Determination of detection and quantification limits for SNP allele frequency estimation in DNA pools using real time PCR

Improvement and application of qPCR assay revealed new insight on early warning of Phaeocystis globosa bloom

Phaeocystis globosa bloom develops from its early solitary cells, providing clues for early warning of its bloom and timely responding to possible consequences. However, the early prediction requires quantification of the solitary cells for a thorough understanding of bloom formation. Therefore, we developed an accurate, sensitive, and specific qPCR assay for this need. Results show that the accuracy of qPCR was significantly enhanced by ameliorating DNA barcode design, improving genomic DNA extraction, and introducing a strategy of internal amplification control (IAC). This approach reached a quantification limit of 1 cell/reaction, making low-abundance cells (10¹-10³ cells/L) detection possible, and we also observed a plunge in the abundance of the solitary cells before the bloom outbreak in two winters in 2019 and 2020 for the first time, which is quite unique from laboratory results showing an increase instead. The plunge in solitary-cell abundance might be associated with the attachment of solitary cells to solid matrices to form non-solitary attached aggregate, the precursor of colonies, which gains supports from other studies and needs more investigations in the future. Therefore, as the plunge in solitary-cell abundance is a sign of colony formation, it can be used as an early warning indicator to P. globosa bloom.

Quantitative RT-PCR Assays for Quantification of Undesirable Mutants in the Novel Type 2 Oral Poliovirus Vaccine

Emergence of mutations is an inherent property of RNA viruses with several implications for their replication, pathogenesis, and evolutionary adaptation. Oral poliovirus vaccine (OPV), developed by Albert Sabin, is composed of live attenuated polioviruses of three serotypes that can revert to neurovirulence during replication in cell culture and in vaccine recipients. Recently, a new modified variant of Sabin 2 virus was developed by introducing changes in its genome, making it more genetically stable to prevent the reversion. The new strain was used to manufacture novel OPV2 (nOPV2), which was approved by the World Health Organization for emergency use to stop outbreaks caused by circulating vaccine-derived poliovirus (cVDPV2). Manufacture of this improved vaccine requires close attention to the genetic heterogenicity to ensure that the levels of the undesirable mutations are limited. Preliminary studies using whole-genome Illumina sequencing (NGS) identified several genomic sites where mutations tend to occur with regularity. They include VP1-I₁₄₃T amino acid change at the secondary attenuation site; VP1-N₁₇₁D, a substitution that modestly increases neurovirulence in mice; and VP1-E₂₉₅K, which may reduce the immunogenicity of the nOPV2. Therefore, to ensure the molecular consistency of vaccine batches, the content of these mutants must be quantified and kept within specifications. To do this, we have developed quantitative, multiplex, one-step reverse-transcriptase polymerase chain reactions (qmosRT-PCRs) as simple methods for quantification of these mutations. Each method uses specific short TaqMan probes with different dyes for the analysis of both mutants and non-mutants in the same sample. The quantification is done using calibration curves developed using validated reference materials. To evaluate the sensitivity and the linearity of the qmosRT-PCR method, the mutant viruses were spiked in non-mutant viruses, and nOPV2 batches were used to validate the method. The spiked samples and the nOPV2 batches were analyzed by qmosRT-PCR and NGS assays. The results showed that qmosRT-PCR is sensitive enough to detect around 1% of mutants. The percentages of mutants determined by qmosRT-PCR correlate well with the results of the NGS. Further, the analysis of the nOPV2 batches showed that the results of qmosRT-PCR correlated well with the results of NGS. In conclusion, the qmosRT-PCR is a specific, sensitive, and linear method. It could be used for quality control of the nOPV2 batches.

Integrated Microfluidic System for Cell-Free DNA Extraction from Plasma for Mutant Gene Detection and Quantification

Ovarian cancer (OvCa) is among the most severe gynecologic cancers, yet individuals may be asymptomatic during its early stages. Routine, early screening for genetic abnormalities associated with OvCa could improve prognoses, and this can be achieved by detecting mutant genes in cell-free DNA (cfDNA). Herein, we developed an integrated microfluidic chip (IMC) that could extract cfDNA from plasma and automatically detect and quantify mutations in the OvCa biomarker BRCA1. The cfDNA extraction module relied on a vortex-type micromixer to mix cfDNA with magnetic beads surface-coated with cfDNA probes and could isolate 76% of molecules from a 200 μL plasma sample in 45 min. The cfDNA quantification module, which comprised a micropump that evenly distributed 4.5 μL of purified cfDNA into the on-chip, allele-specific quantitative polymerase chain reaction (qPCR) zones, was capable of quantifying mutant genes within 90 min. By automating the cfDNA extraction and qPCR processes, this IMC could be used for clinical screening for OvCa-associated mutations.

A digital coding combination analysis for mutational genotyping using pyrosequencing

In the present study, we developed a novel digital coding combination analysis (DCCA) to analyze the gene mutation based on the sample combination principle. The principle is that any numerically named sample is divided into two groups, any two samples are not grouped in the same two groups, and any sample can be tested within the detection limit. Therefore, we proposed a specific combination that N samples were divided into M groups. Then N samples were analyzed, which could obtain the mutation results of M mixed groups. If only two groups showed positive (mutant type) signals, the same sample number from two positive signal groups would be the positive sample, and the remaining samples were negative (wild type). If three groups or more exhibited positive results, the same sample number from three positive signal groups would be the positive sample. If some samples remained uncertain, individual samples could be analyzed on a small scale. In the present study, we used the two genotypes of a mutation site (A5301G) to verify whether it was a useful and promising method. The results showed that we could quantitatively detect mutations and demonstrate 100% consistent results against a panel of defined mixtures with the detection limit using pyrosequencing. This method was suitable, sensitive, and reproducible for screening and analyzing low-frequency mutation samples, which could reduce reagent consumption and cost by approximately 70-80% compared with conventional clinical methods.

Fungicide Resistance Evolution and Detection in Plant Pathogens: Plasmopara viticola as a Case Study

The use of single-site fungicides to control plant pathogens in the agroecosystem can be associated with an increased selection of resistance. The evolution of resistance represents one of the biggest challenges in disease control. In vineyards, frequent applications of fungicides are carried out every season for multiple years. The agronomic risk of developing fungicide resistance is, therefore, high. Plasmopara viticola, the causal agent of grapevine downy mildew, is a high risk pathogen associated with the development of fungicide resistance. P. viticola has developed resistance to most of the fungicide classes used and constitutes one of the most important threats for grapevine production. The goals of this review are to describe fungicide resistance evolution in P. viticola populations and how to conduct proper monitoring activities. Different methods have been developed for phenotyping and genotyping P. viticola for fungicide resistance and the different phases of resistance evolution and life cycles of the pathogen are discussed, to provide a full monitoring toolkit to limit the spread of resistance. A detailed revision of the available tools will help in shaping and harmonizing the monitoring activities between countries and organizations.

The Role of the Liquid Biopsy in Decision-Making for Patients with Non-Small Cell Lung Cancer

Liquid biopsy is a rapidly emerging tool of precision oncology enabling minimally invasive molecular diagnostics and longitudinal monitoring of treatment response. For the clinical management of advanced stage lung cancer patients, detection and quantification of circulating tumor DNA (ctDNA) is now widely adopted into clinical practice. Still, interpretation of results and validation of ctDNA-based treatment decisions remain challenging. We report here our experience implementing liquid biopsies into the clinical management of lung cancer. We discuss advantages and limitations of distinct ctDNA assay techniques and highlight our approach to the analysis of recurrent molecular alterations found in lung cancer. Moreover, we report three exemplary clinical cases illustrating the complexity of interpreting liquid biopsy results in clinical practice. These cases underscore the potential and current limitations of liquid biopsy, focusing on the difficulty of interpreting discordant findings. In our view, despite all current limitations, the analysis of ctDNA in lung cancer patients is an essential and highly versatile complementary diagnostic tool for the clinical management of lung cancer patients in the era of precision oncology.

Next-Generation Sequencing in High-Sensitive Detection of Mutations in Tumors: Challenges, Advances, and Applications

Next-generation sequencing (NGS) technologies have come of age as preferred technologies for screening of genomic variants of pathologic and therapeutic potential. Because of their capability for high-throughput and massively parallel sequencing, they can screen for a variety of genomic changes in multiple samples simultaneously. This has made them platforms of choice for clinical testing of solid tumors and hematological malignancies. Consequently, they are increasingly replacing conventional technologies, such as Sanger sequencing and pyrosequencing, expression arrays, real-time PCR, and fluorescence in situ hybridization methods, for routine molecular testing of tumors. However, one limitation of routinely used NGS technologies is the inability to detect low-level genomic variants with high accuracy. This can be attributed to the frequent occurrence of low-level sequencing errors and artifacts in NGS workflow that need specialized approaches to be identified and eliminated. This review focuses on the origins and nature of these artifacts and recent improvements in the NGS technologies to overcome them to facilitate accurate high-sensitive detection of low-level mutations. Potential applications of high-sensitive NGS in oncology and comparisons with non-NGS technologies of similar capabilities are also summarized.

Surface Enhanced CdSe/ZnS QD/SiNP Electrochemical Immunosensor for the Detection of Mycobacterium Tuberculosis by Combination of CFP10-ESAT6 for Better Diagnostic Specificity

In this study, an electrochemical immunosensor was introduced for the detection of tuberculosis (TB) via utilization of a modified electrode containing a quantum dot (CdSe/ZnS QD) and functionalized silica nanoparticles (SiNPs) on screen-printed carbon electrode (SPCE) CdSe/ZnS QD/SiNPs/SPCE, by employing indirect enzyme-linked immunosorbent assay (ELISA). Here, the fabricated electrode was linked to the biocatalytic action of enzyme catalase through antigen–antibody binding for the detection of the antigen (CFP10–ESAT6) by means of producing a differential pulse voltammetry (DPV) current. The characterization and cyclic voltammetry (CV) of the modified electrode showed good electrochemical behavior and enhanced high electron transfer between the electrode and analyte. Moreover, the active surface area was 4.14-fold higher than the bare SPCE. The developed method showed high selectivity towards CFP10–ESAT6 compared with the other TB proteins. The detection of CFP10–ESAT6 also showed a linear response towards different concentrations of CFP10–ESAT6 with R² = 0.9937, yielding a limit of detection (LOD) of as low as 1.5 × 10⁻¹⁰ g/mL for a linear range of 40 to 100 ng/mL of CFP10–ESAT6 concentration. The proposed method showed good reproducibility of target analyte with a relative standard deviation of 1.45%.

Quantification of HIV-2 DNA in Whole Blood

Time to AIDS infection is longer with HIV-2, compared to HIV-1, but without antiretroviral therapy both infections will cause AIDS-related mortality. In HIV-2 infection, monitoring of antiretroviral treatment (ART) efficacy is challenging since a large proportion of HIV-2-infected individuals displays low or undetectable plasma RNA levels. Hence, quantification of cellular DNA load may constitute an alternative method for monitoring ART efficacy. Moreover, sensitive HIV-2 DNA quantification protocols are also important for the characterization of the HIV-2 reservoirs, and ultimately for the development of HIV-2 cure strategies. We have developed a sensitive and robust HIV-2 DNA quantification protocol based on whole blood as DNA source, including normalization of leukocyte cell numbers using parallel quantification of the single copy porphobilinogen deaminase gene. The specificity and sensitivity of the assay was 100%. The limit of detection was 1 copy and limit of quantification was 5 copies. When applying this protocol to HIV-2 infected, it was found that HIV-2 viral DNA was detectable in individuals in whom viral RNA was undetectable or under quantification level. Thus, this method provides a sensitive approach to HIV-2 DNA viral quantification from whole blood of HIV-2 infected patients.

Distribution pattern and health risk assessment of polycyclic aromatic hydrocarbons in the water and sediment of Algoa Bay, South Africa

Polycyclic aromatic hydrocarbons are amongst the pollutants of major concern in the terrestrial and aquatic habitats. They are mostly characterised by carcinogenic and non-carcinogenic effects. Distribution and potential health risks of sixteen priority PAHs in the water and sediment samples collected between December 2015 and June 2016 from Algoa Bay, South Africa, were evaluated. Water and sediment samples collected were extracted with liquid-liquid and soxhlet extraction methods, respectively, and then cleaned up using glass column loaded with silica gel. Final concentrations of the target PAHs were determined by gas chromatography interfaced with flame ionization detector. Results indicated that individual PAH concentrations in surface water, bottom water and sediment samples ranged from not detected (ND) to 24.66 µg/L, ND to 22.81 µg/L and ND to 5.23 mg/kg correspondingly. Total PAHs concentrations varied as 12.78-78.94 µg/L, 1.20-90.51 µg/L and 1.17-10.47 mg/kg in the three environmental matrices in that order. The non-carcinogenic risk was generally below 1, whereas risk indices (dermal contact) were above the acceptable limit of 1 × 10^-4 in the water column, suggesting possible carcinogenic effects to humans, with adults being the most vulnerable. Similarly, highest contributions to TEQs and MEQs in the sediments were made by benzo(a)pyrene and dibenzo(a,h)anthracene, the two most toxic congeners, signifying the possibility of carcinogenicity and mutagenicity in humans. Diagnostic ratios of PAHs reflect a prevailing pyrogenic input all through. The pollution was albeit moderate, yet regular check is recommended to ensure safe and healthy environment for human and aquatic lives.

Detection of single nucleotide polymorphism by measuring extension kinetics with T7 exonuclease mediated isothermal amplification

Kinetics based detection of single nucleotide polymorphism at room temperature with high sensitivity and specificity.

Petroleum Hydrocarbon Fingerprints of Water and Sediment Samples of Buffalo River Estuary in the Eastern Cape Province, South Africa

Petroleum hydrocarbon status of the Buffalo River Estuary in East London, South Africa, was evaluated from January to May, 2016. Surface water and sediment samples were collected from five points in the estuary and extracted using standard methods. The extracts were subsequently analyzed by gas chromatography-flame ionization detection. Results showed that total petroleum hydrocarbon (TPH) varied from 7.65 to 477 μg/L in the water and 12.59 to 1,100 mg/kg in the sediments, with mean values of 146.50 ± 27.96 μg/L and 209.81 ± 63.82 mg/kg, respectively. Concentrations of TPH in the sediments correlated significantly with organic carbon (OC) in both seasons. TPH and OC levels were slightly lower in summer than in autumn in the two environmental matrices, and the average amount of TPH in the water samples collected from all the sampling stations was generally lower than the EU standard limit of 300 μg/L. However, the levels in the sediments exceeded the EGASPIN target value (50 mg/kg) for mineral oil but were below the intervention value (5,000 mg/kg), indicating a serious impact of industrial growth and urbanization on the area, although the n-alkane ratios and indexes used for source tracking revealed excessive flow from both natural and anthropogenic sources.

Analytical Validation of Quantitative Real-Time PCR Methods for Quantification of Trypanosoma cruzi DNA in Blood Samples from Chagas Disease Patients

An international study was performed by 26 experienced PCR laboratories from 14 countries to assess the performance of duplex quantitative real-time PCR (qPCR) strategies on the basis of TaqMan probes for detection and quantification of parasitic loads in peripheral blood samples from Chagas disease patients. Two methods were studied: Satellite DNA (SatDNA) qPCR and kinetoplastid DNA (kDNA) qPCR. Both methods included an internal amplification control. Reportable range, analytical sensitivity, limits of detection and quantification, and precision were estimated according to international guidelines. In addition, inclusivity and exclusivity were estimated with DNA from stocks representing the different Trypanosoma cruzi discrete typing units and Trypanosoma rangeli and Leishmania spp. Both methods were challenged against 156 blood samples provided by the participant laboratories, including samples from acute and chronic patients with varied clinical findings, infected by oral route or vectorial transmission. kDNA qPCR showed better analytical sensitivity than SatDNA qPCR with limits of detection of 0.23 and 0.70 parasite equivalents/mL, respectively. Analyses of clinical samples revealed a high concordance in terms of sensitivity and parasitic loads determined by both SatDNA and kDNA qPCRs. This effort is a major step toward international validation of qPCR methods for the quantification of T. cruzi DNA in human blood samples, aiming to provide an accurate surrogate biomarker for diagnosis and treatment monitoring for patients with Chagas disease.

Positive effect of reduced aeration rate on growth and stereospecificity of DL-malic acid consumption by Azospirillum brasilense: improving the shelf life of a liquid inoculant formulation

Azospirillum brasilense has significance as a growth promoter in plants of commercial interest. Two industrial native strains (Start and Calf), used as a part of an inoculant formulation in Mexico during the last 15 years, were incubated in laboratory-scale pneumatic bioreactors at different aeration rates. In both strains, the positive effect of decreased aeration was observed. At the lowest (0.1 vvm, air volume/liquid volume×minute), the highest biomass were obtained for Calf (7.8 × 10(10)CFU/ml), and Start (2.9 × 10(9)CFU/ml). These were higher in one magnitude order compared to cultures carried out at 0.5 vvm, and two compared to those at 1.0 vvm. At lower aeration, both stereoisomeric forms of malic acid were consumed, but at higher aeration, just L-malate was consumed. A reduction in aeration allows an increase of the shelf life and the microorganism saved higher concentrations of polyhydroxybutyrate. The selected fermentation conditions are closely related to those prevalent in large-scale bioreactors and offer the possibility of achieving high biomass titles with high shelf life at a reduced costs, due to the complete use of a carbon source at low aeration of a low cost raw material as DL-malic acid mixture in comparison with the L-malic acid stereoisomer.

Allele-specific PCR for quantitative analysis of mutants in live viral vaccines

Monitoring consistency of genetic composition of oral polio vaccine (OPV) is a part of its quality control. It is performed by mutant analysis by PCR and restriction enzyme cleavage (MAPREC) used to quantify neurovirulent revertants in the viral genome. Here an alternative method based on quantitative PCR is proposed. Allele-specific quantitative polymerase chain reaction (asqPCR) uses a "tethered" oligonucleotide primer consisting of two specific parts connected by a polyinosine stretch. Homogeneous DNA from plasmids containing wild Leon/37 and attenuated Sabin 3 sequences with 100% 472(C) and 100% 472(T) could only be amplified using homologous primers. Real-time implementation of the allele-specific PCR resulted in sensitive detection of 472(C) revertants with the limit of quantitation of less than 0.05%. Monovalent vaccine batches and international viral references for MAPREC test were used to validate the method. asqPCR performed with the WHO references and monovalent batches of vaccine showed that the new method could measure accurately and reproducibly the content of revertants producing values comparable to MAPREC results. This suggests that asqPCR could be used as an alternative to MAPREC for lot release of OPV. The method could also be used for the quantitation of other mutants in populations of microorganisms.

Development of a multiplex allele-specific primer PCR assay for simultaneous detection of QoI and CAA fungicide resistance alleles in Plasmopara viticola populations

BACKGROUND

DNA-based diagnosis has become a common tool for the evaluation of fungicide resistance in obligate phytopathogenic fungus Plasmopara viticola.

RESULTS

A multiplex allele-specific primer PCR assay has been developed for the rapid detection of fungicide resistance in P. viticola populations. With this assay, a glycine-to-alanine substitution at codon 143 of the P. viticola cytochrome b gene, which conferred QoI fungicide resistance, and a glycine-to-serine substitution at codon 1105 of the P. viticola cellulose synthase gene PvCesA3, which conferred CAA fungicide resistance, were detected simultaneously.

CONCLUSION

It is suggested that the present assay is a reliable tool for the rapid and simultaneous detection of QoI and CAA fungicide resistance alleles in P. viticola populations. The assay required only 2 h from the sampling of symptoms to the detection of resistance alleles to both fungicides.

Integrated genomic analysis of sézary syndrome

Sézary syndrome (SS) is a rare variant of primary cutaneous T-cell lymphoma. Little is known about the underlying pathogenesis of S. To address this issue, we used Affymetrix 10K SNP microarray to analyse 13 DNA samples isolated from 8 SS patients and qPCR with ABI TaqMan SNP genotyping assays for the validation of the SNP microarray results. In addition, we tested the impact of SNP loss of heterozygosity (LOH) identified in SS cases on the gene expression profiles of SS cases detected with Affymetrix GeneChip U133A. The results showed: (1) frequent SNP copy number change and LOH involving 1, 2p, 3, 4q, 5q, 6, 7p, 8, 9, 10, 11, 12q, 13, 14, 16q, 17, and 20, (2) reduced SNP copy number at FAT gene (4q35) in 75% of SS cases, and (3) the separation of all SS cases from normal control samples by SNP LOH gene clusters at chromosome regions of 9q31q34, 10p11q26, and 13q11q12. These findings provide some intriguing information for our current understanding of the molecular pathogenesis of this tumour and suggest the possibility of presence of functional SNP LOH in SS tumour cells.

Glycosylation and post-translational modification gene expression analysis by DNA microarrays for cultured mammalian cells

DNA microarray analysis of gene expression has become a valuable tool for bioprocessing research aimed at improving therapeutic protein yields. The highly parallel nature of DNA microarray technology allows researchers to assess hundreds of gene simultaneously, essentially enabling genome-wide snapshots. The quality and amount of therapeutic proteins produced by cultured mammalian cells rely heavily on the culture environment. In order to implement beneficial changes to the culture environment, a better understanding of the relationship between the product quality and culture environment must be developed. By analyzing gene expression levels under various environmental conditions, light can be shed on the underlying mechanisms. This paper describes a method for evaluating gene expression changes for cultured NS0 cells, a mouse-derived myeloma cell line, under culture environment conditions, such as ammonia buildup, known to affect product quality. These procedures can be easily adapted to other environmental conditions and any mammalian cell lines cultured in suspension, so long as a sufficient number of gene sequences are publicly available.

Novel quantitative real-time LCR for the sensitive detection of SNP frequencies in pooled DNA: method development, evaluation and application

Background

Single nucleotide polymorphisms (SNP) have proven to be powerful genetic markers for genetic applications in medicine, life science and agriculture. A variety of methods exist for SNP detection but few can quantify SNP frequencies when the mutated DNA molecules correspond to a small fraction of the wild-type DNA. Furthermore, there is no generally accepted gold standard for SNP quantification, and, in general, currently applied methods give inconsistent results in selected cohorts. In the present study we sought to develop a novel method for accurate detection and quantification of SNP in DNA pooled samples.

Methods

The development and evaluation of a novel Ligase Chain Reaction (LCR) protocol that uses a DNA-specific fluorescent dye to allow quantitative real-time analysis is described. Different reaction components and thermocycling parameters affecting the efficiency and specificity of LCR were examined. Several protocols, including gap-LCR modifications, were evaluated using plasmid standard and genomic DNA pools. A protocol of choice was identified and applied for the quantification of a polymorphism at codon 136 of the ovine PRNP gene that is associated with susceptibility to a transmissible spongiform encephalopathy in sheep.

Conclusions

The real-time LCR protocol developed in the present study showed high sensitivity, accuracy, reproducibility and a wide dynamic range of SNP quantification in different DNA pools. The limits of detection and quantification of SNP frequencies were 0.085% and 0.35%, respectively.

Significance

The proposed real-time LCR protocol is applicable when sensitive detection and accurate quantification of low copy number mutations in DNA pools is needed. Examples include oncogenes and tumour suppressor genes, infectious diseases, pathogenic bacteria, fungal species, viral mutants, drug resistance resulting from point mutations, and genetically modified organisms in food.

Assessment of fungicide resistance and pathogen diversity in Erysiphe necator using quantitative real-time PCR assays

BACKGROUND

Management of grapevine powdery mildew Erysiphe necator Schw. requires fungicide treatments such as sterol demethylation inhibitors (DMIs) or mitochondrial inhibitors (QoIs). Recently, reduction in the efficacy of DMIs or QoIs was reported in Europe and the United States. The aim of the present study was to develop real-time qPCR tools to detect and quantify several CYP51 gene variants of E. necator: (i) A versus B groups (G37A) and (ii) sensitive versus resistant to sterol demethylase inhibitor fungicides (Y136F).

RESULTS

The efficacy of the qPCR tools developed was better than the CAPS method, with a limit of 2 pg for E necator DNA, 0.06 ng for genetic group A and 1.4 ng for the DMI-resistant allele. The detection limits of qPCR protocols (LOD) ranged from 0.72 to 0.85%, and the quantification limits (LOQ) ranged from 2.4 to 2.85% for the two alleles G47A and Y136F respectively. The application of qPCR to field isolates from French vineyards showed the presence of DMI-resistant and/or QoI-resistant alleles in French pathogen populations, linked to genetic group B.

CONCLUSION

The real-time PCR assay developed in this study provides a potentially useful tool for efficient quantification of different alleles of interest for fungicide monitoring and for population structure of E. necator.

A simple method using PyrosequencingTM to identify de novo SNPs in pooled DNA samples

A practical way to reduce the cost of surveying single-nucleotide polymorphism (SNP) in a large number of individuals is to measure the allele frequencies in pooled DNA samples. Pyrosequencing^TM has been frequently used for this application because signals generated by this approach are proportional to the amount of DNA templates. The Pyrosequencing^TM pyrogram is determined by the dispensing order of dNTPs, which is usually designed based on the known SNPs to avoid asynchronistic extensions of heterozygous sequences. Therefore, utilizing the pyrogram signals to identify de novo SNPs in DNA pools has never been undertook. Here, in this study we developed an algorithm to address this issue. With the sequence and pyrogram of the wild-type allele known in advance, we could use the pyrogram obtained from the pooled DNA sample to predict the sequence of the unknown mutant allele (de novo SNP) and estimate its allele frequency. Both computational simulation and experimental Pyrosequencing^TM test results suggested that our method performs well. The web interface of our method is available at http://life.nctu.edu.tw/∼yslin/PSM/.

Kinetic effects on signal normalization in oligonucleotide microchips with labeled immobilized probes

Among various factors affecting operation of oligonucleotide microchips, the variations in concentration and in homogeneous distribution of immobilized probes over the cells are one of the most important. The labeling of immobilized probes ensures the complete current monitoring on the probe distribution and is reliable and convenient. Using hydrogel-based oligonucleotide microchips, the applicability of Cy3-labeled immobilized probes for quality control and signal normalization after hybridization with Cy5-labeled target DNA was investigated. This study showed that proper signal normalization should be different in thermodynamic conditions and in transient regime with hybridization far from saturation. This kinetic effect holds for both hydrogel-based and surface oligonucleotide microchips. Besides proving basic features, the technique was assessed on a sampling batch of 50 microchips developed for identifying mutations responsible for rifampicin and isoniazid resistance of Mycobacterium tuberculosis.

Detection and quantification of genetically modified organisms using very short, locked nucleic acid TaqMan probes

Many countries have introduced mandatory labeling requirements on foods derived from genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (PCR) based upon the TaqMan probe chemistry has become the method mostly used to support these regulations; moreover, event-specific PCR is the preferred method in GMO detection because of its high specificity based on the flanking sequence of the exogenous integrant. The aim of this study was to evaluate the use of very short (eight-nucleotide long), locked nucleic acid (LNA) TaqMan probes in 5'-nuclease PCR assays for the detection and quantification of GMOs. Classic TaqMan and LNA TaqMan probes were compared for the analysis of the maize MON810 transgene. The performance of the two types of probes was tested on the maize endogenous reference gene hmga, the CaMV 35S promoter, and the hsp70/cryIA(b) construct as well as for the event-specific 5'-integration junction of MON810, using plasmids as standard reference molecules. The results of our study demonstrate that the LNA 5'-nuclease PCR assays represent a valid and reliable analytical system for the detection and quantification of transgenes. Application of very short LNA TaqMan probes to GMO quantification can simplify the design of 5'-nuclease assays.

SNP, ARMS and SSH authentication of medicinal Dendrobium officinale KIMURA et MIGO and application for identification of Fengdou drugs

Dried stems of Dendrobium officinale have been used as crude drugs in traditional Chinese medicine (TCM) with good tonic efficacy. Sequences of chloroplast, nuclear and mitochondria genes and the method of genomic DNA (gDNA) suppression subtraction hybridization (SSH) were used to authenticate different populations during the process of good agriculture practice (GAP) and crude drug quality control. Six populations could be authenticated successfully by nine single sucleotide polymorphism (SNP) sites and six pairs of diagnostic primers for amplification refractory mutation system (ARMS) were also designed to identify six populations on the basis of single nucleotide polymorphism (SNPs). The remainder two populations (JSR, GGL) with the same sequences could be authenticated by SSH. One population-specific fragment was obtained by SSH and a pair of specific primers (SSH-JB01, SSH-JB02) on the specific sequence was designed to authenticate GGL population from the other populations tested. As the resultants were population-specific, the botanic origins of fifty "Fengdou" drug samples from markets could be classified. It is evident that the combined methods provide a high throughput and reliable approach for identification of D. officinale plants and "Fengdou" drugs.

Expression of two recombinant chloramphenicol acetyltransferase variants in highly reduced genome Escherichia coli strains

Highly reduced E. coli strains, MDS40, MDS41, and MDS42, lacking approximately 15% of the genome, were grown to high cell densities to test their ability to produce a recombinant protein with high yields. These strains lack all transposons and insertion sequences, cryptic prophage and many genes of unknown function. In addition to improving genetic stability, these deletions may reduce the biosynthetic requirements of the cell potentially allowing more efficient production of recombinant protein. Basic growth parameters and the ability of the strains to produce chloramphenicol acetyltransferase (CAT) under high cell density, batch cultivation were assessed. Although growth rate and recombinant protein production of the reduced genome strains are comparable to the parental MG1655 strain, the reduced genome strains were found to accumulate significant amounts of acetate in the medium at the expense of additional biomass. A number of hypotheses were examined to explain the accumulation of acetate, including oxygen limitation, carbon flux imbalance, and metabolic activity of the recombinant protein. Use of a non-catalytic CAT variant identified the recombinant protein activity as the source of this phenomenon; implications for the metabolic efficiency of the reduced genome strains are discussed.

Molecular quantitative analysis of human viruses in California stormwater

Many human pathogenic viruses are transmitted via the oral-fecal route and water is one possible vector, representing a risk for public health. Sixty-one large-volume water samples from storm drains in California were processed by a two-step hollow fiber ultrafiltration procedure followed by molecular analysis for human enterovirus and adenovirus types. Each sample was spiked with a surrogate, the benign bacteriophage PP7. Both surrogate and human viruses were quantified by newly designed TaqMan PCR assays. Equations were developed that account for the main variables in the procedure: recovery of the ultrafiltration, efficiency of nucleic acid extraction, and effect of inhibitors on the amplification of viral targets. Adenovirus 40/41 was detected in one sample at 230 genomes per liter, and no other adenovirus or enterovirus types were found. Samples that resulted in nondetects are reported together with the corresponding sample-specific limit of detection (S(LOD)), a useful tool when estimating the public health risk associated with the contact or ingestion of water. Virus concentrations did not correlate with traditional viable indicator concentrations or any of the physicochemical parameters measured. In contrast, coliform concentrations were correlated with total suspended solids. To our knowledge, this is the first study where all factors known to influence limits of detection have been investigated and integrated into equations that are widely applicable to the quantification of viruses or other microbial targets by PCR.

Electrochemical quantification of single-nucleotide polymorphisms using nanoparticle probes

We report a new approach for electrochemical quantification of single-nucleotide polymorphisms (SNPs) using nanoparticle probes. The principle is based on DNA polymerase I (Klenow fragment)-induced coupling of the nucleotide-modified nanoparticle probe to the mutant sites of duplex DNA under the Watson-Crick base pairing rule. After liquid hybridization events occurred among biotinylated DNA probes, mutant DNA, and complementary DNA, the resulting duplex DNA helixes were captured to the surface of magnetic beads through a biotin-avidin affinity reaction and magnetic separation. A cadmium phosphate-loaded apoferritin nanoparticle probe, which is modified with nucleotides and is complementary to the mutant site, is coupled to the mutant sites of the formed duplex DNA in the presence of DNA polymerase. Subsequent electrochemical stripping analysis of the cadmium component of coupled nanoparticle probes provides a means to quantify the concentration of mutant DNA. The method is sensitive enough to detect 21.5 attomol of mutant DNA, which will enable the quantitative analysis of nucleic acid without polymerase chain reaction preamplification. The approach was challenged with constructed samples containing mutant and complementary DNA. The results indicated that it was possible to accurately determine SNPs with frequencies as low 0.01. The proposed approach has a great potential for realizing an accurate, sensitive, rapid, and low-cost method of SNP detection.

Validation of a real-time PCR for the quantitative estimation of a G143A mutation in the cytochrome bc1 gene of Pyrenophora teres

A single nucleotide polymorphism (SNP) in the cytochrome b gene confers resistance to strobilurin fungicides for several fungal pathogens. Therefore, on the basis of a change at amino acid position 143 from glycine to alanine, a real-time PCR assay was established for the quantitative detection of the analogous SNP in the cytochrome b sequence of Pyrenophora teres Drechsler, which causes barley net blotch. Allelic discrimination was achieved by using allele specific primers with artificially mismatched nucleic acid bases and minor groove binding probes. Validation parameters for the lower limits of the working range, namely limits of detection (LOD) and limits of quantification (LOQ), were statistically determined by the variance of calibration data, as well as by the variance of the 100% non-strobilurin-resistant allele DNA sample (blank values). It was found that the detection was limited by the variance of blank values (five in 801 458 copies; 0.0006%), whereas the quantification was limited by the variance of calibration data (37 in 801 458 copies; 0.0046%). The real-time PCR assay was finally used to monitor strobilurin-resistant cytochrome b alleles in barley net blotch field samples, which were already classified in in vivo biotests to be fully sensitive to strobilurins. All signals for strobilurin-resistant cytochrome b alleles were below the LOD, and therefore the results are in total agreement with the phenotypes revealed by biotests.

Virulence factor activity relationships: challenges and development approaches

Virulence factor activity relationships (VFAR) is a predictive approach proposed by the National Research Council's Committee on Drinking Water Contaminants (Washington, D.C.) to classify and rank waterborne pathogens. It is based on the presumption that health threats of waterborne pathogens can be predicted from descriptors at different levels of cellular organization. This paper summarizes challenges that need to be addressed while developing VFAR, with a focus on genomics, such as genomic variability among related pathogens and the need to incorporate genetic descriptors for persistence and host susceptibility. Three key components of VFAR development and validation are also presented, including (1) compilation of a comprehensive VFAR database, (2) development of predictive mathematical models relating descriptors to health effects and other microbial responses, and (3) high-throughput molecular monitoring of drinking water supplies and sources. Bayesian approach and on-chip polymerase chain reaction are discussed as examples of mathematical models and molecular monitoring.

Assessment of QoI resistance in Plasmopara viticola oospores

QoI fungicides, inhibitors of mitochondrial respiration at the Qo site of cytochrome b in the mitochondrial bc(1) enzyme complex, are commonly applied in vineyards against Plasmopara viticola (Berk. & MA Curtis) Berl. & De Toni. Numerous treatments per year with QoI fungicides can lead to the selection of resistant strains in the pathogen population owing to the very specific and efficient mode of action. In order to evaluate the resistance risk and its development, two different methods, biological and molecular, were applied to measure the sensitivity of oospores differentiated in vineyards, both treated and untreated with azoxystrobin, from 2000 to 2004. Assays using oospores have the advantage of analysing the sensitivity of bulked samples randomly collected in vineyards, describing accurately the status of resistance at the end of the grapevine growing season. Both methods correlated well in describing the resistance situation in vineyards. QoI resistance was not observed in one vineyard never treated with QoI fungicides. In the vineyard where azoxystrobin had been used in mixture with folpet, the selection of QoI-resistant strains was lower, compared with using solely QoI. In vineyards where QoI treatments have been stopped, a decrease in resistance was generally observed.

Real-time quantitative PCR assays for quantification of L1781 ACCase inhibitor resistance allele in leaf and seed pools of Lolium populations

The I1781L amino acid substitution in the target ACCase enzyme causes broad resistance to ACCase inhibitor herbicides in several monocotyledenous weeds of agronomic importance. This mutation results from a substitution of an adenine (A) residue by either a thymine (T) or cytosine (C) at position 5341 in Alopecurus myosuroides Huds and at an equivalent position in Lolium species, Avena fatua L. and Setaria viridis (L.) Beauv. Two different procedures, the PCR-based allele-specific assay (ASA) and the derived cleaved amplified polymorphic sequence (dCAPS) method, have previously been described for detecting this mutation. These methods are, however, only amenable to low sample throughput and are used in the analysis of single plants. Here, an alternative high-throughput ARMS/Scorpion real-time quantitative PCR (Q-PCR) method for measuring levels of the I1781L mutation in pools of leaf and seed samples of Lolium populations is presented. The limit of detection for C and T mutant alleles in a background of wild-type A is 0.02 and 0.0003% respectively. In this study, DNA from batches of 24 leaf segments measuring 0.5 cm from different plants or 1000 seeds could be conveniently extracted and accurately analysed. As part of assay validation, the comparative analysis of five geographically distinct Lolium populations with dCAPS and Q-PCR procedures demonstrated the accuracy of the latter method, and the three possible II1781, IL1781 and LL1781 ACCase genotypes being distributed as predicted by the Hardy-Weinberg principle. Given the dominance of the L1781 over the I1781 allele at recommended field rates for most ACCase inhibitors, the frequency of herbicide survivors in the field owing only to the presence of the I1781L mutation is thus predicted to be 2pq + q(2), where p and q are the frequencies of the I1781 and L1781 alleles as determined by Q-PCR. The Q-PCR assay established allows detection of very low levels of the L1781 ACCase mutation before resistance would normally be discernible in the field. Therefore, it offers the opportunity to tackle resistance at its very onset, potentially avoiding implementation of complicated and often costly weed management practices.

Different real time PCR approaches for the fine quantification of SNP's alleles in DNA pools: assays development, characterization and pre-validation

Single nucleotide polymorphisms (SNPs) are becoming the most common type of markers used in genetic analysis. In the present report a SNP has been chosen to test the applicability of Real Time PCR to discriminate and quantify SNPs alleles on DNA pools. Amplification Refractory Mutation System (ARMS) and Mismatch Amplification Mutation Assay (MAMA) has been applied. Each assay has been pre-validated testing specificity and performances (linearity, PCR efficiency, interference limit, limit of detection, limit of quantification, precision and accuracy). Both the approaches achieve a precise and accurate estimation of the allele frequencies on pooled DNA samples in the range from 5 % to 95 % and don't require standard curves or calibrators. The lowest measurement that could be significantly distinguished from the background noise has been determined around the 1 % for both the approaches, allowing to extend the range of quantifications from 1 % to 99 %. Furthermore applicability of Real Time PCR assays for general diagnostic purposes is discussed.

Dual-probe assay for detection of lamivudine-resistance hepatitis B virus by real-time PCR

A rapid and accurate minor groove binder (MGB) real-time PCR is described for detection lamivudine resistance mutations in hepatitis B virus. The real-time PCR was compared with direct Sanger sequencing in 53 clinical patients samples, the results of the real-time PCR correlate with the nucleotide sequence and the assay has the advantage of detecting a mixture of quasi-species with higher sensitivity than sequencing. As a simple, easy, rapid, accurate and high throughout method, MGB real-time PCR assay should be useful for detecting lamivudine resistance variants during lamivudine therapy in clinical settings.

Haplotyping by capillary electrophoresis

The investigation of the genetic background and phenotype structures of complex diseases, such as cardiovascular or psychiatric disorders and tumors, is one of the most scrutinized fields of the post genomic era. Besides the multiplex analysis of genetic markers and polymorphisms throughout the whole genome, more and more attention is focused on the interaction between the etiological factors of these traits. Haplotype determination, rather than multiplex genotyping seems to be one of the first building blocks of this endeavor. This review focuses on the importance and theoretical background of haplotyping, and summarizes the recent examples of novel and emerging haplotyping techniques by capillary gel electrophoresis based DNA fragment analysis, a powerful tool for the examination of the inheritance of complex traits.

Using cDNA and genomic sequences as tools to develop SNP strategies in cassava (Manihot esculenta Crantz)

Single nucleotide polymorphisms (SNP) are the most abundant type of DNA polymorphism found in animal and plant genomes. They provide an important new source of molecular markers that are useful in genetic mapping, map-based positional cloning, quantitative trait locus mapping and the assessment of genetic distances between individuals. Very little is known on the frequency of SNPs in cassava. We have exploited the recently-developed collection of cassava expressed sequence tags (ESTs) to detect SNPs in the five cultivars of cassava used to generate the sequences. The frequency of intra-cultivar and inter-cultivar SNPs after analysis of 111 contigs was one polymorphism per 905 and one per 1,032 bp, respectively; totaling 1 each 509 bp. We have obtained further information on the frequency of SNPs in six cassava cultivars by analysis of 33 amplicons obtained from 3' EST and BAC end sequences. Overall, about 11 kb of DNA sequence was obtained for each cultivar. A total of 186 SNPs (136 and 50 from ESTs and BAC ends, respectively) were identified. Among these, 146 were intra-cultivar polymorphisms, while 80 were inter-cultivar polymorphisms. Thus the total frequency of SNPs was one per 62 bp. This information will help to develop new strategies for EST mapping as well as their association with phenotypic characteristics.