Comparison of target enrichment strategies for ancient pathogen DNA

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...

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Published inBioTechniques Vol. 69; no. 6; pp. 455 - 459
Main Authors Furtwängler, Anja, Neukamm, Judith, Böhme, Lisa, Reiter, Ella, Vollstedt, Melanie, Arora, Natasha, Singh, Pushpendra, Cole, Stewart T, Knauf, Sascha, Calvignac-Spencer, Sébastien, Krause-Kyora, Ben, Krause, Johannes, Schuenemann, Verena J, Herbig, Alexander
Format Journal Article
LanguageEnglish
Published England Future Science Ltd 01.12.2020
Taylor & Francis Group
Subjects
ancient DNA
high-throughput sequencing
hybridization capture
Mycobacterium leprae
pathogen DNA
target enrichment
pathogen DNA
Mycobacterium leprae
target enrichment
ancient DNA
high-throughput sequencing
hybridization capture
Treponema pallidum
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Summary: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 and 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. We compared three targeted DNA enrichment strategies used in ancient DNA research for the specific enrichment of pathogen DNA regarding their efficiency, specificity and reproducibility for ancient and modern and samples. The three methods – array-based capture and in-solution capture with RNA and DNA baits – were all tested in three independent replicates.
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ISSN:0736-6205
1940-9818
DOI:10.2144/btn-2020-0100