The Neandertal genome and ancient DNA authenticity.
The Neandertal genome and ancient DNA authenticity.
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DOI：
10.1038/emboj.2009.222
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发表时间：
2009-09-02
期刊：
影响因子：
11.4
通讯作者：
Paeaebo, Svante
中科院分区：
文献类型：
--
作者：
Green, Richard E.;Briggs, Adrian W.;Krause, Johannes;Pruefer, Kay;Burbano, Hernan A.;Siebauer, Michael;Lachmann, Michael;Paeaebo, Svante
高通量DNA测序的最新进展使对灭绝生物的基因组进行基因组规模的分析成为可能。随着这些新的机会，在评估检索到的DNA序列的真实性方面出现了新的困难。我们将讨论如何解决这些困难，特别是关于尼安德特人基因组的分析。我们认为，只有直接测定尼安德特人与所有当代人类不同的DNA序列位置，才能作为估计人类污染的可靠手段。间接的测量，如DNA片段化的程度，核苷酸错配，或不同片段大小类别中推导出的等位基因频率的比较，是不可靠的。幸运的是，基于尼安德特人和现代人类之间mtDNA差异的临时方法，通过Y染色体序列检测男性污染，以及从同一化石中重复测序以检测常染色体污染，允许对尼安德特人基因组进行初始大规模测序。这将导致发现尼安德特人和现代人类之间的核基因组中的固定差异，这些差异可以作为未来污染的直接测定。对于其他化石古人类的分析，这可能成为可能在未来，我们建议一个类似的“引导”的方法，其中临时的方法，直到获得足够的数据，更明确的直接测定。
Recent advances in high-thoughput DNA sequencing have made genome-scale analyses of genomes of extinct organisms possible. With these new opportunities come new difficulties in assessing the authenticity of the DNA sequences retrieved. We discuss how these difficulties can be addressed, particularly with regard to analyses of the Neandertal genome. We argue that only direct assays of DNA sequence positions in which Neandertals differ from all contemporary humans can serve as a reliable means to estimate human contamination. Indirect measures, such as the extent of DNA fragmentation, nucleotide misincorporations, or comparison of derived allele frequencies in different fragment size classes, are unreliable. Fortunately, interim approaches based on mtDNA differences between Neandertals and current humans, detection of male contamination through Y chromosomal sequences, and repeated sequencing from the same fossil to detect autosomal contamination allow initial large-scale sequencing of Neandertal genomes. This will result in the discovery of fixed differences in the nuclear genome between Neandertals and current humans that can serve as future direct assays for contamination. For analyses of other fossil hominins, which may become possible in the future, we suggest a similar ‘boot-strap' approach in which interim approaches are applied until sufficient data for more definitive direct assays are acquired.
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