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.

中文翻译：

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古代病原体 DNA 目标富集策略的比较。

在古代 DNA 研究中，样品的降解性质通常会导致高度片段化的 DNA 产量低；因此需要有针对性的 DNA 富集，以最大限度地提高研究成果。三种常用的方法——基于阵列的杂交捕获和使用 RNA 或 DNA 诱饵的溶液内捕获——具有不同的特性，可能会影响捕获效率、特异性和重现性。在这里，我们比较了它们在从 11 个古代样本和 19 个现代样本中富集麻风分枝杆菌和梅毒螺旋体病原体 DNA 方面的性能。我们发现溶液内方法是古代和现代两种病原体样本中最有效的方法，并且 RNA 诱饵通常比 DNA 诱饵表现更好。