Comparison of target enrichment strategies for ancient pathogen DNA

A Furtwängler, J Neukamm, L Böhme, E Reiter… - …, 2020 - Taylor & Francis
In ancient DNA research, the degraded nature of the samples generally results in poor
yields of highly fragmented DNA; targeted DNA enrichment is thus required to maximize …

Parallel detection of ancient pathogens via array-based DNA capture

KI Bos, G Jäger, VJ Schuenemann… - … of the Royal …, 2015 - royalsocietypublishing.org
DNA capture coupled with next generation sequencing is highly suitable for the study of
ancient pathogens. Screening for pathogens can, however, be meticulous when assays are …

Hybridization capture of ancient DNA using RNA baits

AER Soares - Ancient DNA: Methods and Protocols, 2019 - Springer
The majority of DNA recovered from ancient remains is derived from organisms that colonize
the remains post-mortem, such as soil microbes, or from contaminants, such as DNA from …

Emulsion PCR-coupled target enrichment: an effective fishing method for high-throughput sequencing of poorly preserved ancient DNA

M Kihana, F Mizuno, R Sawafuji, L Wang, S Ueda - Gene, 2013 - Elsevier
Due to the difficulties in deep sequencing, high-throughput sequencing of ancient DNA has
been limited to exceptionally well-preserved ancient materials. The primary factor is …

Comparison and optimization of ancient DNA extraction

N Rohland, M Hofreiter - Biotechniques, 2007 - Taylor & Francis
Ancient DNA analyses rely on the extraction of the tiny amounts of DNA remaining in
samples that are hundreds to tens of thousands of years old. Despite the critical role …

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

C Gamba, K Hanghøj, C Gaunitz… - Molecular Ecology …, 2016 - Wiley Online Library
The DNA molecules that can be extracted from archaeological and palaeontological
remains are often degraded and massively contaminated with environmental microbial …

Quantifying and reducing cross‐contamination in single‐and multiplex hybridization capture of ancient DNA

EI Zavala, A Aximu‐Petri, J Richter… - Molecular Ecology …, 2022 - Wiley Online Library
The use of hybridization capture has enabled a massive upscaling in sample sizes for
ancient DNA studies, allowing the analysis of hundreds of skeletal remains or sediments in …

Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded …

MT Gansauge, A Aximu-Petri, S Nagel, M Meyer - Nature Protocols, 2020 - nature.com
It has been shown that highly fragmented DNA is most efficiently converted into DNA
libraries for sequencing if both strands of the DNA fragments are processed independently …

Whole-genome capture of ancient DNA using homemade baits

G González Fortes, JLA Paijmans - Ancient DNA: Methods and protocols, 2019 - Springer
For many archaeological and paleontological samples, the relative content of endogenous
compared to contaminant DNA is low. In such cases, enriching sequencing libraries for …

Experimental conditions improving in‐solution target enrichment for ancient DNA

DI Cruz‐Dávalos, B Llamas, C Gaunitz… - Molecular ecology …, 2017 - Wiley Online Library
High‐throughput sequencing has dramatically fostered ancient DNA research in recent
years. Shotgun sequencing, however, does not necessarily appear as the best‐suited …