两种全血基因组DNA提取法的比较

目的比较经典的酚／氯仿法和人全血基因组DNA小量快速提取试剂盒抽提法两种方法提取人全血基因组DNA的纯度及总量的差异。方法收集静脉血5毫升,共132人份。分别采用上述两种方法提取基因组DNA,用紫外分光光度仪及琼脂糖凝胶电泳检测其纯度和总量,采用统计学t检验,数据以均数±标准差（x±s）表示。结果经典的酚／氯仿法和人全血基因组DNA小量快速提取试剂盒抽提法两种方法提取基因组DNA纯度用0D260／OD280表示分别为：1．65＋0．12,1．86＋0．15。基因组DNA总量分别为28．3＋3．02,33．8＋3．24。结论从提取的基因组DNA纯度和总量来比较,人全血基因组DNA小量快速提取试剂盒抽提法抽提方法较好。     

TRIzol（或TriPure）试剂结合QIAamp Viral RNA Mini试剂盒用于血标本中病毒RNA提取的研究

目的 建立一种安全、简便、可靠的适用于血标本中有包膜RNA病毒核酸提取的方法,保证埃博拉病毒核酸筛查的实验室安全,提高标本的核酸检测效率.方法 根据已发表可完全灭活埃博拉病毒的方法,通过实时荧光逆转录聚合酶链反应（real-time RT-PCR）方法,比较分析QIAamp Viral RNA Mini试剂盒、TRIzol（或TriPure）试剂裂解样本并用或不用氯仿萃取后结合QIAamp Viral RNA Mini试剂盒等3种方法提取核酸的效率,优化反应步骤,建立一种安全、简便的血标本中病毒RNA提取方法.结果 血标本经TRIzol（或TriPure）试剂处理后,不经氯仿萃取,与QIAamp Viral RNA Mini试剂盒结合,提取病毒RNA,RNA提取效率优于QIAamp Viral RNA Mini试剂盒和美国CDC推荐的方法.结论 采用TRIzol（或TriPure）试剂裂解病毒,结合QIAamp Viral RNAMini试剂盒提取病毒RNA的方法简便、可靠,可用于埃博拉出血热相关标本的核酸检测.     

不同方法提取基因组DNA的比较

目的通过对不同方法的比较建立一种遗传工程鼠基因组DNA鉴定提取最简单快速的方法。方法以大鼠和小鼠的鼠尾及脚趾为实验材料,采用酚氯仿、煮沸法、涡旋离心法提取基因组DNA;通过琼脂糖凝胶的方法检验DNA质量,通过对时间的统计分析比较3种方法提取DNA的速率。利用PCR技术检测DNA的扩增效果。结果煮沸法、涡旋离心法和酚氯仿提取的DNA比较,电泳条带均较弱。涡旋离心法所耗费的时间最短,煮沸法次之,酚氯仿法耗时最长。除了煮沸法外,涡旋离心法和酚氯仿方法提取的DNA在用于PCR检测时都能得到清晰的目的条带。结论在使用PCR进行基因型初步鉴定时,涡旋离心法是三种方法中最简单快速的首选方法。     

改进TRIZOL法提取基因组DNA

目的建立一种在提取总RNA的同时又能制备基因组DNA的方法。方法利用TR IZOL法收集水相沉淀总RNA后余下的中间层和有机相,合并去除蛋白质,再提取基因组DNA。通过紫外分光光度法和电泳法予以鉴定,并以之为模板进行PCR扩增鉴定。结果提取的基因组DNA纯度和浓度俱佳,用于PCR扩增效果良好。结论改进的TR IZOL法可以更加充分地利用实验材料,且可靠易行。     

PUREGENE DNA 提取试剂盒快速克提取全血DNA

目的对于人类基因组的研究,寻求快速、经济地从外周血中提取高产量、高纯度的DNA的试剂盒及切实有效的实验方案.方法应用PUREGENE DNA提取试剂盒(Gentra Systems,Minneapolis,MN,USA)快速提取全血DNA的3种推荐实验方案.结果与结论通过应用3种推荐实验方案,对600人份全血DNA的提取,讨论并总结了所推荐的3ml实验方案减半为最佳高效、快速、经济方案.     

不同试剂盒对乙脑病毒RNA提取效能的比较

目的比较常见的3种商售RNA提取试剂对乙脑病毒检测的相对效率、耗时和成本,为实验室应用及检测结果的评价提供依据。方法对乙脑病毒参考株悬液作10^-1～10^-4系列稀释,选用QIAGEN公司的QIAamp Viral RNA Mini Kit、Sangon生物公司的RNA提取试剂盒和Invitrogen公司的Trizol试剂3种核酸提取方法提取上述样本RNA．用TaqMan实时荧光定量反转录聚合酶链反应对其提取效率进行评价,并比较3种试剂（盒）的耗费时间和价格。结果对不同稀释度乙脑病毒样本的检测,均以QIAGEN公司QIAamp Viral RNA Mini Kit检测的敏感度最高。以该试剂盒的提取效率为100％,则Invitrogen和Sangon生物公司RNA提取试剂（盒）的提取效率分别为77．4％～86．8％和64．2％～74．1％。3种试剂（盒）对cDNA起始模板量的估计也有明显的影响,差别达到1～3个数量级,以QIAGEN公司的试剂盒最敏感。3种试剂（盒）提取RNA耗时分别为60min、100min和70min,价格效率比分别为46元、23元和20元。结论RNA提取试剂可影响JEV荧光定量PCR检测的结果,各实验室应根据实验目的和实验室条件．合理选择病毒RNA提取试剂盒。     

四种石蜡包埋组织DNA提取方法的比较

背景:由于在甲醛固定石蜡包埋组织的制作及保存过程中对DNA造成的损害,影响了后续的聚合酶链反应等研究。选择一种简便有效且经济实用的石蜡包埋组织DNA提取方法成为研究者们关注和亟待解决的问题。目的:比较甲醛固定石蜡包埋组织中4种提取DNA的方法对DNA质量的影响,探讨一种操作简便、污染少、经济实用的石蜡包埋组织中提取DNA的方法。方法:取手术切除的普通甲醛固定石蜡包埋的非小细胞肺癌组织标本20例,分别以二甲苯脱蜡-酚氯仿法、改良TES水浴脱蜡-酚氯仿法、试剂盒法和改良TES水浴脱蜡-试剂盒抽提DNA法提取其DNA,然后进行电泳分析、紫外分光光度计测定A260/A280比值及PCR扩增。结果与结论:改良TES水浴脱蜡-酚氯仿法和改良TES水浴脱蜡-试剂盒抽提DNA法可获得较大的DNA片段,且两种方法与试剂盒法所提取DNA的A260/A280值相比较,均有显著性意义(P0.05),4种方法的提取效率差异无显著性意义(P0.1),以改良TES水浴脱蜡-酚氯仿法所得DNA为模板,扩增的目的条带亮度与阳性对照相当。结果证实改良TES水浴脱蜡-酚氯仿法简便有效,所用试剂价格低廉,是一种经济实用的石蜡包埋组织DNA提取方法。     

近交系小鼠体细胞核移植囊胚的微卫星DNA鉴定

目的 利用微卫星DNA技术进行体细胞核移植囊胚的鉴定。方法 根据Mouse Genome Database设计小鼠微卫星DNA多态聚合酶链反应引物,提取近交系小鼠体细胞核移植囊胚、供体BALB/c小鼠、受体C57BL/6小鼠及昆明小鼠的基因组DNA,使用巢式聚合酶链反应扩增4个微卫星位点DNA片段,即D3Mit28、D11Mit258、D12Mit136及D14Mit50。对反应产物进行琼脂糖凝胶电泳验证。结果 巢式聚合酶链反应可扩增微量基因组DNA,通过微卫星DNA序列的扩增,证明核移植囊胚的微卫星DNA与供体细胞完全相同,而与受体细胞或者对照细胞无亲缘关系。结论 体细胞核移植囊胚基因组来源于供体BALB/c小鼠。     

粪便不同保存方法对动物基因组DNA提取效果的影响

目的为了探索一种既能使野外采集的粪便样品DNA保存完好,又方便带回实验室用于分子水平研究的粪便保存方法。方法本研究通过将普氏原羚的粪便在野外分别采取60℃干燥后低温保存,75％乙醇保存,100％乙醇保存,直接低温(保温箱中加生物冰袋)保存,在1个月内、5个月后、8个月后对粪便DNA进行抽提,并将提取的DNA作为模板进行PCR扩增,基因克隆测序。结果短期内均可得到高质量的DNA,DNA大小在23kb左右,电泳带型整齐,无降解,线粒体的扩增结果也完全一致,而用100％乙醇保存粪便DNA的时间更为长久。结论不同的保存方法提取动物基因组效果不一样。     

IgA肾病组蛋白H3K4三甲基化和DNA甲基化基因修饰的相关性

目的: 探讨IgA肾病(IgAN)外周血单个核细胞(PBMCs)组蛋白H3赖氨酸4 (H3K4)三甲基化与DNA甲基化之间的关系。方法: 采用染色质免疫共沉淀联合芯片技术(ChIP-chip)对40例IgAN患者和40例健康者的PBMCs H3K4三甲基化进行高通量筛选,染色质免疫共沉淀-实时定量聚合酶链反应 (ChIP-qPCR) 验证芯片结果,定量反转录聚合酶链反应(qRT-PCR)检测阳性基因的mRNA表达水平,采用甲基化DNA免疫共沉淀定量聚合酶链反应(MeDIP-qPCR)检测DNA甲基化水平。结果: IgAN病人PBMCs 基因组H3K4三甲基化水平升高,基因组DNA甲基化水平降低。 4个阳性基因H3K4三甲基化水平和DNA甲基化水平与正常对照组相比,显著差异(P<0.05)。结论: IgAN患者PBMCs基因组H3K4三甲基化和DNA甲基化水平存在显著改变,DNA甲基化和组蛋白H3K4三甲基化基因修饰存在相互作用。     

PCR detection of Escherichia coli O157:H7 directly from stools: evaluation of commercial extraction methods for purifying fecal DNA

Rapid identification of Escherichia coli O157:H7 is important for patient management and for prompt epidemiological investigations. We evaluated one in-house method and three commercially available kits for their ability to extract E. coli O157:H7 DNA directly from stool specimens for PCR. Of the 153 stool specimens tested, 107 were culture positive and 46 were culture negative. The sensitivities and specificities of the in-house enrichment method, IsoQuick kit, NucliSens kit, and QIAamp kit were comparable, as follows: 83 and 98%, 85 and 100%, 74 and 98%, and 86 and 100%, respectively. False-negative PCR results may be due to the presence of either inherent inhibitors or small numbers of organisms. The presence of large amounts of bacteria relative to the amount of the E. coli O157:H7 target may result in the lower sensitivities of the assays. All commercial kits were rapid and easy to use, although DNA extracted with the QIAamp kit did not require further dilution of the DNA template prior to PCR.     

Efficient extraction of viral DNA and viral RNA by the Chemagic viral DNA/RNA kit allows sensitive detection of cytomegalovirus, hepatitis B virus, and hepatitis G virus by PCR

The Chemagic Viral DNA/RNA kit was evaluated for extraction of cytomegalovirus (CMV), hepatitis B virus (HBV), and hepatitis G virus (HGV) by using the QIAamp DNA Blood Mini kit and the QIAamp Viral RNA Mini kit as reference protocols. The extraction efficiencies of the different kits for CMV DNA and HBV DNA were not distinguishable, but the extraction efficiency for HGV RNA was better with the Chemagen protocol. All clinical specimens tested HBV DNA- or HGV RNA-positive after QIAGEN protocols for extraction were confirmed by using the Chemagen protocol. The Chemagen kit failed to confirm one of 75 CMV DNA-positive specimens. Thus, a new competitive extraction method using a technology with a high potential for automation is available.     

Comparison of seven commercial DNA extraction kits for the recovery of <Emphasis Type="Italic">Brucella</Emphasis> DNA from spiked human serum samples using real-time PCR

We compared the relative recovery of extraction of bacterial DNA from serum using seven commercial kits (UltraClean DNA BloodSpin Kit, Puregene DNA Purification System, Wizard Genomic DNA Purification Kit, High Pure PCR Template Preparation Kit, GFX™ Genomic Blood DNA Purification Kit, NucleoSpin Tissue Kit, and QIAamp DNA Blood Mini Kit). Human serum samples were spiked with known concentrations of Brucella melitensis Rev 1; the DNA was extracted and tested in genus-specific LightCycler polymerase chain reaction (PCR). The UltraClean DNA BloodSpin Kit proved to be as sensitive as the QIAamp DNA Blood Mini Kit isolation method and could detect down to 100 fg of DNA, though only the former had no contamination. All the other procedures yielded DNA isolation results that were less sensitive and were always contaminated. Our results show that the UltraClean DNA Blood Spin Kit was the commercially available assay tested that yielded the best sensitivity, purity, and lack of contamination for Brucella DNA isolation from serum.     

Comparison of six commercial DNA extraction kits for recovery of cytomegalovirus DNA from spiked human specimens

We evaluated six commercially available DNA extraction kits for their ability to recover DNA from various dilutions of cytomegalovirus (CMV) added to four different specimens: bronchoalveolar lavage, cerebral spinal fluid, plasma, and whole blood. The kits evaluated included the Puregene DNA isolation kit (PG), Generation Capture Column kit, MasterPure DNA purification kit, IsoQuick nucleic acid extraction kit, QIAamp blood kit, and NucliSens isolation kit (NS). All six kits evaluated effectively removed PCR inhibitors from each of the four specimen types and produced consistently positive results down to a spiked concentration of 200 PFU of whole CMV per ml. However, the NS and PG resulted in the most consistently positive results at the lowest concentrations of spiked CMV (4 and 0.4 PFU/ml) and, in this evaluation, offered the most sensitive methods for extracting CMV DNA from the four different spiked specimens. Processing time and cost were also evaluated.     

Evaluation of DNA extraction kits for molecular diagnosis of human <Emphasis Type="Italic">Blastocystis</Emphasis> subtypes from fecal samples

Blastocystis sp. is now recognized as one of the most common intestinal parasite in human fecal examinations. Recently, PCR-based diagnostic methods of Blastocystis infection using direct DNA extraction from fresh fecal samples with commercially available kits are reported. Several kits have been developed, but little has been done in comparing the detective sensitivity between PCR methods using the commercial kits. In this study, we compared the detective sensitivity among five commercially available kits (MagNA Pure LC DNA Isolation Kit I, Roche; QuickGene SP Kit DNA, FujiFilm; NucleoSpin Plant II, Macherey-Nagel; QIAamp DNA Stool Mini Kit, Qiagen; ZR Fecal DNA Kit, Zymo Research) and fecal culture method. In a preliminary test, the DNA isolated with two kits (FujiFilm and Macherey-Nagel) showed negative PCR, while the other three kits showed positive PCR. Then, DNA from 50 clinical samples that was Blastocystis-positive in the examination of fecal culture method were isolated with the three kits and 1.1 kbp SSU rRNA gene was detected with PCR. The positive rates of the three kits (Roche, Qiagen, and Zymo Research) were 10, 48 and 94%, respectively. The present study indicated that there is different detective sensitivity among the commercial kits, and fecal culture method is superior in detection rate and cost performance than DNA-elution kits for diagnosis of Blastocystis sp. subtypes.     

DNA extraction and PCR assays for detection of Toxoplasma gondii

For detection of Toxoplasma gondii we compared the sensitivity of two different DNA extraction methods and three different PCR assays. Sensitivities of DNA extraction by QIAamp DNA mini Kit or MagNa pure followed by PCR, nested PCR and oligochromatography or Light Cycler PCR using either SYBR green chemistry or TaqMan probe were compared. No significant difference between extraction methods was found using pure T. gondii tachyzoites. Spiked blood samples, 10(4) to 10 parasites per sample, generated no difference in sensitivity between the two DNA extraction methods when analysed by nested PCR detected by oligochromatography or analysed by Light Cycler PCR TaqMan. In spiked blood samples Light Cycler PCR SYBR green was unable to detect the parasite and a reduction in sensitivity was observed with the TaqMan assay. Conventional PCR was more sensitive when DNA was extracted from the spiked samples using the QIAamp DNA mini Kit. Conventional and nested PCR were found to be more sensitive than Light Cycler PCR TaqMan using the QIAamp DNA mini Kit. It was not possible to use Light Cycler PCR SYBR green in blood samples. Conventional PCR was more sensitive for detection of T. gondii in spiked blood samples using QIAamp DNA mini Kit DNA extraction, suggesting that the choice of DNA extraction method may affect PCR assays differently.     

Comparison of Methods for the Extraction of DNA from Formalin-Fixed,Paraffin-Embedded Archival Tissues

Aim: Discussing a protocol involving xylene-ethanol deparaffinization on slides followed by a kit-based extraction that allows for the extraction of high quality DNA from FFPE tissues.Methods: DNA was extracted from the FFPE tissues of 16 randomly selected blocks. Methods involving deparaffinization on slides or tubes, enzyme digestion overnight or for 72 hours and isolation using phenol chloroform method or a silica-based commercial kit were compared in terms of yields, concentrations and the amplifiability.Results: The highest yield of DNA was produced from the samples that were deparaffinized on slides, digested for 72 hours and isolated with a commercial kit. Samples isolated with the phenol-chloroform method produced DNA of lower purity than the samples that were purified with kit. The samples isolated with the commercial kit resulted in better PCR amplification.Conclusion: Silica-based commercial kits and deparaffinized on slides should be considered for DNA extraction from FFPE.     

A 5' nuclease PCR (TaqMan) high-throughput assay for detection of the mecA gene in staphylococci

In an effort to find a rapid, efficient, and reliable method of screening large numbers of bacterial isolates for specific antimicrobial resistance genes, we compared conventional PCR results to the results generated using the TaqMan 5' nuclease PCR kit in conjunction with an ABI Prism 7700 Sequence Detector for detecting the mecA gene in various species of staphylococci. DNA was extracted using two techniques. The first used a high-salt extraction method suitable for conventional PCR but resulted in a 7.2% rate of PCR inhibition with the TaqMan technique. PCR inhibition could be overcome by diluting samples 1:5 prior to testing. The second method used the Qiagen QIAamp Tissue Kit; no instances of PCR inhibition were encountered with this method. A total of 197 (96%) of the 206 samples with no inhibition showed agreement between the two methods. Eight of the nine disagreements were likely the result of low-level DNA cross contamination caused by frequent specimen handling. Target DNA in all eight of these samples was first detected in the initial tests only after >30 PCR cycles, and all were negative upon repeat testing even after 40 PCR cycles using freshly extracted DNA. Among those positive samples in agreement, target DNA was invariably detected before 30 PCR cycles. The TaqMan assay eliminated the need to load, run, stain, and read agarose gels and provided the advantage of instant detection of PCR product by laser-activated fluorescence. Thus, final results were obtained 2 h after PCR was initiated, as opposed to a requirement of 2 days to examine 96 samples by agarose gel electrophoresis.     

Comparison of different methods of isolation of DNA of commonly encountered Candida species and its quantitation by using a real-time PCR-based assay

Molecular diagnosis based on genomic amplification methods such as real-time PCR assay has been reported as an alternative to conventional culture for early detection of invasive candidiasis. However, a major limitation of the molecular method is the difficulty associated with breaking fungal cell walls since the DNA extraction step still requires more than half of a working day. It has been suggested that PCR detection of free template DNA in serum is preferred over the use of whole blood for the diagnosis of systemic candidiasis. In this study, two conventional procedures (the first [the HLGT method] consists of boiling sera in an alkaline guanidine-phenol-Tris reagent, and the second [the PKPC method] uses proteinase K digestion, followed by organic extraction) and three commercially available kits for DNA isolation were evaluated for sensitivity, purity, cost, and use of template for most clinically important Candida species in a TaqMan-based PCR assay. To optimize these procedures, we evaluated the effect of adding 0.5% bovine serum albumin to DNA extracts and found that it decreased the effects of inhibitors. The QIAamp DNA blood kit did significantly shorten the duration of the DNA isolation but was among the most expensive procedures. Furthermore, the QIAamp DNA blood kit proved to be as sensitive as the HLGT DNA isolation method for PCR amplification from 52 serum samples from hematology or oncology patients with clinically proven or suspected systemic Candida infections. All PCR-positive samples showed approximately the same Candida species load by both procedures (100% correspondence), whereas one discordant result was obtained between PCR and blood culture.     

A modified extraction method of circulating free DNA for epidermal growth factor receptor mutation analysis

Purpose

Circulating free DNA (cfDNA) in plasma is promising to be a surrogate for tumor tissue DNA. However, not all epidermal growth factor receptor (EGFR) mutations in tumor tissue DNA has been detected in matched cfDNA, at least partly due to inefficient cfDNA extraction method. The purpose of this study was to establish an efficient plasma cfDNA extraction protocol.

Materials and Methods

The yield of plasma cfDNA extracted by our modified phenol-chloroform (MPC) method from non-small-cell lung cancer (NSCLC) patients was compared with that by QIAamp MinElute Virus Spin kit (Qiagen kit) as control, using the Wilcoxon rank-sum test. TaqMan quantitative polymerase chain reaction (qPCR) assays were used to quantify the plasma cfDNA extracted. Both Mutant-enriched PCR (ME-PCR) coupled sequencing and DxS EGFR mutation test kit were used to evaluate the impact of extraction method on EGFR mutation analysis.

Results

MPC method extracted more plasma cfDNA than Qiagen kit method (p=0.011). The proportion of longer fragment (≥202 bp) in cfDNA extracted by MPC method was significantly higher than by Qiagen kit method (p=0.002). In the sequencing maps of ME-PCR products, a higher mutant peak was observed on plasma cfDNA extracted by MPC method than by Qiagen kit method. In DxS EGFR mutation test kit results, plasma cfDNA extracted by MPC method contained more tumor-origin DNA than by Qiagen kit method.

Conclusion

An improved plasma cfDNA extraction method of MPC is provided, which will be beneficial for EGFR mutation analysis for patients with NSCLC.