Single-tube-genotyping of gastric cancer related SNPs by directly using whole blood and paper-dried blood as starting materials

AIM: To demonstrate an inexpensive method for typing gastric cancer related single nucleotide polymorphisms (SNPs) using whole blood or paper-dried blood as starting materials. METHODS: PCR amplification is directly carried out from the whole blood or paper-dried blood sample without any DNA extraction step. Before PCR, a blood sample, four primers, and all of biological reagents necessary for PCR were added at a time; After PCR, the amplified products were directly separated by slab gel electrophoresis or microchip CE without any purification. SNP typing was performed by tetra-primer PCR with two inner primers specific to each allele and two outer primers defining the length of allele-specific amplicons. Genotypes were directly discriminated by the size of amplicons specific to each allele, thereby avoiding any post-PCR process. RESULTS: Using a special PCR buffer, inhibitory substances in blood (including the anticoagulant in blood) and filter paper were effectively suppressed; a "true" single-tube-genotyping is thus realized. We successfully determined genotypes IL-1B-511 and IL-1B-31 polymorphisms at the gene IL-1B by using whole-blood and paper-dried blood samples as starting materials respectively. The method is so sensitive that 0.5-1.0μL of blood sample is enough to give a satisfactory typing results. The genotyping results were confirmed by RFLP-PCR using purified genome DNA, indicating that amplification specificity was not affected by inhibitory components (including coagulants) in blood or filter paper. CONCLUSION: Compared with SNP typing methods based on purified DNA, the proposed method is labor saving, simple, inexpensive, and less cross-contaminated. It is promising to use this method to type other SNPs.     

Single-tube-genotyping of gastric cancer related SNPs by directly using whole blood and paper-dried blood as starting material

AIM: To demonstrate an inexpensive method for typing gastric cancer related single nucleotide polymorphisms (SNPs) using whole blood or paper-dried blood as starting materials. METHODS: PCR amplification is directly carried out from the whole blood or paper-dried blood sample without any DNA extraction step. Before PCR, a blood sample, four primers, and all of biological reagents necessary for PCR were added at a time; After PCR, the amplified products were directly separated by slab gel electrophoresis or microchip CE without any purification. SNP typing was performed by tetra-primer PCR with two inner primers specific to each allele and two outer primers defining the length of allele-specific amplicons. Genotypes were directly discriminated by the size of amplicons specific to each allele, thereby avoiding any post-PCR process. RESULTS: Using a special PCR buffer, inhibitory substances in blood (including the anticoagulant in blood) and filter paper were effectively suppressed; a "true" single-tube-genotyping is thus realized. We successfully determined genotypes IL-1B-511 and IL-1B-31 polymorphisms at the gene IL-1B by using whole-blood and paper-dried blood samples as starting materials respectively. The method is so sensitive that 0.5-1.0 microL of blood sample is enough to give a satisfactory typing results. The genotyping results were confirmed by RFLP-PCR using purified genome DNA, indicating that amplification specificity was not affected by inhibitory components (including coagulants) in blood or filter paper. CONCLUSION: Compared with SNP typing methods based on purified DNA, the proposed method is labor-saving, simple, inexpensive, and less cross-contaminated. It is promising to use this method to type other SNPs.     

Comprehensive human genome amplification using multiple displacement amplification

Fundamental to most genetic analysis is availability of genomic DNA of adequate quality and quantity. Because DNA yield from human samples is frequently limiting, much effort has been invested in developing methods for whole genome amplification (WGA) by random or degenerate oligonucleotide-primed PCR. However, existing WGA methods like degenerate oligonucleotide-primed PCR suffer from incomplete coverage and inadequate average DNA size. We describe a method, termed multiple displacement amplification (MDA), which provides a highly uniform representation across the genome. Amplification bias among eight chromosomal loci was less than 3-fold in contrast to 4-6 orders of magnitude for PCR-based WGA methods. Average product length was >10 kb. MDA is an isothermal, strand-displacing amplification yielding about 20-30 microg product from as few as 1-10 copies of human genomic DNA. Amplification can be carried out directly from biological samples including crude whole blood and tissue culture cells. MDA-amplified human DNA is useful for several common methods of genetic analysis, including genotyping of single nucleotide polymorphisms, chromosome painting, Southern blotting and restriction fragment length polymorphism analysis, subcloning, and DNA sequencing. MDA-based WGA is a simple and reliable method that could have significant implications for genetic studies, forensics, diagnostics, and long-term sample storage.     

A simple method for extraction and purification of genomic DNA from dried blood spots on filter paper

We have developed an efficient and simple method for extracting and purifying genomic DNA from dried blood stored on filter paper. The quality of the genomic DNA extracted is tested by PCR amplification of a 255-bp fragment of the PAX8 gene sequence and the PCR products are determined for further genetic studies by single strand conformation polymorphism (SSCP) analysis. Larger DNA sequences of the 674-bp of the PAX8 gene and the 1,039-bp of the human beta-globin gene, a housekeeping gene, have also been amplified from the extracted DNA, thus indicating the high quality of the genomic DNA extracted by the developed method for subsequent genetic studies of any gene of interest. The method developed can also be used for the purification of genomic DNA from dried blood specimens stored under different conditions. Moreover, the genomic DNA products can be stored for long-term use due to the highly purified procedure. Therefore, the method is efficient and appropriate for the extraction and purification of genomic DNA from dried blood specimens, which has become an increasingly important tool for genetic and epidemiological studies.     

Evaluation of the BeTha Gene 1 Kit for the Qualitative Detection of the Eight Most Common Mediterranean β-Thalassemia Mutations

We describe the evaluation of the Bio-Rad BeTha Gene 1 kit (Bio-Rad Laboratories, Hercules, CA), a DNA-probe assay designed for the qualitative determination of the eight most common Mediteranean β-thalassemia mutations. The kit utilizes the principle of allele-specific oligonucleotide (ASO) hybridization. Following sample preparation and in vitro DNA amplification by the polymerase chain reaction (PCR), an allele-specific detection of the amplified products by a nonradioactive enzymatic assay is performed. Genomic DNA is prepared from an individual's whole blood with a DNA purification matrix. In a second step, the β-globin gene is amplified in a multiplex PCR reaction containing four 5′ biotinylated oligonucleotide primers. In a final step, an aliquot of the PCR reaction is first chemically denatured and then captured in two eight-well strips of a 96-well enzyme-linked immunosorbent assay (ELISA) plate by hybridization to an immobilized ASO probe. Each DNA sequence at each of the eight mutation sites is represented by one normal and one mutant ASO. During this capture/hybridization step, which is performed at 37°C, only perfectly matched PCR products will be captured by an ASO. Subsequently, the allele-specific captured biotin-labeled PCR products are detected by a colorimetric enzymatic reaction. The system permits the detection of 16 β-thalassemia alleles using a high-throughput format that can be automated easily. A clinical feasibility study was performed to evaluate the functionality (method camparison study, assay validity using samples previously collected and stored at various temperatures for different periods of time, interference on kit performance, and assay validity for prenatal diagnosis) and the usability (ease of use, sample throughput) of the kit. The analysis of 110 samples previously studied with reference methods showed 100% clinical sensitivity and specificity. We demonstrate here that the procedure not only increases the throughput of β-thalassemia allele genotyping but also provides an accurate, rapid, reliable, and nonisotopic diagnostic tool. Am. J. Hematol. 59:214–222, 1998. © 1998 Wiley-Liss, Inc.     

A simple method to detect Plasmodium falciparum directly from blood samples using the polymerase chain reaction.

We have developed a simple method for treating blood samples permitting direct detection of Plasmodium falciparum parasites using the P. falciparum-specific DNA probe pPF14 after polymerase chain reaction (PCR) amplification of target DNA sequences, and have compared this method with microscopic examination of thick blood smears. For PCR amplification, blood samples were lysed, then filtered onto filter paper. After drying, a piece of the filter paper was added directly to the PCR mixture for amplification. The presence of PCR products was detected using nonisotopically labeled probe. This method permits detection of less than than 10 parasites in a 20-microliters sample, and minimizes the effects of PCR inhibitors generally found in blood. Samples were collected from patients presenting at malaria clinics in Mae Sod and Mae Ramat, Thailand, and 626 were analyzed both by the PCR method and by conventional microscopy. Of these, 157 were positive both by microscopy and by PCR, while 297 were negative by both methods. PCR detected 131 samples that were negative by microscopy, and failed to detect 41 samples identified as positive by microscopy. All discordant samples were re-analyzed by microscopy and by PCR. Upon re-examination at a higher sensitivity, microscopy identified five additional positive cases, while six previously positive cases were found to be negative. This method of treating blood samples for PCR may also be useful in other diagnostic assays.     

Applications of polymerase chain reaction in rheumatology

Polymerase chain reaction (PCR) is a highly sensitive and specific method for detection and quantification of specific nucleic acids from a clinical sample. With its use, genetic, infectious, neoplastic, and autoimmune diseases can be diagnosed and managed with a high level of sensitivity, accuracy, and rapidity. This technique exactly reproduces unlimited copies of DNA, even if only a small amount are present initially. PCR assays can detect presence of fastidious and slow-growing microorganisms, such as chlamydia, mycoplasmas, mycobacterias, and viruses directly from clinical specimens and also can detect antimicrobial resistance. The value of viral load measurement by nucleic acid amplification in the management of patients with HIV infection or hepatitis C has also been well established. From the point of view of a clinician, the applications of PCR are focused mainly in the amplification and detection of diagnostic DNA segments from the genomes of both pathogens and patients.     

Storage duration and polymerase chain reaction detection of Plasmodium falciparum from blood spots on filter paper

To evaluate the effect of long-term storage of sample filters on the sensitivity of polymerase chain reaction (PCR) detection of malaria, 252 blood spots from patients with microscopically confirmed Plasmodium falciparum malaria were analyzed and stratified by storage duration. The spots were collected between 1996 and 2000 on filter paper and stored at room temperature. A Chelex-based method was used to extract the DNA. Unexpectedly, after the first purification, the sensitivity of the PCR from recently stored samples was low and showed progressively increased with time storage (P = 0.003, by chi-square test for linear trend). This suggested that PCR inhibitors were easier to dissolve from the more recent blood spots (< 4 years old) than from blood spots > or = 4 years old, thus leading to a time-dependent increase in PCR sensitivity. However, if DNA was purified again (when the first PCR result was negative), the cumulative sensitivity was not influenced by storage duration. This indicated that length of storage is not a critical issue providing purification is sufficient.     

基于SSUrRNA基因序列的间日疟原虫LAMP检测技术的建立

目的克隆分析间日疟原虫小亚基亚单位核糖体核糖核酸(SSUrRNA)特异性基因序列,建立间日疟原虫环介导等温扩增(LAMP)检测技术。方法针对间日疟原虫SSUrRNA种特异性基因序列设计1对引物,采用聚合酶链反应(PCR)从血样核酸提取物中扩增SSUrRNA基因片段,纯化后与pGEM-Teasy载体连接,构建重组质粒并转化大肠埃希菌JM109,PCR与双酶切鉴定筛选阳性克隆并测序,设计6条寡核苷酸片段,LAMP检测感染血样中间日疟原虫DNA,扩增产物作琼脂糖电泳分析或直接荧光染色肉眼观察。结果间日疟原虫SSUrRNA基因扩增片段大小约为235 bp;阳性克隆重组质粒插入的SSUrRNA基因扩增片段含有235个核苷酸,与GenBank中的Sal-1株、Belem株间日疟原虫相同序列进行比对,同源性为100%,与PV2008/TR/DEL株、PVK1294株、E1 Salvador株的同源性均为99%,与三日疟原虫、卵形疟原虫及恶性疟原虫的序列同源性均低于95%。将含有SSUrRNA靶基因的重组质粒以蒸馏水倍比稀释后做LAMP,试验的灵敏度为10 copy/μl;特异性检验显示间疟原虫患者血样DNA呈阳性反应,恶性...     

A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities

We present a programmable droplet-based microfluidic device that combines the reconfigurable flow-routing capabilities of integrated microvalve technology with the sample compartmentalization and dispersion-free transport that is inherent to droplets. The device allows for the execution of user-defined multistep reaction protocols in 95 individually addressable nanoliter-volume storage chambers by consecutively merging programmable sequences of picoliter-volume droplets containing reagents or cells. This functionality is enabled by "flow-controlled wetting," a droplet docking and merging mechanism that exploits the physics of droplet flow through a channel to control the precise location of droplet wetting. The device also allows for automated cross-contamination-free recovery of reaction products from individual chambers into standard microfuge tubes for downstream analysis. The combined features of programmability, addressability, and selective recovery provide a general hardware platform that can be reprogrammed for multiple applications. We demonstrate this versatility by implementing multiple single-cell experiment types with this device: bacterial cell sorting and cultivation, taxonomic gene identification, and high-throughput single-cell whole genome amplification and sequencing using common laboratory strains. Finally, we apply the device to genome analysis of single cells and microbial consortia from diverse environmental samples including a marine enrichment culture, deep-sea sediments, and the human oral cavity. The resulting datasets capture genotypic properties of individual cells and illuminate known and potentially unique partnerships between microbial community members.     

DNA profiling: a valuable tool for quality control of sample logistics including occurrences of suspected sample confusion in a blood donation centre

BACKGROUND AND OBJECTIVES: A molecular method for analysing whole-blood samples should be established for quality control of plasma sample logistics. MATERIALS AND METHODS: DNA profiles of retention samples (plasma) were compared to profiles of recent donations (whole blood). DNA extraction, amplification and detection were performed using the Qiagen DNA Blood Mini kit, the AmpFFISTR Profiler Plus Kit and capillary electrophoresis, respectively. RESULTS: Matched pairs of full profiles were obtained for all samples investigated, therefore no deviation from the standardized procedures was detected. CONCLUSIONS: Modified extraction and amplification protocols enabled DNA profiling to be used for the quality control of plasma samples. Hence, DNA profiling can be used in the blood bank as a safe and easy method for quality control of sample logistics.     

荧光定量PCR快速检测鼠疫耶尔森氏菌的实验研究

目的　利用LightCycler建立一种简便、特异的荧光定量PCR检测方法 ,用于鼠疫耶尔森氏菌的快速检测。 方法　采用SYBRGreenI随机掺入法 ,以Roche试剂盒为标准 ,比较两公司的DNA聚合酶 ,用鼠疫菌 310 0 4建立荧光PCR反应体系 ;针对鼠疫耶尔森氏菌特异的染色体标识序列和质粒上F1抗原基因设计引物 ,检测其灵敏度和特异性 ,以盲测试验进行验证 ;在此基础上鉴定 2 75株鼠疫耶尔森氏菌 ,并测试该法检测脏器污染模拟标本的灵敏度。结果　建立以一个公司试剂为主较低成本的PCR反应体系 ;EV76的检测灵敏度可达每反应体系 1.6个菌 ;检测我国 18个生态型共计 2 75株鼠疫耶尔森氏菌及 2 8株非鼠疫菌株的PCR扩增结果表明 ,鼠疫菌株均出现特异的扩增结果 ,2 8株对照菌株均为阴性 ;肝、脾、肺模拟标本检测灵敏度可达每反应体系 4 0 0 0个菌。结论　该方法对于检测鼠疫耶尔森氏菌具有简便、快捷、高敏感性和特异性的特点 ,适用于鼠疫紧急疫情时的快速诊断和疫源地监测     

Microfluidic approaches to malaria detection

Microfluidic systems are under development to address a variety of medical problems. Key advantages of micrototal analysis systems based on microfluidic technology are the promise of small size and the integration of sample handling and measurement functions within a single, automated device having low mass-production costs. Here, we review the spectrum of methods currently used to detect malaria, consider their advantages and disadvantages, and discuss their adaptability towards integration into small, automated micro total analysis systems. Molecular amplification methods emerge as leading candidates for chip-based systems because they offer extremely high sensitivity, the ability to recognize malaria species and strain, and they will be adaptable to the detection of new genotypic signatures that will emerge from current genomic-based research of the disease. Current approaches to the development of chip-based molecular amplification are considered with special emphasis on flow-through PCR, and we present for the first time the method of malaria specimen preparation by dielectrophoretic field-flow-fractionation. Although many challenges must be addressed to realize a micrototal analysis system for malaria diagnosis, it is concluded that the potential benefits of the approach are well worth pursuing.     

外周血游离DNA检测非小细胞肺癌患者EGFR基因突变研究进展

外周血游离DNA检测非小细胞肺癌人群表皮生长因子受体基因突变法因受到标本质量、采集运输分离条件、DNA提取方法、基因突变检测方法的多种限制,检测敏感性低,假阴性比例较高,但特异性较好。因此,外周血游离DNA的基因突变检测需针对特殊人群,优化采集运输分离步骤,并尝试使用较好的DNA提取（如改良酚一氯仿法、QIAmpCirculatingNucleicAcidKit）及基因检测方法（如蝎形探针扩增阻滞突变系统、高效液相色谱法、高分辨溶解曲线分析技术、突变一富集PCR等）。本文就外周血游离DNA表皮生长因子受体基因突变检测的现状及发展方向进行综述。     

Comparison of whole genome amplification methods for detecting pathogenic bacterial genomic DNA using microarray

The genetic diagnosis of pathogenic agents using microarrays has the advantage of high-throughput detection, but a relatively large amount of DNA sample is required. To obtain a sufficient amount of DNA for molecular diagnoses, several whole genome amplification (WGA) methods have been proposed. In this study, using Francisella tularensis and Escherichia coli as models, we compared four WGA methods in terms of their efficiency of amplification of whole genomic DNA in order to identify the most suitable method for preparing DNA to be used for microarray analysis. It was possible to obtain more than 1.5 microg of products from 10 ng of F. tularensis and E. coli genomic DNA using four methods, but biases in the amplification of bacterial genes were least prominent in the multiple displacement amplification (MDA) or OmniPlex WGA. When the amplified DNAs were applied to microarray slides consisting of 32 different genes probes, DNAs amplified by Phi29 v2 of MDA and OmniPlex WGA showed high signal intensity as well as a high signal-to-noise ratio for all 32 genes. These results indicate that Phi29 v2 and OmniPlex WGA are useful methods for obtaining sufficient DNA from a limited amount of samples for the detection of microbes using microarrays.     

Simplified diagnosis of malaria infection: GFM/PCR/ELISA a simplified nucleic acid amplification technique by PCR/ELISA

We report an adaptation of a technique for the blood sample collection (GFM) as well as for the extraction and amplification of Plasmodium DNA for the diagnosis of malaria infection by the PCR/ELISA. The method of blood sample collection requires less expertise and saves both time and money, thus reducing the cost by more than half. The material is also suitable for genetic analysis in either fresh or stored specimens prepared by this method.     

疟疾复合PCR检测系统的建立

目的：建立简易、快速的复合ＰＣＲ系统,用于检测间日疟、恶性疟及混合感染。方法：以疟原虫小亚单位核糖体核糖核酸基因为靶片段,设计疟原虫属特异性上游引物Ｓ１和间日疟原虫、恶性疟原虫种特异性下游引物Ｓ２和Ｓ３,建立双温度点复合ＰＣＲ扩增系统并用于临床血样的检测。结果：从间日疟原虫和恶性疟原虫感染血样中分别扩增出７０５ｂｐ和５７５ｂｐ特定扩增带,而食蟹猴疟原虫、诺氏疟原虫及健康人血样均未见扩增带。检测原虫水平达２－１０虫／μｌ全血。限制性内切酶酶切分析证实扩增产物为目的片段。检测１０４份镜检确诊疟疾患者血样,其中８１份与镜检结果相符,并查出镜检未发现的１７份混合感染和２份虫种鉴别失误的恶性疟。结论：本系统敏感性高,特异性强,操作简便,可在一次扩增中同时检出间日疟和恶性疟两种原虫。     

多重聚合酶链式反应检测C、D型肉毒神经毒素基因

目的为了建立检测Ｃ、Ｄ型肉毒神经素基因的ＰＣＲ方法。方法用人工合成的两对寡核苷酸引物于同一反应管中扩增Ｃ、Ｄ型肉毒素基因的一段ＤＮＡ片断,建立了用于Ｃ、Ｄ型肉毒神经毒素基因检测的多重ＰＣＲ方法。用多重聚合酶链式反应对梭状芽胞杆菌属的１０种２６株菌进行了鉴定,并对其特异性及灵敏度进行了检查。结果当样本中同时含有Ｃ、Ｄ型的模板ＤＮＡ时用该ＰＣＲ系统可同时扩增出Ｃ、Ｄ型的目的片段,分别为９９９ｂｐ和４０４ｂｐ,其它各型肉毒酸梭菌及其它梭菌均为阴性,灵敏度较Ｃ、Ｄ型分别扩增偏低,Ｃ型为４５０ｐｇ,Ｄ型为１０ｐｇ。结论该ＰＣＲ系统可用于Ｃ、Ｄ型肉毒梭菌的鉴定、定型     

Shaping acoustic fields as a toolset for microfluidic manipulations in diagnostic technologies

Ultrasonics offers the possibility of developing sophisticated fluid manipulation tools in lab-on-a-chip technologies. Here we demonstrate the ability to shape ultrasonic fields by using phononic lattices, patterned on a disposable chip, to carry out the complex sequence of fluidic manipulations required to detect the rodent malaria parasite Plasmodium berghei in blood. To illustrate the different tools that are available to us, we used acoustic fields to produce the required rotational vortices that mechanically lyse both the red blood cells and the parasitic cells present in a drop of blood. This procedure was followed by the amplification of parasitic genomic sequences using different acoustic fields and frequencies to heat the sample and perform a real-time PCR amplification. The system does not require the use of lytic reagents nor enrichment steps, making it suitable for further integration into lab-on-a-chip point-of-care devices. This acoustic sample preparation and PCR enables us to detect ca. 30 parasites in a microliter-sized blood sample, which is the same order of magnitude in sensitivity as lab-based PCR tests. Unlike other lab-on-a-chip methods, where the sample moves through channels, here we use our ability to shape the acoustic fields in a frequency-dependent manner to provide different analytical functions. The methods also provide a clear route toward the integration of PCR to detect pathogens in a single handheld system.