Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing

Cristina Gamba; Kristian Ebbesen Hanghøj; Charleen Gaunitz; Ahmed H. Alfarhan; Saleh A. Alquraishi; Khaled A. S. Al-Rasheid; Daniel G. Bradley; Ludovic Antoine Alexandre Orlando

doi:10.1111/1755-0998.12470

Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing

Cristina Gamba, Kristian Ebbesen Hanghøj, Charleen Gaunitz, Ahmed H. Alfarhan, Saleh A. Alquraishi, Khaled A. S. Al-Rasheid, Daniel G. Bradley, Ludovic Antoine Alexandre Orlando^*

^*Corresponding author af dette arbejde

81 Citationer (Scopus)

Abstract

The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs of high-throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning a ~30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules retrieved but also the relative importance of endogenous DNA fragments and their molecular diversity. Therefore, these methods provide a cost-effective solution for downstream applications, including DNA sequencing on HTS platforms.

Originalsprog	Engelsk
Tidsskrift	Molecular Ecology Resources
Vol/bind	16
Udgave nummer	2
Sider (fra-til)	459-469
Antal sider	11
ISSN	1755-098X
DOI	https://doi.org/10.1111/1755-0998.12470
Status	Udgivet - 1 mar. 2016

Adgang til dokumentet

10.1111/1755-0998.12470

Citationsformater

@article{1eed721912b34196b9ba58fa4e01568a,

title = "Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing",

abstract = "The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs of high-throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning a ~30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules retrieved but also the relative importance of endogenous DNA fragments and their molecular diversity. Therefore, these methods provide a cost-effective solution for downstream applications, including DNA sequencing on HTS platforms.",

keywords = "Ancient DNA, DNA extraction, Palaeogenomics, Ultrashort fragments",

author = "Cristina Gamba and Hangh{\o}j, {Kristian Ebbesen} and Charleen Gaunitz and Alfarhan, {Ahmed H.} and Alquraishi, {Saleh A.} and Al-Rasheid, {Khaled A. S.} and Bradley, {Daniel G.} and Orlando, {Ludovic Antoine Alexandre}",

year = "2016",

month = mar,

day = "1",

doi = "10.1111/1755-0998.12470",

language = "English",

volume = "16",

pages = "459--469",

journal = "Molecular Ecology Resources",

issn = "1755-098X",

publisher = "Wiley-Blackwell",

number = "2",

}

TY - JOUR

T1 - Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing

AU - Gamba, Cristina

AU - Hanghøj, Kristian Ebbesen

AU - Gaunitz, Charleen

AU - Alfarhan, Ahmed H.

AU - Alquraishi, Saleh A.

AU - Al-Rasheid, Khaled A. S.

AU - Bradley, Daniel G.

AU - Orlando, Ludovic Antoine Alexandre

PY - 2016/3/1

Y1 - 2016/3/1

N2 - The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs of high-throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning a ~30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules retrieved but also the relative importance of endogenous DNA fragments and their molecular diversity. Therefore, these methods provide a cost-effective solution for downstream applications, including DNA sequencing on HTS platforms.

AB - The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs of high-throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning a ~30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules retrieved but also the relative importance of endogenous DNA fragments and their molecular diversity. Therefore, these methods provide a cost-effective solution for downstream applications, including DNA sequencing on HTS platforms.

KW - Ancient DNA

KW - DNA extraction

KW - Palaeogenomics

KW - Ultrashort fragments

U2 - 10.1111/1755-0998.12470

DO - 10.1111/1755-0998.12470

M3 - Journal article

C2 - 26401836

SN - 1755-098X

VL - 16

SP - 459

EP - 469

JO - Molecular Ecology Resources

JF - Molecular Ecology Resources

IS - 2

ER -

Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing

Abstract

Adgang til dokumentet

Fingeraftryk

Citationsformater