Combining bleach and mild predigestion improves ancient DNA recovery from bones

Sanne Boessenkool; Kristian Ebbesen Hanghøj; Heidi M. Nistelberger; Clio Der Sarkissian; Agata T. Gondek; Ludovic Antoine Alexandre Orlando; James H. Barrett; Bastiaan Star

doi:10.1111/1755-0998.12623

Combining bleach and mild predigestion improves ancient DNA recovery from bones

Sanne Boessenkool, Kristian Ebbesen Hanghøj, Heidi M. Nistelberger, Clio Der Sarkissian, Agata T. Gondek, Ludovic Antoine Alexandre Orlando, James H. Barrett, Bastiaan Star

34 Citations (Scopus)

Abstract

The feasibility of genome-scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA. In the majority of cases, this represents a few per cent of the DNA extract, at most. A number of specific pre-extraction protocols for bone powder aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal. years before present. Using high-throughput sequencing, we show that combined together, bleach wash and predigestion consistently yield DNA libraries with higher endogenous content than either of these methods alone. Additionally, the molecular complexity of these libraries is improved and endogenous DNA templates show larger size distributions. Other library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre-extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains and will reduce the cost of whole-genome sequencing.

Original language	English
Journal	Molecular Ecology Resources
Volume	17
Issue number	4
Pages (from-to)	742–751
Number of pages	10
ISSN	1755-098X
DOIs	https://doi.org/10.1111/1755-0998.12623
Publication status	Published - Jul 2017

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title = "Combining bleach and mild predigestion improves ancient DNA recovery from bones",

abstract = "The feasibility of genome-scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA. In the majority of cases, this represents a few per cent of the DNA extract, at most. A number of specific pre-extraction protocols for bone powder aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal. years before present. Using high-throughput sequencing, we show that combined together, bleach wash and predigestion consistently yield DNA libraries with higher endogenous content than either of these methods alone. Additionally, the molecular complexity of these libraries is improved and endogenous DNA templates show larger size distributions. Other library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre-extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains and will reduce the cost of whole-genome sequencing.",

author = "Sanne Boessenkool and Hangh{\o}j, {Kristian Ebbesen} and Nistelberger, {Heidi M.} and {Der Sarkissian}, Clio and Gondek, {Agata T.} and Orlando, {Ludovic Antoine Alexandre} and Barrett, {James H.} and Bastiaan Star",

note = "{\textcopyright} 2016 John Wiley & Sons Ltd.",

year = "2017",

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doi = "10.1111/1755-0998.12623",

language = "English",

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AU - Boessenkool, Sanne

AU - Hanghøj, Kristian Ebbesen

AU - Nistelberger, Heidi M.

AU - Der Sarkissian, Clio

AU - Gondek, Agata T.

AU - Orlando, Ludovic Antoine Alexandre

AU - Barrett, James H.

AU - Star, Bastiaan

PY - 2017/7

Y1 - 2017/7

N2 - The feasibility of genome-scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA. In the majority of cases, this represents a few per cent of the DNA extract, at most. A number of specific pre-extraction protocols for bone powder aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal. years before present. Using high-throughput sequencing, we show that combined together, bleach wash and predigestion consistently yield DNA libraries with higher endogenous content than either of these methods alone. Additionally, the molecular complexity of these libraries is improved and endogenous DNA templates show larger size distributions. Other library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre-extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains and will reduce the cost of whole-genome sequencing.

AB - The feasibility of genome-scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA. In the majority of cases, this represents a few per cent of the DNA extract, at most. A number of specific pre-extraction protocols for bone powder aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal. years before present. Using high-throughput sequencing, we show that combined together, bleach wash and predigestion consistently yield DNA libraries with higher endogenous content than either of these methods alone. Additionally, the molecular complexity of these libraries is improved and endogenous DNA templates show larger size distributions. Other library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre-extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains and will reduce the cost of whole-genome sequencing.

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DO - 10.1111/1755-0998.12623

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SN - 1755-098X

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EP - 751

JO - Molecular Ecology Resources

JF - Molecular Ecology Resources

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ER -

Combining bleach and mild predigestion improves ancient DNA recovery from bones

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