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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA. / Avila Arcos, Maria del Carmen; Cappellini, Enrico; Romero-Navarro, J. Alberto; Wales, Nathan; Moreno Mayar, José Victor; Rasmussen, Morten; Fordyce, Sarah Louise; Montiel, Rafael; Vielle-Calzada, Jean-Philippe; Willerslev, Eske; Gilbert, Tom.

In: Scientific Reports, Vol. 1, 74, 2011.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Avila Arcos, MDC, Cappellini, E, Romero-Navarro, JA, Wales, N, Moreno Mayar, JV, Rasmussen, M, Fordyce, SL, 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, vol. 1, 74. https://doi.org/10.1038/srep00074

APA

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, [74]. https://doi.org/10.1038/srep00074

Vancouver

Avila Arcos MDC, Cappellini E, Romero-Navarro JA, Wales N, Moreno Mayar JV, Rasmussen M et al. Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA. Scientific Reports. 2011;1. 74. https://doi.org/10.1038/srep00074

Author

Avila Arcos, Maria del Carmen ; Cappellini, Enrico ; Romero-Navarro, J. Alberto ; Wales, Nathan ; Moreno Mayar, José Victor ; Rasmussen, Morten ; Fordyce, Sarah Louise ; Montiel, Rafael ; Vielle-Calzada, Jean-Philippe ; Willerslev, Eske ; Gilbert, Tom. / Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA. In: Scientific Reports. 2011 ; Vol. 1.

Bibtex

@article{df36039ff70d46848364edd372f5ef4d,
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.",
author = "{Avila Arcos}, {Maria del Carmen} and Enrico Cappellini and Romero-Navarro, {J. Alberto} and Nathan Wales and {Moreno Mayar}, {Jos{\'e} Victor} and Morten Rasmussen and Fordyce, {Sarah Louise} and Rafael Montiel and Jean-Philippe Vielle-Calzada and Eske Willerslev and Tom Gilbert",
year = "2011",
doi = "10.1038/srep00074",
language = "English",
volume = "1",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "nature publishing group",

}

RIS

TY - JOUR

T1 - Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

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

DO - 10.1038/srep00074

M3 - Journal article

C2 - 22355593

VL - 1

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

M1 - 74

ER -

ID: 46089600