收稿日期: 2024-08-06
录用日期: 2024-12-09
网络出版日期: 2025-04-28
基金资助
国家重点研发计划(2021YFF1200300);国家自然科学基金(22174094)
Comparison of DNA and RNA extraction efficiency from blood
Received date: 2024-08-06
Accepted date: 2024-12-09
Online published: 2025-04-28
Supported by
National Key Research and Development Program of China(2021YFF1200300);National Natural Science Foundation of China(22174094)
目的·全面评估不同试剂盒及不同方法对血液样本中DNA与RNA提取的效率。方法·收集来自阿尔茨海默病(20例)、纤维化(5例)、结直肠癌患者(108例)及健康个体(12例)的血液样本,共145例。采用柱法试剂盒(Kit A)和核酸提取仪来提取血液中白细胞的基因组DNA(genomic DNA,gDNA)。使用5种试剂盒(Kit B~F),通过柱法(Kit B、E)或磁珠法(Kit C、D、F)对血浆中的游离DNA(cell-free DNA,cfDNA)和游离RNA(cell-free RNA,cfRNA)进行提取。对Kit B提取过程进行优化,包括增加血浆上样体积和延长洗脱孵育时间,并且采用该方案对100例结直肠癌患者血浆样本cfDNA进行提取。使用实时荧光定量PCR(quantitative real-time PCR,qPCR)对提取出的DNA和RNA进行定量分析,比较提取的DNA或RNA分子的数量以评估提取效率,并结合成本及操作时间等进行综合评价。结果·在gDNA提取中,尽管核酸提取仪缩短了操作时间,但Kit A(柱法)提取的DNA分子数的中位数是其25.36倍(P<0.001)。对于cfDNA提取,3种试剂盒(Kit B~D)的总体效率相近,但Kit B(柱法)在低浓度样本中的表现较为突出,其DNA提取量的平均值分别是基于磁珠法的Kit D和Kit C的4.24倍和1.18倍。提取步骤优化后的Kit B进一步提高了cfDNA的提取效率。对比3例样本在不同血浆上样体积下的cfDNA提取量,结果显示大上样体积提取的cfDNA量分别为小上样体积的3.98倍、2.38倍和3.82倍;对100例结直肠癌患者血浆样本cfDNA提取结果表明,该提取方案可在临床样本中稳定提取足够量的cfDNA。在cfRNA提取方面,Kit E(柱法)因其高效、便捷且经济性好,被广泛推荐;其提取的cfRNA含量中位数是Kit F(磁珠法)的5.01倍。比较血浆中cfDNA与cfRNA的拷贝数,结果显示每毫升血浆中cfRNA的拷贝数平均数是cfDNA的27.65倍。结论·Kit A、Kit B和Kit E分别在白细胞gDNA、血浆cfDNA以及血浆cfRNA提取方面表现出更高的效率。然而,尽管Kit E在提取效率和成本上具有优势,其安全性仍需进一步评估。
宿星蕾 , 路平 , 彭俊杰 , 汪滋民 , 宋萍 , 韩达 . 血液样本中DNA与RNA提取效率的研究[J]. 上海交通大学学报(医学版), 2025 , 45(4) : 476 -486 . DOI: 10.3969/j.issn.1674-8115.2025.04.010
Objective ·To comprehensively evaluate the efficiency of different kits and methods for DNA and RNA extraction from blood samples. Methods ·A total of 145 blood samples were collected, including those from patients with Alzheimer's disease (20 cases), fibrosis (5 cases), colorectal cancer (108 cases), and healthy individuals (12 cases). A column-based kit (Kit A) and a nucleic acid extraction instrument were used to extract genomic DNA (gDNA) from leukocytes in the blood. Cell-free DNA (cfDNA) and cell-free RNA (cfRNA) in plasma were extracted using five different kits (Kit B‒F), which employed either column-based (Kit B, E) or magnetic bead-based methods (Kit C, D, F). The extraction process of Kit B was optimized by increasing the plasma sample volume and extending the elution incubation time. Furthermore, this protocol was applied to extracting cfDNA from plasma samples of 100 colorectal cancer patients. Quantitative real-time PCR (qPCR) was used to quantify the extracted DNA and RNA, and the molecular yields were compared to evaluate the extraction efficiency. A comprehensive assessment was conducted, considering factors such as cost and operation time. Results ·In gDNA extraction, although the the operation time was shortened by using the nucleic acid extraction instrument, the median number of DNA molecules extracted using Kit A (column-based method) was 25.36-fold higher than that obtained with the instrument (P<0.05). For cfDNA extraction, while the overall efficiency of the three kits (Kit B‒D) was similar, Kit B (column-based method) showed superior performance in low-concentration samples, with average DNA yields 4.24-fold and 1.18-fold higher than those of Kit D and Kit C (both magnetic bead-based). Optimization of Kit B's extraction protocol further improved cfDNA yield. When comparing three samples, the cfDNA yields from larger plasma input volumes was 3.98-fold, 2.38-fold, and 3.82-fold higher than those from smaller input volumes, respectively. The results of cfDNA extraction from 100 colorectal cancer patients indicated that this extraction protocol reliably extracted sufficient amounts of cfDNA from clinical samples. For cfRNA extraction, Kit E (column-based method) was widely recommended due to its high efficiency, convenience, and cost-effectiveness. The median RNA content extracted using Kit E was 5.01-fold higher than that of Kit F (magnetic bead-based method). Lastly, a comparison of the copy numbers of cfDNA and cfRNA in plasma revealed that the average copy number of cfRNA per milliliter of plasma was 27.65-fold higher than that of cfDNA. Conclusion ·Kit A, Kit B, and Kit E show outstanding performance in leukocyte gDNA extraction, plasma cfDNA extraction, and plasma cfRNA extraction, respectively. However, although Kit E has advantages in extraction efficiency and cost, its safety requires further evaluation.
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