用于捕获血浆中游离肿瘤DNA的单链DNA相较于双链DNA文库制备的优势。
Advantages of Single-Stranded DNA Over Double-Stranded DNA Library Preparation for Capturing Cell-Free Tumor DNA in Plasma.
作者信息
Zhu Jing, Huang Jinyong, Zhang Peng, Li Qianxia, Kohli Manish, Huang Chiang-Ching, Wang Liang
机构信息
Laboratory of Medical Genetics, Harbin Medical University, and The Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Chinese Ministry of Education, 157 Baojian Road, Harbin, 150081, Heilongjiang, China.
Department of Pathology and MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA.
出版信息
Mol Diagn Ther. 2020 Feb;24(1):95-101. doi: 10.1007/s40291-019-00429-7.
BACKGROUND
Single-stranded DNA (ssDNA) libraries have been shown to enrich shorter and more degraded DNA fragments than double-stranded DNA (dsDNA) libraries.
OBJECTIVE
In this study, we evaluated whether ssDNA libraries captured more circulating tumor DNA (ctDNA) in plasma cell-free DNA (cfDNA).
METHODS
We prepared dsDNA, ssDNA and pure-ssDNA (capture the preexisting ssDNA) libraries using ten plasma cfDNA samples. After low-pass whole genome sequencing, we calculated a duplicate rate to estimate library complexity and compared the library insert sizes between the different library methods. Finally, we estimated the ctDNA content and plasma genomic abnormality (PGA) score, an indicator of ctDNA burden.
RESULTS
27 libraries were prepared and sequenced from the ten cfDNA samples. The duplicate rate in the ssDNA and pure-ssDNA libraries was significantly lower than in the dsDNA libraries (p < 0.001 and p < 0.01, respectively). ctDNA content and PGA scores were consistently higher in the ssDNA and pure-ssDNA libraries than in the matched dsDNA libraries (p < 0.005). The higher ctDNA content in ssDNA libraries was associated with smaller library insert size.
CONCLUSIONS
ssDNA libraries preserve more diversity and capture more ctDNA than dsDNA libraries. The ssDNA library method is preferred when performing genomic analysis of ctDNA.
背景
与双链DNA（dsDNA）文库相比，单链DNA（ssDNA）文库已被证明能富集更短且降解程度更高的DNA片段。
目的
在本研究中，我们评估了ssDNA文库是否能在血浆游离DNA（cfDNA）中捕获更多的循环肿瘤DNA（ctDNA）。
方法
我们使用10份血浆cfDNA样本制备了dsDNA、ssDNA和纯ssDNA（捕获预先存在的ssDNA）文库。在进行低通量全基因组测序后，我们计算重复率以评估文库复杂性，并比较不同文库方法之间的文库插入片段大小。最后，我们估计了ctDNA含量和血浆基因组异常（PGA）评分，这是一个反映ctDNA负担的指标。
结果
从10份cfDNA样本中制备并测序了27个文库。ssDNA和纯ssDNA文库中的重复率显著低于dsDNA文库（分别为p < 0.001和p < 0.01）。ssDNA和纯ssDNA文库中的ctDNA含量和PGA评分始终高于匹配的dsDNA文库（p < 0.005）。ssDNA文库中较高的ctDNA含量与较小的文库插入片段大小相关。
结论
与dsDNA文库相比，ssDNA文库保留了更多的多样性并捕获了更多的ctDNA。在进行ctDNA的基因组分析时，ssDNA文库方法更受青睐。
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