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

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Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA. / Ávila-Arcos, María C.; Cappellini, Enrico; Romero-Navarro, J. Alberto; Wales, Nathan; Moreno-Mayar, J. Víctor; Rasmussen, Morten; Fordyce, Sarah L.; Montiel, Rafael; Vielle-Calzada, Jean Philippe; Willerslev, Eske; Gilbert, M. Thomas P.

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

Research output: Contribution to journalArticlepeer-review

Harvard

Ávila-Arcos, MC, Cappellini, E, Romero-Navarro, JA, Wales, N, Moreno-Mayar, JV, Rasmussen, M, Fordyce, SL, Montiel, R, Vielle-Calzada, JP, Willerslev, E & Gilbert, MTP 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

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

Vancouver

Ávila-Arcos MC, 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

Ávila-Arcos, María C. ; Cappellini, Enrico ; Romero-Navarro, J. Alberto ; Wales, Nathan ; Moreno-Mayar, J. Víctor ; Rasmussen, Morten ; Fordyce, Sarah L. ; Montiel, Rafael ; Vielle-Calzada, Jean Philippe ; Willerslev, Eske ; Gilbert, M. Thomas P. / Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA. In: Scientific Reports. 2011 ; Vol. 1.

Bibtex - Download

@article{a62cc27dccdb494ab3feec212a1fb4dc,
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 = "{\'A}vila-Arcos, {Mar{\'i}a C.} and Enrico Cappellini and Romero-Navarro, {J. Alberto} and Nathan Wales and Moreno-Mayar, {J. V{\'i}ctor} and Morten Rasmussen and Fordyce, {Sarah L.} and Rafael Montiel and Vielle-Calzada, {Jean Philippe} and Eske Willerslev and Gilbert, {M. Thomas P.}",
year = "2011",
doi = "10.1038/srep00074",
language = "English",
volume = "1",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Springer Nature ",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

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

AU - Ávila-Arcos, María C.

AU - Cappellini, Enrico

AU - Romero-Navarro, J. Alberto

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.

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.

UR - http://www.scopus.com/inward/record.url?scp=84859608437&partnerID=8YFLogxK

U2 - 10.1038/srep00074

DO - 10.1038/srep00074

M3 - Article

C2 - 22355593

AN - SCOPUS:84859608437

VL - 1

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

M1 - 74

ER -