Comparison of target enrichment strategies for ancient pathogen DNA.
- Furtwängler A Institute for Archaeological Sciences, Archaeo- & Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany.
- Neukamm J Institute for Archaeological Sciences, Archaeo- & Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany.
- Böhme L Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany.
- Reiter E Institute for Archaeological Sciences, Archaeo- & Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany.
- Vollstedt M Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany.
- Arora N Zurich Institute of Forensic Medicine, University of Zurich, 8057 Zurich, Switzerland.
- Singh P Indian Council of Medical Research National Institute of Research in Tribal Health, Jabalpur 482003, MP, India.
- Cole ST Institut Pasteur, 75015 Paris, France.
- Knauf S Deutsches Primatenzentrum GmbH, Leibniz-Institute for Primate Research, 37077 Goettingen, Germany.
- Calvignac-Spencer S Robert Koch Institut, 13353 Berlin, Germany.
- Krause-Kyora B Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany.
- Krause J Institute for Archaeological Sciences, Archaeo- & Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany.
- Schuenemann VJ Institute for Archaeological Sciences, Archaeo- & Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany.
- Herbig A Institute for Archaeological Sciences, Archaeo- & Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany.
- 2020-11-02
Published in:
- BioTechniques. - 2020
Mycobacterium leprae
Treponema pallidum
ancient DNA
high-throughput sequencing
hybridization capture
pathogen DNA
target enrichment
English
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 research outcomes. The three commonly used methods - array-based hybridization capture and in-solution capture using either RNA or DNA baits - have different characteristics that may influence the capture efficiency, specificity and reproducibility. Here we compare their performance in enriching pathogen DNA of Mycobacterium leprae and Treponema pallidum from 11 ancient and 19 modern samples. We find that in-solution approaches are the most effective method in ancient and modern samples of both pathogens and that RNA baits usually perform better than DNA baits.
- Language
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- English
- Open access status
- gold
- Identifiers
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- DOI 10.2144/btn-2020-0100
- PMID 33135465
- Persistent URL
- https://folia.unifr.ch/global/documents/203883
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