从野外到实验室:高通量测序时代人类古代DNA研究中的DNA污染控制

B. Llamas, Guido Valverde, Lars Fehren-Schmitz, L. Weyrich, A. Cooper, W. Haak
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引用次数: 120

摘要

高通量DNA测序(HTS)技术已经改变了我们在古代DNA研究中检测和评估DNA污染的方式。研究人员利用计算方法挖掘大量的测序数据来检测DNA损伤的特征模式,并评估结果的真实性。我们认为,除非计算方法能够自信地将真实的古代DNA序列与在独立衰变过程中显示损伤模式的污染DNA分离开来,否则DNA污染的预防和控制应该仍然是古代人类DNA研究的核心和关键方面。理想情况下,DNA污染可以通过在挖掘,样本采集和/或随后的处理过程中遵循最小的指导方针来早期预防。古DNA实验室也应使用专门的设备和严格的实验程序监测或尽量减少DNA污染。在本文中,我们更新了从现场到实验室控制DNA污染的建议,试图促进现场考古学家,人类学家和古代DNA研究人员之间的交流。我们还为基于hts的研究提供了古代DNA真实性的最新标准。我们相信,这里概述的程序将来将增加从有价值的考古人类遗骸中检索更高比例的真实遗传信息。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
From the field to the laboratory: Controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era
Abstract High-Throughput DNA Sequencing (HTS) technologies have changed the way in which we detect and assess DNA contamination in ancient DNA studies. Researchers use computational methods to mine the large quantity of sequencing data to detect characteristic patterns of DNA damage, and to evaluate the authenticity of the results. We argue that unless computational methods can confidently separate authentic ancient DNA sequences from contaminating DNA that displays damage patterns under independent decay processes, prevention and control of DNA contamination should remain a central and critical aspect of ancient human DNA studies. Ideally, DNA contamination can be prevented early on by following minimal guidelines during excavation, sample collection and/or subsequent handling. Contaminating DNA should also be monitored or minimised in the ancient DNA laboratory using specialised facilities and strict experimental procedures. In this paper, we update recommendations to control for DNA contamination from the field to the laboratory, in an attempt to facilitate communication between field archaeologists, anthropologists and ancient DNA researchers. We also provide updated criteria of ancient DNA authenticity for HTS-based studies. We are confident that the procedures outlined here will increase the retrieval of higher proportions of authentic genetic information from valuable archaeological human remains in the future.
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