefitted the field of ancient DNA (aDNA). Its application can be further exploited by the use of targeted capture-enrichment methods to overcome restrictions posed by low endogenous and contaminating DNA in ancient samples. We tested the performance of Agilent's SureSelect and Mycroarray's MySelect in-solution capture systems on Illumina sequencing libraries built from ancient maize to identify key factors influencing aDNA capture experiments. High levels of clonality as well as the presence of multiple-copy sequences in the capture targets led to biases in the data regardless of the capture method. Neither method consistently outperformed the other in terms of average target enrichment, and no obvious difference was observed either when two tiling designs were compared. In addition to demonstrating the plausibility of capturing aDNA from ancient plant material, our results also enable us to provide useful recommendations for those planning targeted-sequencing on aDNA.",

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AU - Avila Arcos, Maria del Carmen

AU - Cappellini, Enrico

AU - Romero-Navarro, J. Alberto

AU - Wales, Nathan

AU - Moreno Mayar, José Victor

AU - Rasmussen, Morten

AU - Fordyce, Sarah Louise

AU - Montiel, Rafael

AU - Vielle-Calzada, Jean-Philippe

AU - Willerslev, Eske

AU - Gilbert, Tom

PY - 2011

Y1 - 2011

N2 - The development of second-generation sequencing technologies has greatly benefitted the field of ancient DNA (aDNA). Its application can be further exploited by the use of targeted capture-enrichment methods to overcome restrictions posed by low endogenous and contaminating DNA in ancient samples. We tested the performance of Agilent's SureSelect and Mycroarray's MySelect in-solution capture systems on Illumina sequencing libraries built from ancient maize to identify key factors influencing aDNA capture experiments. High levels of clonality as well as the presence of multiple-copy sequences in the capture targets led to biases in the data regardless of the capture method. Neither method consistently outperformed the other in terms of average target enrichment, and no obvious difference was observed either when two tiling designs were compared. In addition to demonstrating the plausibility of capturing aDNA from ancient plant material, our results also enable us to provide useful recommendations for those planning targeted-sequencing on aDNA.

AB - The development of second-generation sequencing technologies has greatly benefitted the field of ancient DNA (aDNA). Its application can be further exploited by the use of targeted capture-enrichment methods to overcome restrictions posed by low endogenous and contaminating DNA in ancient samples. We tested the performance of Agilent's SureSelect and Mycroarray's MySelect in-solution capture systems on Illumina sequencing libraries built from ancient maize to identify key factors influencing aDNA capture experiments. High levels of clonality as well as the presence of multiple-copy sequences in the capture targets led to biases in the data regardless of the capture method. Neither method consistently outperformed the other in terms of average target enrichment, and no obvious difference was observed either when two tiling designs were compared. In addition to demonstrating the plausibility of capturing aDNA from ancient plant material, our results also enable us to provide useful recommendations for those planning targeted-sequencing on aDNA.

U2 - 10.1038/srep00074

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JO - Scientific Reports

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ER -

Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

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