Comparison of target enrichment strategies for ancient pathogen DNA

BioTechniques

Ella Reiter¹  Pushpendra Singh¹  Judith Neukamm¹  Verena J Schuenemann²  Lisa Böhme³  Natasha Arora³  Anja Furtwängler³  Stewart T Cole⁴  Melanie Vollstedt⁴  Alexander Herbig⁴  Sascha Knauf⁵  Sébastien Calvignac-Spencer⁶  Ben Krause-Kyora⁷  Johannes Krause⁸ 

[1] Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany;11Robert Koch Institut, 13353 Berlin, Germany;;1Institute for Archaeological Sciences, Archaeo- &5Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany;6Zurich Institute of Forensic Medicine, University of Zurich, 8057 Zurich, Switzerland;7Indian Council of Medical Research National Institute of Research in Tribal Health, Jabalpur 482003, MP, India;8Institut Pasteur, 75015 Paris, France;9Deutsches Primatenzentrum GmbH, Leibniz-Institute for Primate Research, 37077 Goettingen, Germany;

关键词: ancient DNA;    high-throughput sequencing;    hybridization capture;    Mycobacterium leprae;    pathogen DNA;    target enrichment;   

DOI  :  10.2144/btn-2020-0100

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown