Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples.

IF 2.2 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS BioTechniques Pub Date : 2024-05-01 Epub Date: 2024-03-26 DOI:10.2144/btn-2023-0107
Reyhan Yaka, Maja Krzewińska, Vendela Kempe Lagerholm, Anna Linderholm, Füsun Özer, Mehmet Somel, Anders Götherström
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Abstract

Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results.

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比较和优化古代 DNA 样本的方案和全基因组捕获条件。
从人类遗骸中获取的古 DNA(aDNA)通常是片段化的,且含量相对较低。在这里,我们通过比较硅基 DNA 提取和 aDNA 文库制备方案,研究了一套生成 aDNA 数据的最佳方法。我们还通过修改一些参数组合来测试古人类样本的全基因组富集(WGC)效率。我们发现,Dabney 提取方案的性能明显优于其他方案。我们进一步观察到,BEST 文库方案的阳性趋势表明克隆性较低。值得注意的是,我们的研究结果表明,WGC 能有效地提取内源性 DNA,尤其是从保存较差的人类样本中提取,能将人类内源性比例提高 5 倍。因此,aDNA 研究最有可能从我们的结果中获益。
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来源期刊
BioTechniques
BioTechniques 工程技术-生化研究方法
CiteScore
4.40
自引率
0.00%
发文量
68
审稿时长
3.3 months
期刊介绍: BioTechniques is a peer-reviewed, open-access journal dedicated to publishing original laboratory methods, related technical and software tools, and methods-oriented review articles that are of broad interest to professional life scientists, as well as to scientists from other disciplines (e.g., chemistry, physics, computer science, plant and agricultural science and climate science) interested in life science applications for their technologies. Since 1983, BioTechniques has been a leading peer-reviewed journal for methods-related research. The journal considers: Reports describing innovative new methods, platforms and software, substantive modifications to existing methods, or innovative applications of existing methods, techniques & tools to new models or scientific questions Descriptions of technical tools that facilitate the design or performance of experiments or data analysis, such as software and simple laboratory devices Surveys of technical approaches related to broad fields of research Reviews discussing advancements in techniques and methods related to broad fields of research Letters to the Editor and Expert Opinions highlighting interesting observations or cautionary tales concerning experimental design, methodology or analysis.
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