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

María C. Ávila-Arcos; Enrico Cappellini; J. Alberto Romero-Navarro; Nathan Wales; J. Víctor Moreno-Mayar; Morten Rasmussen; Sarah L. Fordyce; Rafael Montiel; Jean Philippe Vielle-Calzada; Eske Willerslev; M. Thomas P. Gilbert

doi:10.1038/srep00074

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

María C. Ávila-Arcos, Enrico Cappellini, J. Alberto Romero-Navarro, Nathan Wales, J. Víctor Moreno-Mayar, Morten Rasmussen, Sarah L. Fordyce, Rafael Montiel, Jean Philippe Vielle-Calzada, Eske Willerslev, M. Thomas P. Gilbert^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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
DOIs	https://doi.org/10.1038/srep00074
Publication status	Published - 2011

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Ávila-Arcos, M. 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, M. T. P. (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 - Wales, Nathan

AU - Moreno-Mayar, J. Víctor

AU - Rasmussen, Morten

AU - Fordyce, Sarah L.

AU - Montiel, Rafael

AU - Vielle-Calzada, Jean Philippe

AU - Willerslev, Eske

AU - Gilbert, M. Thomas P.

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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.

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

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