Ligation bias in Illumina next-generation DNA libraries: implications for sequencing ancient genomes

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Ligation bias in Illumina next-generation DNA libraries : implications for sequencing ancient genomes. / Seguin-Orlando, Andaine; Schubert, Mikkel; Clary, Joel; Stagegaard, Julia; Alberdi, Maria T.; Prado, José Luis; Prieto, Alfredo; Willerslev, Eske; Orlando, Ludovic Antoine Alexandre.

I: PLoS ONE, Bind 8, Nr. 10, e78575, 29.10.2013.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

Harvard

Seguin-Orlando, A, Schubert, M, Clary, J, Stagegaard, J, Alberdi, MT, Prado, JL, Prieto, A, Willerslev, E & Orlando, LAA 2013, 'Ligation bias in Illumina next-generation DNA libraries: implications for sequencing ancient genomes', PLoS ONE, bind 8, nr. 10, e78575. https://doi.org/10.1371/journal.pone.0078575

APA

Seguin-Orlando, A., Schubert, M., Clary, J., Stagegaard, J., Alberdi, M. T., Prado, J. L., ... Orlando, L. A. A. (2013). Ligation bias in Illumina next-generation DNA libraries: implications for sequencing ancient genomes. PLoS ONE, 8(10), [e78575]. https://doi.org/10.1371/journal.pone.0078575

Vancouver

Seguin-Orlando A, Schubert M, Clary J, Stagegaard J, Alberdi MT, Prado JL o.a. Ligation bias in Illumina next-generation DNA libraries: implications for sequencing ancient genomes. PLoS ONE. 2013 okt 29;8(10). e78575. https://doi.org/10.1371/journal.pone.0078575

Author

Seguin-Orlando, Andaine ; Schubert, Mikkel ; Clary, Joel ; Stagegaard, Julia ; Alberdi, Maria T. ; Prado, José Luis ; Prieto, Alfredo ; Willerslev, Eske ; Orlando, Ludovic Antoine Alexandre. / Ligation bias in Illumina next-generation DNA libraries : implications for sequencing ancient genomes. I: PLoS ONE. 2013 ; Bind 8, Nr. 10.

Bibtex

@article{89fb70f752aa400dbfeb1fa4a97ae43b,
title = "Ligation bias in Illumina next-generation DNA libraries: implications for sequencing ancient genomes",
abstract = "Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate that library preparation based on adapter ligation at AT-overhangs are biased against DNA templates starting with thymine residues, contrarily to blunt-end adapter ligation. We observe the same bias on fresh DNA extracts sheared on Bioruptor, Covaris and nebulizers. This contradicts previous reports suggesting that this bias could originate from the methods used for shearing DNA. This also suggests that AT-overhang adapter ligation efficiency is affected in a sequence-dependent manner and results in an uneven representation of different genomic contexts. We then show how this bias could affect the base composition of ancient DNA libraries prepared following AT-overhang ligation, mainly by limiting the ability to ligate DNA templates starting with thymines and therefore deaminated cytosines. This results in particular nucleotide misincorporation damage patterns, deviating from the signature generally expected for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.",
author = "Andaine Seguin-Orlando and Mikkel Schubert and Joel Clary and Julia Stagegaard and Alberdi, {Maria T.} and Prado, {Jos{\'e} Luis} and Alfredo Prieto and Eske Willerslev and Orlando, {Ludovic Antoine Alexandre}",
year = "2013",
month = "10",
day = "29",
doi = "10.1371/journal.pone.0078575",
language = "English",
volume = "8",
journal = "P L o S One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "10",

}

RIS

TY - JOUR

T1 - Ligation bias in Illumina next-generation DNA libraries

T2 - implications for sequencing ancient genomes

AU - Seguin-Orlando, Andaine

AU - Schubert, Mikkel

AU - Clary, Joel

AU - Stagegaard, Julia

AU - Alberdi, Maria T.

AU - Prado, José Luis

AU - Prieto, Alfredo

AU - Willerslev, Eske

AU - Orlando, Ludovic Antoine Alexandre

PY - 2013/10/29

Y1 - 2013/10/29

N2 - Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate that library preparation based on adapter ligation at AT-overhangs are biased against DNA templates starting with thymine residues, contrarily to blunt-end adapter ligation. We observe the same bias on fresh DNA extracts sheared on Bioruptor, Covaris and nebulizers. This contradicts previous reports suggesting that this bias could originate from the methods used for shearing DNA. This also suggests that AT-overhang adapter ligation efficiency is affected in a sequence-dependent manner and results in an uneven representation of different genomic contexts. We then show how this bias could affect the base composition of ancient DNA libraries prepared following AT-overhang ligation, mainly by limiting the ability to ligate DNA templates starting with thymines and therefore deaminated cytosines. This results in particular nucleotide misincorporation damage patterns, deviating from the signature generally expected for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.

AB - Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate that library preparation based on adapter ligation at AT-overhangs are biased against DNA templates starting with thymine residues, contrarily to blunt-end adapter ligation. We observe the same bias on fresh DNA extracts sheared on Bioruptor, Covaris and nebulizers. This contradicts previous reports suggesting that this bias could originate from the methods used for shearing DNA. This also suggests that AT-overhang adapter ligation efficiency is affected in a sequence-dependent manner and results in an uneven representation of different genomic contexts. We then show how this bias could affect the base composition of ancient DNA libraries prepared following AT-overhang ligation, mainly by limiting the ability to ligate DNA templates starting with thymines and therefore deaminated cytosines. This results in particular nucleotide misincorporation damage patterns, deviating from the signature generally expected for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.

U2 - 10.1371/journal.pone.0078575

DO - 10.1371/journal.pone.0078575

M3 - Journal article

VL - 8

JO - P L o S One

JF - P L o S One

SN - 1932-6203

IS - 10

M1 - e78575

ER -

ID: 65450044