Advances in approaches to DNA-based diagnostics

Rapid and quantitative detection of Shiga toxin1 and Shiga toxin2 based on multiple targets UPT-LF assay

Shiga toxin-producing Escherichia coli (STEC) infection causes a series of diseases that are highly pathogenic and deadly in humans and animals, seriously endangering public health. Of the pathogenic factors within STEC, the two groups of Shiga toxin (Stx) consisting Stx1 and Stx2 plays a prominent role in the pathogenesis of STEC infection. In this study, we developed single-target up-converting phosphor technology-based lateral flow assay (Stx-UPT-LFA) for the rapid detection of Stx1 and Stx2, respectively, and also developed a dual-target Stx1/2-UPT-LFA based on single-target strips to detect of Stx1 and Stx2 at the meantime within 20 min. We choose the purified Stx1 and Stx2 standard samples, and the optimum monoclonal antibody (namely 8E7-E6, 2F6-F8 for Stx1 and S1D8, S2C4 for Stx2) were selected for use in Stx-UPT-LFA in double-antibody-sandwich mode. The sensitivities of single-target Stx-UPT-LFA for both Stx1 and Stx2 were 1 ng mL-1 with accurate quantitation ranges of 1-1000 ng mL-1 and 1-800 ng mL-1 respectively. No false-negative result was found in the Stx2-UPT-LFA even with a high-test concentration up to 1000 ng mL-1. Meanwhile, both targets detection sensitivities for dual-target Stx1/2-UPT-LFA were 5 ng mL-1, and accurate quantitation ranges were 5-1000 ng mL-1 and 5-800 ng mL-1 for standard Stx1 and Stx2 solutions without cross-interference between two targets. Both techniques showed good linearities, with a linear fitting coefficient of determination(r) of 0.9058-0.9918. Therefore, the UPT-LFA could realize simultaneous detection for multiple targets on a single strip and thus to quickly determine the type of infectious Stxs. In addition, the single-target Stx1-UPT-LFA and Stx2-UPT-LFA showed excellent specificity to six toxins, even at high concentrations of 1000 ng mL-1. In conclusion, the developed Stx-UPT-LFA allows the rapid, quantitative, reliable and simultaneous detection of Stx1 and Stx2 within 20 min, providing an alternative method for clinical diagnosis of STEC infection.

A SYBR Green based multiplex Real-Time PCR assay for rapid detection and differentiation of ocular bacterial pathogens

PURPOSE

Ocular bacterial pathogenesis is a serious sight threatening infection due to several bacterial species like Staphylococcus aureus, Streptococcus pneumoniae and Pseudomonas aeruginosa which are predominant. It is necessary to expedite diagnosis of pathogens for early treatment. Hence, a SYBR Green based multiplex Real-Time PCR assay coupled with melting curve analysis has been developed for rapid detection and differentiation of Staphylococcus aureus, Streptococcus pneumoniae and Pseudomonas aeruginosa in a single reaction.

METHODS

The assay was designed for simultaneous detection and differentiation of pathogens based on their distinct melting curve. The analytical specificity, sensitivity and reproducibility of the assay were examined using various reference strains. Clinical validation was carried out with 100 ocular samples collected from patients suffering from ocular infections.

RESULT

Each reaction tested for the targets individually generated three non overlapping melting curves with well alienated peaks corresponding to each gene. Among 100 ocular samples tested, 40 samples diagnosed with positive results in RT-PCR. Thus assay showed 100% specificity with high sensitivity and reproducibility.

CONCLUSION

The developed assay consistently established as a rapid and accurate diagnosis of ocular bacterial pathogens compared to the conventional laboratory techniques. Such precise method would aid greatly in clinical management of devastating ocular infections.

Rapid Detection and Identification of Uveitis Pathogens by Qualitative Multiplex Real-Time PCR

Purpose

Infectious uveitis is a serious sight-threatening infection commonly caused by herpesviruses and Toxoplasma gondii. Etiologic diagnosis based on the clinical evaluation is often challenging. We developed and validated a multiplex real-time PCR assay coupled with high-resolution melting (HRM) for rapid detection and identification of herpes simplex viruses 1 and 2 (HSV-1 and HSV-2), varicella-zoster virus (VZV), cytomegalovirus (CMV), and T. gondii.

Methods

The assay was designed to target pathogen genome regions that yield products with distinct melting temperatures. Analytical specificity, sensitivity, and precision of HRM identification were determined. Clinical validation was performed by testing 108 intraocular fluids collected from eyes suffering with infectious uveitis (n = 30) and controls (n = 78).

Results

A nonoverlapping high-precision profile for each pathogen was generated following HRM (coefficient of variation 0%). The assay was highly sensitive, with a limit of detection of 20 genome copies for herpesviruses and 200 genome copies for T. gondii. The intra- and interassay variability of cycle threshold (Ct) measurement was ≤4% and ≤6%, respectively. Thirteen intraocular specimens collected from suspected cases of infectious uveitis were positive (mean Ct values varied from 19.4 to 27.7). Melting profiles of positive cases were consistent with HSV-2 (n = 5), VZV (n = 5), CMV (n = 2), and T. gondii (n = 1). Amplicon identities were confirmed by sequencing. Control intraocular samples from patients without a clinical diagnosis of infectious uveitis were all negative.

Conclusions

This assay allows rapid, sensitive, and reliable detection and identification of the most common known causes of infectious uveitis, making early pathogen information-based intervention possible.

DNA Chips: The Future of Biomarkers

DNA chips are small, solid supports such as microscope slides onto which thousands of cDNAs or oligonucleotides are arrayed, representing known genes or simply EST clones, or covering the entire sequence of a gene with all its possible mutations. Fluorescently labeled DNA or RNA extracted from tissues is hybridized to the array. Laser scanning of the chip permits quantitative evaluation of each individual complementary sequence present in the sample.

DNA chip technology is currently being proposed for qualitative and quantitative applications, firstly for the detection of point mutations, small deletions and insertions in genes involved in human diseases or affected during cancer progression; secondly, to determine on a genome-wide basis the pattern of gene expression in tumors, as well as in a number of experimental situations.

The extraordinary power of DNA chips will have a strong impact on medicine in the near future, both in the molecular characterization of tumors and genetic diseases and in drug discovery and evaluation. Quantitative applications will soon spread through all fields of biology.

Droplet-Based Microfluidics Digital PCR for the Detection of KRAS Mutations

We demonstrate an accurate and sensitive quantification of mutated KRAS oncogene in genomic DNA, using droplet-based microfluidics and digital PCR.

Quantitative and sensitive detection of rare mutations using droplet-based microfluidics

Somatic mutations within tumoral DNA can be used as highly specific biomarkers to distinguish cancer cells from their normal counterparts. These DNA biomarkers are potentially useful for the diagnosis, prognosis, treatment and follow-up of patients. In order to have the required sensitivity and specificity to detect rare tumoral DNA in stool, blood, lymph and other patient samples, a simple, sensitive and quantitative procedure to measure the ratio of mutant to wild-type genes is required. However, techniques such as dual probe TaqMan(®) assays and pyrosequencing, while quantitative, cannot detect less than ∼1% mutant genes in a background of non-mutated DNA from normal cells. Here we describe a procedure allowing the highly sensitive detection of mutated DNA in a quantitative manner within complex mixtures of DNA. The method is based on using a droplet-based microfluidic system to perform digital PCR in millions of picolitre droplets. Genomic DNA (gDNA) is compartmentalized in droplets at a concentration of less than one genome equivalent per droplet together with two TaqMan(®) probes, one specific for the mutant and the other for the wild-type DNA, which generate green and red fluorescent signals, respectively. After thermocycling, the ratio of mutant to wild-type genes is determined by counting the ratio of green to red droplets. We demonstrate the accurate and sensitive quantification of mutated KRAS oncogene in gDNA. The technique enabled the determination of mutant allelic specific imbalance (MASI) in several cancer cell-lines and the precise quantification of a mutated KRAS gene in the presence of a 200,000-fold excess of unmutated KRAS genes. The sensitivity is only limited by the number of droplets analyzed. Furthermore, by one-to-one fusion of drops containing gDNA with any one of seven different types of droplets, each containing a TaqMan(®) probe specific for a different KRAS mutation, or wild-type KRAS, and an optical code, it was possible to screen the six common mutations in KRAS codon 12 in parallel in a single experiment.

Real-time polymerase chain reaction test to discriminate between contamination and intraocular infection after cataract surgery

PURPOSE

To determine the usefulness of real-time polymerase chain reaction (PCR) assays in the diagnosis of postoperative bacterial endophthalmitis in clinically diagnosed infectious cases and to test for bacterial DNA in control samples collected from noninfected eyes.

SETTING

Federal University of São Paulo, Brazil.

DESIGN

Evaluation of diagnostic test or technology.

METHODS

This study comprised patients with clinically diagnosed infectious endophthalmitis after cataract surgery and vitreous samples (from noninflamed eyes obtained through vitrectomy) and aqueous samples (at end of phacoemulsification) from control patients at a single university setting. Universal and gram-specific real-time PCR, Gram staining, and culture were performed. Sensitivity and cycle thresholds were determined. Clinical and microbiologic data were also assessed.

RESULTS

The study evaluated 11 patients with infectious endophthalmitis (9 vitreous and 7 aqueous samples), 12 control vitreous samples, and 50 control aqueous samples. Gram and culture identified 80% and 75%, respectively, of patients with infectious endophthalmitis. Real-time PCR assays were positive in 91% of patients with a clinical diagnosis of endophthalmitis using aqueous samples, vitreous samples, or both. None of the 12 vitreous controls were positive by PCR. Two aqueous control samples were positive by real-time PCR. The cycle threshold cutoff value was 36 for universal PCR (sensitivity 93.8%; specificity 100%) and 38 for gram-specific PCR (sensitivity 93.8%; specificity 100%). Gram-positive microorganisms prevailed, and visual acuity varied according to the causative bacteria.

CONCLUSIONS

Real-time PCR provided fast and accurate diagnosis of bacterial endophthalmitis. As a quantitative technique, it may be useful in distinguishing between contamination and infection based on the cycle thresholds value.

Is molecular biology the best alternative for diagnosis of malaria to microscopy? A comparison between microscopy, antigen detection and molecular tests in rural Kenya and urban Tanzania

OBJECTIVE

To assess the agreement of different diagnostic methods for the diagnosis and confirmation of the clinical suspicion of Plasmodium infection in children in Tanzania and Kenya.

METHOD

Blood samples were collected by the finger prick method from 338 children. Blood samples were collected from 338 children with the clinical suspicion of uncomplicated malaria in health clinics in Tanzania and Kenya. The presence of Plasmodium parasites was assessed with microscopy, rapid diagnostic tests (RDTs) and the molecular assays, quantitative nucleic acid sequence based amplification (QT-NASBA) and polymerase chain reaction (PCR). The results were compared and analysed for agreement.

RESULTS

There was a high degree of agreement (88.6-100%) between RDTs or molecular tests and microscopy. In rural Kenya, with a high incidence of malaria cases, the correlation coefficient ranged from 0.94 for RDTs to 0.76 for PCR. In urban Tanzania, where there was a low incidence of cases, R for RDTs was 1.0 but only 0.25 for PCR and 0.33 for NASBA.

CONCLUSION

Malaria is overestimated if the diagnosis is based solely on clinical signs. Therefore, laboratory confirmation is essential. Microscopy is a reliable method in rural areas where malaria is prevalent, but RDTs offer a good alternative with the advantage that it is an easy and rapid method. Molecular tests are more sensitive but difficult to implement in rural areas. In areas with lower incidence, molecular tests detect a significantly higher number of Plasmodium infections than RDTs or microscopy. Although implementation of molecular tools can be difficult, the prospect of an easy and cheap detection system makes them promising tools for the near future.

Digital quantification of mutant DNA in cancer patients

PURPOSE OF REVIEW

The accumulation of somatic mutations is the major driving force for tumorigenesis. These mutations uniquely differentiate tumor cells from their normal counterparts. Mutations within tumor cells and mutant DNA released by tumor cells into blood, lymph, stool, tissues and other bodily compartments can thereby be used for cancer detection. Here we discuss technologies available for the detection and quantification of mutant DNA in clinical samples and the value of such measurements for patient management.

RECENT FINDINGS

Conventional mutation detection technologies are either qualitative or only roughly estimate the abundance of mutant DNA molecules. Recently-developed approaches, however, use single molecule counting to determine the genotype of each individual member of a DNA population, providing a more accurate and precise digital output.

SUMMARY

In this review, we discuss the clinical utility of mutant DNA quantification in cancer patients in the context of recent technical advances made in digital mutation detection.

Sensitive sequencing method for KRAS mutation detection by Pyrosequencing

Both benign and malignant tumors represent heterogenous tissue containing tumor cells and non-neoplastic mesenchymal and inflammatory cells. To detect a minority of mutant KRAS alleles among abundant wild-type alleles, we developed a sensitive DNA sequencing assay using Pyrosequencing, ie, nucleotide extension sequencing with an allele quantification capability. We designed our Pyrosequencing assay for use with whole-genome-amplified DNA from paraffin-embedded tissue. Assessing various mixtures of DNA from mutant KRAS cell lines and DNA from a wild-type KRAS cell line, we found that mutation detection rates for Pyrosequencing were superior to dideoxy sequencing. In addition, Pyrosequencing proved superior to dideoxy sequencing in the detection of KRAS mutations from DNA mixtures of paraffin-embedded colon cancer and normal tissue as well as from paraffin-embedded pancreatic cancers. Quantification of mutant alleles by Pyrosequencing was precise and useful for assay validation, monitoring, and quality assurance. Our Pyrosequencing method is simple, robust, and sensitive, with a detection limit of approximately 5% mutant alleles. It is particularly useful for tumors containing abundant non-neoplastic cells. In addition, the applicability of this assay for DNA amplified by whole-genome amplification technique provides an expanded source of DNA for large-scale studies.

Parallel dual-color fluorescence cross-correlation spectroscopy using diffractive optical elements

Dual-color cross-correlation spectroscopy allows the detection and quantification of labeled biomolecules at ultra-low concentrations, whereby the sensitivity of the assay correlates with the measurement time. We now describe a parallel multifocal dual-color spectroscopic configuration employing multiple avalanche photodiodes and hardware correlators. Cross-correlation curves are obtained from several dual-color excitation foci simultaneously. Multifocal dual-color excitation is achieved by splitting each of two laser beams (488 and 633 nm) into four sub-beams with the help of two 2x2 fan-out diffractive optical elements (DOEs), and subsequent superposition of the two sets of four foci. The fluorescence emission from double-labeled biomolecules is detected by two 2x2 fiber arrays.

Plasmodium falciparum: evaluation of a quantitative nucleic acid sequence-based amplification assay to predict the outcome of sulfadoxine-pyrimethamine treatment of uncomplicated malaria

A quantitative nucleic acid sequence-based amplification (QT-NASBA) assay was employed to predict retrospectively the outcome of sulfadoxine-pyrimethamine (SP) treatment of uncomplicated malaria in children aged <6 years in an endemic region. Blood samples were collected at initial diagnosis and during follow-up. Mutation-specific nested PCR methods to analyse DHFR (Arg-59) and DHPS (Glu-540) mutations that are associated with SP drug resistance were applied. Parasite genotyping was performed to distinguish between re-infection and recrudescence. Eighty-six patients were recruited of which 66 were available for follow-up. Nine children were classified as early treatment failure, 13 cases were classified as late clinical failure, 32 as late parasitological failure, and only 12 children had an adequate clinical and parasitological response. DHFR and DHPS mutations conferring SP resistance were abundant in the Plasmodium population. Blood samples obtained 7 days after treatment were used to predict retrospectively the outcome of SP treatment. QT-NASBA was able to give a correct prediction of treatment outcome in 85.7% of the cases. Positive predictive value (PPV) of QT-NASBA case was 95% (95% confidence interval = 88.3-100) and negative predictive value (NPV) was 63% (95% CI = 39.5-86.5). In contrast, microscopy correctly predicted outcome in only 37.5% of the cases. PPV of microscopy was 100% (95% CI = 73.9-100) and the NPV was 25.5% (95% CI = 13.0-38.0). The analysis of a day 7 blood sample with QT-NASBA allows for the prediction of late clinical or parasitological treatment failure in the majority of the cases analysed in the present study.

A new approach to revealing point mutations in DNA analyzed by colorimetric detection

A new approach to detection of point mutations in an amplified DNA was developed. The approach is based on highly selective ligation (T4 DNA ligase) of a tandem of short oligonucleotides one of which contains the biotin group. The ligation product is formed only when the hybridization complex DNA/tandem is formed and the tandem is perfect. The hybridization complex DNA/(biotinylated ligation product) was separated from the biotinylated component of the tandem by UV-immobilization of the reaction mixture on a nylon membrane. The immobilized hybridization complex was detected colorimetrically by a streptavidin-alkaline phosphatase cojugate with a chromogenic substrate.

A strategy for establishing accurate quantitation standards of oligonucleotides: quantitation of phosphorus of DNA phosphodiester bonds using inductively coupled plasma-optical emission spectroscopy

A novel approach for quantitation of DNA (oligonucleotides) with an unprecedented accuracy of approximately 1% is reported. Quantitation of DNA is commonly performed by measuring UV absorption or fluorescence from dyes intercalated into DNA. Both methods need accurate quantitation standards to yield more comparable results between laboratories. For establishing technically authentic standards for DNA quantitation, a new measurement approach carrying an inherent capability of absolute quantitation is demanded. The proposed approach is based on the stoichiometric existence of phosphorus (P) in DNA. The quantity of P from the phosphodiester backbone of a purified oligonucleotide was accurately determined using inductively coupled plasma-optical emission spectroscopy (ICP-OES) with yttrium internal standard via acid digestion. The number of moles of oligonucleotides was then calculated from that of P using the stoichiometry. The major issues regarding the validity of the suggested approach were (i) effective removal of extra P sources, (ii) quantitative recovery of P through the digestion process, and (iii) oligomeric purity of the target oligonucleotide. These issues were investigated experimentally using various analytical techniques such as matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), capillary electrophoresis, electrical conductometry, UV spectrometry, and gravimetry. In conclusion, it is feasible to certify pure oligonucleotide reference materials with uncertainties less than 1% using the proposed approach.

Lateral-flow and up-converting phosphor reporters to detect single-stranded nucleic acids in a sandwich-hybridization assay

Up-converting Phosphor Technology (UPT) particles were used as reporters in lateral-flow (LF) assays to detect single-stranded nucleic acids. The 400-nm phosphor particles exhibit strong visible luminescence upon excitation with infrared (IR) light resulting in the total absence of background autofluorescence from other biological compounds. A sandwich-type hybridization assay was applied using two sequence-specific oligonucleotides. One of the oligonucleotides probes was covalently bound to the UPT particle (reporter) for direct labeling and detection, whereas the second oligonucleotide probe contained biotin for capture by avidin during LF. The whole procedure of hybridization, UPT-LF detection, and analysis required a minimum time of 20 min. Moreover, aiming at minimal equipment demands, the hybridization conditions were chosen such that the entire assay could be performed at ambient temperature. During lateral flow, only targets hybridized to both capture and detection oligonucleotide were trapped and detected at an avidin capture line on the LF strip. Analysis (IR scanning) of the strips was performed in an adapted microtiter plate reader provided with a 980-nm IR laser for excitation of the phosphor particles (a portable reader was also available). Visible luminescence was measured and presented as relative fluorescence units (RFU) allowing convenient quantitation of the phosphor signal. With the assay described here as little as 0.1 fmol of a specific single-stranded nucleic acid target was detected in a background of 10 microg fish sperm DNA.

Progress in high throughput SNP genotyping methods

Most current single nucleotide polymorphism (SNP) genotyping methods are still too slow and expensive for routine use in large association studies with hundreds or more SNPs in a large number of DNA samples. However, SNP genotyping technology is rapidly progressing with the emergence of novel, faster and cheaper methods as well as improvements in the existing methods. In this review, we focus on technologies aimed at high throughput uses, and discuss the technical advances made in this field in the last few years. The rapid progress in technology, in combination with the discovery of millions of SNPs and the development of the human haplotype map, may enable whole genome association studies to be initiated in the near future.

Parallel flow measurements in microstructures by use of a multifocal 4 x 1 diffractive optical fan-out element

We have developed a multifocal optical fluorescence correlation spectroscopy system for parallel flow analyses. Multifocal excitation was made possible through a 4 x 1 diffractive optical fan-out element, which produces uniform intensity in all four foci. Autocorrelation flow analyses inside a 20 microm x 20 microm square microchannel, with the 4 x 1 fan-out foci perpendicular to the flow direction, made it possible to monitor different flows in all four foci simultaneously. We were able to perform cross-correlation flow analyses by turning the microstructure, thereby having all four foci parallel to the direction of flow. Transport effects of the diffusion as a function of flow and distance could then also be studied.

Tripartite molecular beacons

Molecular beacons (MBs) are hairpin-like fluorescent DNA probes that have single-mismatch detection capability. Although they are extremely useful for many solution-based nucleic acid detections, MBs are expensive probes for applications that require the use of a large number of different DNA probes due to the high cost and tedious procedures associated with probe synthesis and purification. In addition, since both ends of MB probes are covalently modified with chromophores, they do not offer the flexibility for fluorophore change and the capability for surface immobilization through free DNA ends. In this report, we describe an alternative form of MB, denoted tripartite molecular beacon (TMB), that may help overcome these problems. A TMB uses an unmodified oligodeoxyribonucleotide that forms a MB-like structure with two universal single-stranded arms to bring on a universal pair of oligodeoxyribonucleotides modified separately with a fluorophore and a quencher. We found that TMBs are as effective as standard MBs in signaling the presence of matching nucleic acid targets and in precisely discriminating targets that differ by a single nucleotide. TMBs have the necessary flexibility that may make MBs more affordable for various nucleic acid detection applications.

Parallel fluorescence detection of single biomolecules in microarrays by a diffractive-optical-designed 2 x 2 fan-out element

We have developed a multifocal diffractive-optical fluorescence correlation spectroscopy system for parallel excitation and detection of single tetramethylrhodamine biomolecules in microarrays. Multifocal excitation was made possible through the use of a 2 x 2 fan-out diffractive-optical element with uniform intensity in all foci. Characterization of the 2 x 2 fan-out diffractive-optical element shows formation of almost perfect Gaussian foci of submicrometer lateral diameter, as analyzed by thermal motion of tetramethylrhodamine dye molecules in solution. Results of parallel excitation and detection in a high-density microarray of circular wells show single-biomolecule sensitivity in all four foci simultaneously.

A strategy for examining complex mixtures of deoxyoligonucleotides using ion-pair-reverse-phase high-performance liquid chromatography, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, and informatics

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and ion-pair-reverse-phase high-performance liquid chromatography (IP-RP HPLC) techniques were combined to determine the sequence identity of short single-stranded deoxyoligonucleotides. This methodology is demonstrated using a commercially available multiplex set of eight primer pairs. The primer pairs were separated and collected by IP-RP HPLC. Partial sequence information for IP-RP HPLC fractions was obtained from analyzing exonuclease digestion products by MALDI-TOF MS. IP-RP HPLC, MALDI-TOF MS, exonuclease digests, and a simple computational algorithm provide an integrated strategy for determining the sequence of short nucleic acid oligomers.

Nucleic acid biotechnology

Driven by advances in the acquisition of genetic sequence information and the ability to manipulate small quantities of nucleic acid, a number of technologies are emerging that exploit nucleic acids for research, diagnostic, and therapeutic utility. In this review, we cover three technologies based on nucleic acids--DNA microarrays, antisense technology, and gene therapy--that are especially promising and may make a substantial impact in the laboratory and in the clinic during the coming years. For each of these areas, an overview of the current status and applications is provided, followed by a discussion of critical issues and challenges to be faced for further advancement of the technology; an emphasis is placed on quantitative and engineering aspects.

High-throughput genetic analysis using time-resolved fluorometry and closed-tube detection

Robust methods for genetic analysis are required for efficient exploitation of the constantly accumulating genetic information. We describe a closed-tube genotyping method suitable for high-throughput screening of genetic markers. The method is based on allele-specific probes labeled with an environment-sensitive lanthanide chelate, the fluorescence intensity of which is significantly increased upon PCR amplification of a complementary target. Genomic DNA samples were analyzed in an insulin gene single nucleotide polymorphism (SNP) assay using universal amplification primers and probes that recognized the two different alleles. The feasibility of dry reagent based all-in-one PCR assays was tested using another diabetes-related genetic marker, human leukocyte antigen DQB1 allele *0302 as a model analyte in a dual-color, closed-tube end-point assay. There was a 100% correlation between the novel SNP assay and a conventional PCR restriction fragment length polymorphism assay. It was also demonstrated that using real-time monitoring, accurate genotyping results can be obtained despite strongly cross-reacting probes, minimizing the time and effort needed for optimization of probe sequence. Throughput can be maximized by using predried PCR mixtures that are stable for at least 6 months. This homogenous, all-in-one dry reagent assay chemistry permits cost-effective genetic screening on a large scale.

Use of a thin film biosensor for rapid visual detection of PCR products in a multiplex format

Rapid, sensitive assays for nucleic acid amplification products have utility for the identification of bacterial or viral infections. We have developed a nucleic acid hybridization assay utilizing thin film technology that permits visual detection of hybrids. The silicon-based biosensor detects the presence of target sequences by enzymatically transducing the formation of nucleic acid hybrids into molecular thin films. These films alter the interference pattern of light on the biosensor surface, producing a perceived color change. We have applied this technology to the development of a chip containing capture probes specific for human respiratory virus sequences including respiratory syncytial virus, influenza virus A and B, parainfluenza virus types 1 and 3, and rhinovirus. In a ten-minute assay, the biosensor permits unambiguous identification of viral-specific RT/PCR products from infected cell lysates.

Flow-through polymerase chain reactions in chip thermocyclers

The miniaturization of analytical devices by micromachining technology is destined to have a major impact on medical and bioanalytical fields. To meet the current demands for rapid DNA amplification, various instruments and innovative technologies have been introduced by several groups in recent years. The development of the devices was extended in different directions and adapted to corresponding applications. In this review the development of a variety of devices and components for performing DNA amplification as well as the comparison of batch-process thermocyclers with reaction chambers and flow-through devices for different purposes are discussed. The main attention is turned to a flow device concept for thermocycling using microfabricated elements for local heat flow management, for which simulations and considerations for further improvement regarding design, material choice and applied technology were performed. The present review article mainly discusses and compares thermocycling devices for rapid thermocycling made of silicon or of silicon and glass with a short excursion to the possibility of plastic chip devices. In order to perform polymerase chain reactions (PCRs) in the microreactors, special attention must be paid to the conditions of the internal surfaces. For microchips, surface effects are generally pronounced because the surface to volume ratio increases upon miniaturization. Solutions for solving this problem are presented. We propose an overview of layouts for batch-process thermocyclers with different parallelization of reaction chambers and also of different designs of continuous flow thermocycling chips, paying particular attention to the parameters which influence the efficiency of such chip devices. Finally we point out some recent issues for applications in the field of clinical diagnostics.

DNA microarrays with stem-loop DNA probes: preparation and applications

We have developed DNA microarrays containing stem-loop DNA probes with short single-stranded overhangs immobilized on a Packard HydroGel chip, a 3-dimensional porous gel substrate. Microarrays were fabricated by immobilizing self-complementary single-stranded oligonucleotides, which adopt a partially duplex structure upon denaturing and re-annealing. Hybridization of single-stranded DNA targets to such arrays is enhanced by contiguous stacking interactions with stem-loop probes and is highly sequence specific. Subsequent enzymatic ligation of the targets to the probes followed by stringent washing further enhances the mismatched base discrimination. We demonstrate here that these microarrays provide excellent specificity with signal-to-background ratios of from 10- to 300-fold. In a comparative study, we demonstrated that HydroGel arrays display 10-30 times higher hybridization signals than some solid surface DNA microarrays. Using Sanger sequencing reactions, we have also developed a method for preparing nested 3'-deletion sets from a target and evaluated the use of stem-loop DNA arrays for detecting p53 mutations in the deletion set. The stem-loop DNA array format is simple, robust and flexible in design, thus it is potentially useful in various DNA diagnostic tests.

Use of Up-Converting Phosphor Reporters in Lateral-Flow Assays to Detect Specific Nucleic Acid Sequences: A Rapid, Sensitive DNA Test to Identify Human Papillomavirus Type 16 Infection

Background: A lateral-flow (LF) device using the new reporter up-converting phosphor technology (UPTTM) was applied to DNA (hybridization) assays for the detection of specific nucleic acid sequences, thereby aiming to perform the test outside well-equipped laboratories. The methodology reported here is sensitive and provides a rapid alternative for more elaborate gel electrophoresis and Southern blotting. In a preliminary study, it was applied to screen for the presence of human papillomavirus type 16 (HPV16) in a defined series of cervical carcinomas.

Methods: A LF assay was used to capture haptenized DNA molecules and hybrids, which were immunolabeled (before LF) with 400-nm UPT particles. These particles emit visible light after excitation with infrared in a process called up-conversion. Because up-conversion occurs in only the phosphor lattice, autofluorescence of other assay components is virtually nonexistent.

Results: The use of the UPT reporter in LF-DNA tests, as compared with colloidal gold, improved the detection limit at least 100-fold. UPT LF-DNA tests were successfully applied to detect (in a blind test) the presence of HPV16 in DNA extracts obtained from cervical carcinomas. Test results matched 100% with previous characterization of these carcinomas.

Conclusions: The use of UPT in LF assays to detect specific nucleic acids provides low attamole-range sensitivity. Hybridization and consecutive detection of PCR-amplified HPV16 sequences were successful in a background of 10 μg of fish-sperm DNA. The sensitivity of UPT detection in these complex mixtures indicates that detection of viral infections without PCR or other amplification technique is achievable.

Quantitative detection of single nucleotide polymorphisms for a pooled sample by a bioluminometric assay coupled with modified primer extension reactions (BAMPER)

A new method for SNP analysis based on the detection of pyrophosphate (PPi) is demonstrated, which is capable of detecting small allele frequency differences between two DNA pools for genetic association studies other than SNP typing. The method is based on specific primer extension reactions coupled with PPi detection. As the specificity of the primer-directed extension is not enough for quantitative SNP analysis, artificial mismatched bases are introduced into the 3'-terminal regions of the specific primers as a way of improving the switching characteristics of the primer extension reactions. The best position in the primer for such artificial mismatched bases is the third position from the primer 3'-terminus. Contamination with endogenous PPi, which produces a large background signal level in SNP analysis, was removed using PPase to degrade the PPi during the sample preparation process. It is possible to accurately and quantitatively analyze SNPs using a set of primers that correspond to the wild-type and mutant DNA segments. The termini of these primers are at the mutation positions. Various types of SNPs were successfully analyzed. It was possible to very accurately determine SNPs with frequencies as low 0.02. It is very reproducible and the allele frequency difference can be determined. It is accurate enough to detect meaningful genetic differences among pooled DNA samples. The method is sensitive enough to detect 14 amol ssM13 DNA. The proposed method seems very promising in terms of realizing a cost-effective, large-scale human genetic testing system.

Solid-phase, single nucleotide primer extension of DNA/RNA hybrids by reverse transcriptases

A method for RNA analysis based on primer extension by reverse transcriptase is described.

Miniaturized flow-through PCR with different template types in a silicon chip thermocycler

Flow-through chip thermocyclers can be used in miniaturized rapid polymerase chain reaction (PCR) despite their high surface to volume ratio of samples. We demonstrated that a thermocycler made of silicon and glass chips and containing thin film transducers for heating and temperature control can be adapted to the amplification of various DNA templates of different sources and properties. Therefore, the concept of serial flow in a liquid/liquid two-phase system was combined with a surface management of inner side walls of the microchannel and an adaptation of PCR mixture composition. In addition, the process temperatures and the flow rates were optimized. Thus, a synthetic template originating from investigations on nucleic acid evolution with 106 base pairs [cooperative amplification of templates by cross hybridization (CATCH)], a house keeping gene with 379 base pairs [glutaraldehyde 3-phosphate dehydrogenase (GAPDH)] and a zinc finger protein relevant in human pathogenesis with 700 base pairs [Myc-interacting zinc finger protein-1, knock-out (Miz1-KO)] were amplified successfully. In all three cases the selectivity of priming and amplification could be shown by gel electrophoresis. The typical amplification time was 1 min per temperature cycle. So, the typical residence time of a sample volume inside the 25 cycle device amounts to less then half an hour. The energy consumption of the PCR chip for a 35 min PCR process amounts to less than 0.012 kW h.

Pharmacogenetics, race, and ethnicity: social identities and individualized medical care

Social categories such as race and ethnicity have long been used in interpreting patient symptoms, diagnosing disease, and predicting therapeutic response. DNA-based diagnostic tests and pharmacogenetic screens could make these uses of social categories largely irrelevant by allowing clinicians to base diagnosis and treatment decisions on the unique genetic features of individual patients. Despite this attractive vision of individualized care, however, social categories are likely to continue playing a significant role in the coming era of genetic medicine. Current uses of social categories in pharmacogenetic research, for example, illustrate how drug development and marketing will perpetuate the use of social categories such as race and ethnicity. Those uses may unintentionally blunt the precision of genetic technologies and pose new threats to socially identifiable populations. These implications suggest the need for greater caution in using social categories as indicators for specific tests or therapies and for federal legislation to protect against discriminatory uses of individuals' genetic information. In addition, more precise social classifications than those presently in use may allow us to realize the full potential of DNA-based technologies, thus minimizing social disparities in health care. Those more precise social classifications should reflect extended patient pedigrees and not the self-reported claims of racial and/or ethnic affiliation.

3'-nitrophenylpropyloxycarbonyl (NPPOC) protecting groups for high-fidelity automated 5' --> 3' photochemical DNA synthesis

[structure: see text]. The most powerful DNA microarrays would be prepared by photolithography with free 3'-ends that could be processed enzymatically. A photoremovable group that could be removed in quantitative yield would ensure high purity of the synthesized probes. We have developed new pyrimidine building blocks for 5' --> 3' DNA synthesis with high cycle yields using the NPPOC (3'-nitrophenylpropyloxycarbonyl) protecting group. These phosphoramidites were proved in automated photochemical DNA synthesis on a modified synthesizer.

Direct detection of Legionella species from bronchoalveolar lavage and open lung biopsy specimens: comparison of LightCycler PCR, in situ hybridization, direct fluorescence antigen detection, and culture

We developed a rapid thermocycling, real-time detection (also known as real-time PCR) method for the detection of Legionella species directly from clinical specimens. This method uses the LightCycler (Roche Molecular Biochemicals, Indianapolis, Ind.) and requires approximately 1 to 2 h to perform. Both a Legionella genus PCR assay and Legionella pneumophila species-specific PCR assay were designed. A total of 43 archived specimens from 35 patients were evaluated, including 19 bronchoalveolar lavage (BAL) specimens and 24 formalin-fixed, paraffin-embedded open lung biopsy specimens. Twenty-five of the specimens were culture-positive for Legionella (9 BAL specimens and 16 tissue specimens). BAL specimens were tested by LightCycler PCR (LC-PCR) methods and by a direct fluorescent antibody (DFA) assay, which detects L. pneumophila serogroups 1 to 6 and several other Legionella species. Tissue sections were tested by the two LC-PCR methods, by DFA, by an in situ hybridization (ISH) assay, specifically designed to detect L. pneumophila, and by Warthin-Starry (WS) staining. The results were compared to the "gold standard" method of bacterial culture. With BAL specimens the following assays yielded the indicated sensitivities and specificities, respectively: Legionella genus detection by Legionella genus LC-PCR, 100 and 100%; Legionella genus detection by DFA assay, 33 and 100%; and L. pneumophila detection by L. pneumophila species-specific LC-PCR, 100 and 100%. With open lung biopsy specimens the following assays yielded the indicated sensitivities and specificities, respectively: Legionella genus detection by LC-PCR 68.8 and 100%; Legionella genus detection by DFA assay, 44 and 100%; Legionella genus detection by WS staining, 63 and 100%; L. pneumophila species-specific detection by LC-PCR, 17 and 100%; and L. pneumophila species-specific detection by ISH, 100 and 100%. The analytical sensitivity of both LC-PCR assays was <10 CFU/reaction. LC-PCR is a reliable method for the direct detection of Legionella species from BAL specimens. The Legionella genus LC-PCR assay could be performed initially; if positive, L. pneumophila species-specific LC-PCR could then be performed (if species differentiation is desired). The speed with which the LC-PCR procedure can be performed offers significant advantages over both culture-based methods and conventional PCR techniques. In contrast, for the methods evaluated, culture was the best for detecting multiple Legionella species in lung tissue. WS staining, Legionella genus LC-PCR, and L. pneumophila species-specific ISH were useful as rapid tests with lung tissue.

A commented dictionary of techniques for genotyping

Several tools, differing in their technical and practical parameters, are available for the detection of point mutations as well as small deletions and insertions. In this article, a dictionary featuring over fifty methods for detection of mutation is presented. The distinguishing principle for each method is briefly explained. Sorting of and discussion on the methods give the reader a brief introduction to the field of genotyping.

Nonenzymatic autoligation in direct three-color detection of RNA and DNA point mutations

Enzymatic ligation methods are useful in diagnostic detection of DNA sequences. Here we describe the investigation of nonenzymatic phosphorothioate-iodide DNA autoligation chemistry as a method for detection and identification of both RNA and DNA sequences. Combining ligation specificity with the hybridization specificity of the ligated product is shown to yield discrimination of a point mutation as high as >10(4)-fold. Unlike enzymatic ligations, this reaction is found to be equally efficient on RNA or DNA templates. The reaction is also shown to exhibit a significant level of self-amplification, with the template acting in catalytic fashion to ligate multiple pairs of probes. A strategy for fluorescence labeling of three autoligating energy transfer (ALET) probes and directly competing them for autoligation on a target sequence is described. The method is tested in several formats, including solution phase, gel, and blot assays. The ALET probe design offers direct RNA detection, combining high sequence specificity with an easily detectable color change by fluorescence resonance energy transfer (FRET).

Advances in the analysis of DNA sequence variations using oligonucleotide microchip technology

The analysis of DNA variation (polymorphisms and mutations) on a genome-wide scale is becoming both increasingly important and technically challenging. An integration of a growing number of molecular biological methods of DNA-sequence analysis with the high-throughput feature of oligonucleotide microarray-based technologies is one of the most promising current directions of research and development.

Interference-based detection of nucleic acid targets on optically coated silicon

Sequence-specific detection of polynucleotides typically requires modified reporter probes that are labeled with radioactive, fluorescent, or luminescent moieties. Although these detection methods are capable of high sensitivity, they require instrumentation for signal detection. In certain settings, such as clinical point of care, instrumentation might be impractical or unavailable. Here we describe a detection approach in which formation of a nucleic acid hybrid is enzymatically transduced into a molecular thin film that can be visually detected in white light. The system exploits a flat, optically coated silicon-based surface to which capture oligonucleotides are covalently attached. The optimized system is capable of detection of nucleic acid targets present at sub-attomole levels. To supplement visual detection, signals can be quantitated by a charge-coupled device. The design and composition of the optical surface, optimization of immobilization chemistry for attachment of capture probes, and characterization of the efficiency of the hybridization process are presented. We describe the application of this system to detection of a clinically relevant target, the mecA gene present in methicillin-resistant Staphylococcus aureus.

Large-scale SNP scoring from unamplified genomic DNA

Discoveries from the Human Genome Project (HGP) continue to spur changes in medical technology that will lead to new diagnostic procedures in the clinical lab. As more single nucleotide polymorphisms (SNPs) are discovered and correlated to human diseases, demands for genetic tests will increase. The enormity of the number of SNPs makes developing inexpensive and reliable high-throughput methods for SNP scoring imperative. High-throughput screening (HTS) means, at a minimum, a production rate of thousands of assays per day. Ideally, the technology will be easy, inexpensive and amenable to automation. The Invader assay offers a simple diagnostic platform to detect single nucleotide changes with high specificity and sensitivity from unamplified, genomic DNA. The Invader assay uses a structure-specific 5' nuclease (or flap endonuclease) to cleave sequence-specific structures in each of two cascading reactions. The cleavage structure forms when two synthetic oligonucleotide probes hybridise in tandem to a target. One of the probes cycles on and off the target and is cut by the nuclease only when the appropriate structure forms. These cleaved probes then participate in a second Invader reaction involving a dye-labelled fluorescence resonance energy transfer (FRET) probe. Cleavage of this FRET probe generates a signal, which can be readily analysed by fluorescence microtitre plate readers. The two cascading reactions amplify the signal significantly; each original target molecule can lead to more than 10(6) cleaved signal probes in one hour. This signal amplification permits identification of single base changes directly from genomic DNA without prior target amplification. The sequences of the oligonucleotide components of the secondary reaction are independent of the target of interest and permit the development of universal secondary reaction components useful to identify any target.

K-Ras mutations and benign pancreatic disease

This review addresses the history of the ras oncogene, the techniques used to detect molecular alterations in the ras oncogene, and the application of polymerase chain reaction (PCR)-based methods to determine point mutations in clinical samples of patients with pancreatic diseases, namely pancreatic carcinoma and chronic pancreatitis. The frequency of ras mutations in pancreatic carcinoma is high, ranging from 70 to almost 100%. The frequence of ras mutations in chronic pancreatitis, either in pancreatic tissue or pancreatic secretions, vary between 0 and 100%. This wide range in part may be owing to differences in sampling, DNA extraction, or PCR method. The meaning of a k-ras mutation is under debate. Taking into account the positivity of ductal hyperplasias in normal pancreas and ras mutations in normal appearing duct cells, this molecular finding may not mean anything. In contrast, ras mutations are associated with smoking, one acknowledged risk factor for pancreatic carcinoma. The need for large prospective cohort studies is emphasized.

Screening unlabeled DNA targets with randomly ordered fiber-optic gene arrays

We have developed a randomly ordered fiber-optic gene array for rapid, parallel detection of unlabeled DNA targets with surface immobilized molecular beacons (MB) that undergo a conformational change accompanied by a fluorescence change in the presence of a complementary DNA target. Microarrays are prepared by randomly distributing MB-functionalized 3-microm diameter microspheres in an array of wells etched in a 500-microm diameter optical imaging fiber. Using several MBs, each designed to recognize a different target, we demonstrate the selective detection of genomic cystic fibrosis related targets. Positional registration and fluorescence response monitoring of the microspheres was performed using an optical encoding scheme and an imaging fluorescence microscope system.

Digital PCR

The identification of predefined mutations expected to be present in a minor fraction of a cell population is important for a variety of basic research and clinical applications. Here, we describe an approach for transforming the exponential, analog nature of the PCR into a linear, digital signal suitable for this purpose. Single molecules are isolated by dilution and individually amplified by PCR; each product is then analyzed separately for the presence of mutations by using fluorescent probes. The feasibility of the approach is demonstrated through the detection of a mutant ras oncogene in the stool of patients with colorectal cancer. The process provides a reliable and quantitative measure of the proportion of variant sequences within a DNA sample.