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Experimental conditions improving in‐solution target enrichment for ancient DNA
Abstract
High‐throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best‐suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA . DNA capture‐enrichment methods represent cost‐effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MY baits in‐solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA , probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self‐annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains.
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Probe design must attend to base compositional and structural considerations to avoid biasing recovery of sequence variants.
“However, probe design must attend to base compositional and structural considerations 159 to avoid biasing the recovery of sequence variants.”
From Ancient DNA analysis (2021) · cites this paper as [159]
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Metadata
- Authors
- Cruz‐Dávalos, D. I., Llamas, B., Gaunitz, C., Fages, A., Gamba, C., Soubrier, J., Librado, P., Seguin‐Orlando, A., Pruvost, M., Alfarhan, A. H., Alquraishi, S. A., Al‐Rasheid, K. A. S., Scheu, A., Beneke, N., Ludwig, A., Cooper, A., Willerslev, E., & Orlando, L.
- Affiliations
- Centre for GeoGenetics Natural History Museum of Denmark University of Copenhagen Øster Voldgade 5‐7 1350K Copenhagen Denmark
- The University of Adelaide (AU)
- University of Copenhagen (DK)
- Centre National de la Recherche Scientifique (FR)
- King Saud University (SA)
- Johannes Gutenberg University Mainz (DE)
- Naturwissenschaftliches Referat an der Zentrale Deutsches Archäologisches Institut Im Dol 2‐6 14195 Berlin Germany
- Leibniz Institute for Zoo and Wildlife Research (DE)
- Corresponding author
- Orlando, Ludovic
- ORCID
- Venue
- Molecular Ecology Resources
- Publisher
- Wiley
- Published
- 2016-09-18
- Volume
- 17
- Issue
- 3
- Pages
- 508-522
- ISSN
- 1755-098X (ISSN-L)
- 1755-0998
- OpenAlex
- W2517291540
- Cited by
- 90
- References
- 13
- Citations by year
- 2026: 7 · 2025: 7 · 2024: 9 · 2023: 8 · 2022: 7 · 2021: 8 · 2020: 12 · 2019: 7 · 2018: 16 · 2017: 9
- FWCI
- 6.22
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Molecular Ecology Resources (publishedVersion)
- PubMed (publishedVersion)
- ANU Open Research (Australian National University) (acceptedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- Griffith Research Online (submittedVersion)
- Funders
- Natur og Univers, Det Frie Forskningsråd (4002‐00152B)
- Danmarks Grundforskningsfond (DNRF94)
- King Saud University
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- ancient DNA, DNA capture, probe design, hybridization temperature, GC content, CpG, self-annealing, degraded DNA
- MeSH terms
- DNA, Ancient, Base Composition, Nucleic Acid Hybridization, DNA Probes, Sequence Analysis, DNA, CpG Islands, High-Throughput Nucleotide Sequencing
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