Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA

Johanna L. A. Paijmans; Gloria González Fortes; Daniel W. Förster

doi:10.1007/978-1-4939-9176-1_14

Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA

Johanna L. A. Paijmans, Gloria González Fortes, Daniel W. Förster

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Abstract

Genetic studies that include ancient samples are often hampered by the low amount of endogenous DNA that ancient samples often contain, relative to co-extracted “contaminant” DNA from other organisms. One approach to mitigate this challenge is to perform hybridization-based capture of target genomic regions using DNA or RNA baits. Such baits are designed to have high sequence similarity to the target genomic regions and can reduce the off-target fraction in DNA sequencing libraries. Here, we present a protocol to use Agilent SureSelect microarrays to enrich ancient DNA libraries for small-to-medium-sized target loci, such as mitochondrial genomes, from ancient DNA extracts. The protocol that we present builds on previously published work by introducing improvements that improve recovery of short DNA fragments while minimizing the cost and duration of the experiment.

Original language	English
Title of host publication	Ancient DNA
Editors	Beth Shapiro, Axel Barlow, Peter D. Heintzman, Michael Hofreiter, Johanna L. A. Paijmans, André E. R. Soares
Place of Publication	New York, NY
Publisher	Springer New York
Pages	129-139
Number of pages	11
Volume	1963
ISBN (Print)	978-1-4939-9175-4 978-1-4939-9176-1
DOIs	https://doi.org/10.1007/978-1-4939-9176-1_14
Publication status	Published - 16 Mar 2019
Externally published	Yes

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Paijmans, J. L. A., González Fortes, G., & Förster, D. W. (2019). Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA. In B. Shapiro, A. Barlow, P. D. Heintzman, M. Hofreiter, J. L. A. Paijmans, & A. E. R. Soares (Eds.), Ancient DNA (Vol. 1963, pp. 129-139). Springer New York. https://doi.org/10.1007/978-1-4939-9176-1_14

Paijmans, Johanna L. A. ; González Fortes, Gloria ; Förster, Daniel W. / Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA. Ancient DNA. editor / Beth Shapiro ; Axel Barlow ; Peter D. Heintzman ; Michael Hofreiter ; Johanna L. A. Paijmans ; André E. R. Soares. Vol. 1963 New York, NY : Springer New York, 2019. pp. 129-139

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abstract = "Genetic studies that include ancient samples are often hampered by the low amount of endogenous DNA that ancient samples often contain, relative to co-extracted “contaminant” DNA from other organisms. One approach to mitigate this challenge is to perform hybridization-based capture of target genomic regions using DNA or RNA baits. Such baits are designed to have high sequence similarity to the target genomic regions and can reduce the off-target fraction in DNA sequencing libraries. Here, we present a protocol to use Agilent SureSelect microarrays to enrich ancient DNA libraries for small-to-medium-sized target loci, such as mitochondrial genomes, from ancient DNA extracts. The protocol that we present builds on previously published work by introducing improvements that improve recovery of short DNA fragments while minimizing the cost and duration of the experiment.",

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Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA. / Paijmans, Johanna L. A.; González Fortes, Gloria; Förster, Daniel W.
Ancient DNA. ed. / Beth Shapiro; Axel Barlow; Peter D. Heintzman; Michael Hofreiter; Johanna L. A. Paijmans; André E. R. Soares. Vol. 1963 New York, NY: Springer New York, 2019. p. 129-139.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

TY - CHAP

T1 - Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA

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AU - González Fortes, Gloria

AU - Förster, Daniel W.

PY - 2019/3/16

Y1 - 2019/3/16

N2 - Genetic studies that include ancient samples are often hampered by the low amount of endogenous DNA that ancient samples often contain, relative to co-extracted “contaminant” DNA from other organisms. One approach to mitigate this challenge is to perform hybridization-based capture of target genomic regions using DNA or RNA baits. Such baits are designed to have high sequence similarity to the target genomic regions and can reduce the off-target fraction in DNA sequencing libraries. Here, we present a protocol to use Agilent SureSelect microarrays to enrich ancient DNA libraries for small-to-medium-sized target loci, such as mitochondrial genomes, from ancient DNA extracts. The protocol that we present builds on previously published work by introducing improvements that improve recovery of short DNA fragments while minimizing the cost and duration of the experiment.

AB - Genetic studies that include ancient samples are often hampered by the low amount of endogenous DNA that ancient samples often contain, relative to co-extracted “contaminant” DNA from other organisms. One approach to mitigate this challenge is to perform hybridization-based capture of target genomic regions using DNA or RNA baits. Such baits are designed to have high sequence similarity to the target genomic regions and can reduce the off-target fraction in DNA sequencing libraries. Here, we present a protocol to use Agilent SureSelect microarrays to enrich ancient DNA libraries for small-to-medium-sized target loci, such as mitochondrial genomes, from ancient DNA extracts. The protocol that we present builds on previously published work by introducing improvements that improve recovery of short DNA fragments while minimizing the cost and duration of the experiment.

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DO - 10.1007/978-1-4939-9176-1_14

M3 - Chapter

SN - 978-1-4939-9175-4 978-1-4939-9176-1

VL - 1963

SP - 129

EP - 139

BT - Ancient DNA

A2 - Shapiro, Beth

A2 - Barlow, Axel

A2 - Heintzman, Peter D.

A2 - Hofreiter, Michael

A2 - Paijmans, Johanna L. A.

A2 - Soares, André E. R.

PB - Springer New York

CY - New York, NY

ER -

Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA

Abstract

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