Marciniak Stephanie, Klunk Jennifer, Devault Alison, Enk Jacob, Poinar Hendrik N
McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada.
McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, ON, Canada.
J Hum Evol. 2015 Feb;79:21-34. doi: 10.1016/j.jhevol.2014.11.003. Epub 2015 Jan 15.
High-throughput sequencing (HTS) has radically altered approaches to human evolutionary research. Recent contributions highlight that HTS is able to reach depths of the human lineage previously thought to be impossible. In this paper, we outline the methodological advances afforded by recent developments in DNA recovery, data output, scalability, speed, and resolution of the current sequencing technology. We review and critically evaluate the 'DNA pipeline' for ancient samples: from DNA extraction, to constructing immortalized sequence libraries, to enrichment strategies (e.g., polymerase chain reaction [PCR] and hybridization capture), and finally, to bioinformatic analyses of sequence data. We argue that continued evaluations and improvements to this process are essential to ensure sequence data validity. Also, we highlight the role of contamination and authentication in ancient DNA-HTS, which is particularly relevant to ancient human genomics, since sequencing the genomes of hominins such as Homo erectus and Homo heidelbergensis may soon be within the realm of possibility.
高通量测序（HTS）已从根本上改变了人类进化研究的方法。近期的研究成果表明，HTS能够达到之前认为不可能达到的人类谱系深度。在本文中，我们概述了当前测序技术在DNA回收、数据输出、可扩展性、速度和分辨率方面的最新进展所带来的方法学进步。我们回顾并批判性地评估了古代样本的“DNA流程”：从DNA提取，到构建永生化序列文库，再到富集策略（如聚合酶链反应[PCR]和杂交捕获），最后到序列数据的生物信息学分析。我们认为，持续评估和改进这一过程对于确保序列数据的有效性至关重要。此外，我们强调了污染和鉴定在古代DNA- HTS中的作用，这与古代人类基因组学尤为相关，因为对直立人、海德堡人等古人类基因组进行测序可能很快就会成为现实。
