Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing
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Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing. / Gamba, Cristina; Hanghøj, Kristian Ebbesen; Gaunitz, Charleen; Alfarhan, Ahmed H.; Alquraishi, Saleh A.; Al-Rasheid, Khaled A. S.; Bradley, Daniel G.; Orlando, Ludovic Antoine Alexandre.
I: Molecular Ecology Resources, Bind 16, Nr. 2, 2016, s. 459-469.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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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
Y1 - 2016
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
VL - 16
SP - 459
EP - 469
JO - Molecular Ecology
JF - Molecular Ecology
SN - 0962-1083
IS - 2
ER -
ID: 154401225