Reducing microbial and human contamination in DNA extractions from ancient bones and teeth
Reducing microbial and human contamination in DNA extractions from ancient bones and teeth
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DOI：
10.2144/000114320
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发表时间：
2015-08-01
期刊：
影响因子：
2.7
通讯作者：
Meyer, Matthias
中科院分区：
文献类型：
--
作者：
Korlevic, Petra;Gerber, Tobias;Meyer, Matthias
虽然在改进从古代生物样本中产生DNA序列的方法方面已经取得了很大的进展，但由于受到微生物或现代人DNA的严重污染，许多样本(如果不是大多数的话)仍然无法进行分析。在这里，我们探索不同的DNA去污染程序，用于在DNA文库准备和高通量测序之前使用的古代骨骼和牙齿。有两种方法显示了有希望的结果：(I)用磷酸盐缓冲液释放表面结合的DNA，(Ii)用次氯酸钠处理去除DNA污染。暴露在磷酸盐环境中，平均可以去除骨粉中微生物的DNA，但只有37%的内源DNA(从研究中的生物体中)被去除，信息序列的百分比平均增加了两倍。平均4.6倍的增长，在一个案例中达到24倍，是通过次氯酸钠治疗实现的，尽管代价是破坏保存在骨骼中的63%的内源性DNA。虽然这两种预处理方法由于有效地耗尽了微生物DNA而大大降低了从古代材料中进行基因组测序的成本，但我们发现去除人类DNA污染仍然是一个具有挑战性的问题。
Although great progress has been made in improving methods for generating DNA sequences from ancient biological samples, many, if not most, samples are still not amenable for analyses due to overwhelming contamination with microbial or modern human DNA. Here we explore different DNA decontamination procedures for ancient bones and teeth for use prior to DNA library preparation and high-throughput sequencing. Two procedures showed promising results: (i) the release of surface-bound DNA by phosphate buffer and (ii) the removal of DNA contamination by sodium hypochlorite treatment. Exposure to phosphate removes on average 64% of the microbial DNA from bone powder but only 37% of the endogenous DNA (from the organism under study), increasing the percentage of informative sequences by a factor of two on average. An average 4.6-fold increase, in one case reaching 24-fold, is achieved by sodium hypochlorite treatment, albeit at the expense of destroying 63% of the endogenous DNA preserved in the bone. While both pretreatment methods described here greatly reduce the cost of genome sequencing from ancient material due to efficient depletion of microbial DNA, we find that the removal of human DNA contamination remains a challenging problem.