Molecular diagnostics by microelectronic microchips

Lab-on-a-chip: emerging analytical platforms for immune-mediated diseases

Miniaturization of analytical procedures has a significant impact on diagnostic testing since it provides several advantages such as: reduced sample and reagent consumption, shorter analysis time and less sample handling. Lab-on-a-chip (LoC), usually silicon, glass, or silicon-glass, or polymer disposable cartridges, which are produced using techniques inherited from the microelectronics industry, could perform and integrate the operations needed to carry out biochemical analysis through the mechanical realization of a dedicated instrument. Analytical devices based on miniaturized platforms like LoC may provide an important contribution to the diagnosis of high prevalence and rare diseases. In this paper we review some of the uses of Lab-on-a-chip in the clinical diagnostics of immune-mediated diseases and we provide an overview of how specific applications of these technologies could improve and simplify several complex diagnostic procedures.

Integrated PCR amplification and detection processes on a Lab-on-Chip platform: a new advanced solution for molecular diagnostics

BACKGROUND

Several microdevices have been developed to perform only a single step of a genotyping process, such as PCR or detection by probe hybridization. Here, we describe a Lab-on-Chip (LoC) platform integrating a PCR amplification microreactor with a customable microarray for the detection of sequence variations on human genomic DNA.

METHODS

Preliminary work was focused on developing the single analytical steps including PCR and labeling strategies of the amplified product by conventional reference systems. The optimized protocols included a 1:4 forward:reverse primer ratio for asymmetric PCR, and Cy5-dCTP multiple incorporation for the generation of a labeled PCR product to be hybridized to complementary probes bound to the chip surface.

RESULTS

Final conditions were applied to the fully integrated LoC platform for the detection of the IVSI-110 G > A mutation in the human beta-globin (HBB) gene associated with beta-thalassemia, used as a model of genetic application, allowing for correct genotyping of 25 samples that were heterozygous, homozygous or wild-type for this mutation.

CONCLUSIONS

The overall results show that the present platform is very promising for rapid identification of DNA sequence variations in an integrated, cost effective and convenient silicon chip format.

Process Evaluation of a Fully Automated Molecular Diagnostics System

Molecular diagnostics presents challenges to clinical laboratories that are under pressure to consolidate and automate. There is a need to evaluate molecular automation for process efficiency and suitability for high-throughput environments in core laboratories.

A fully automated molecular instrument platform (the BD Viper System with XTR Technology in extracted mode [BD Viper System with XTR]), was evaluated for automation efficiency, labor requirements, and system robustness. System productivity was predicted using time and motion studies as well as process simulation.

Preanalytical steps required 15 min of skilled operator time. The BD Viper System with XTR fully automated DNA extraction, amplification, and analysis of 368 specimens (736 results for Chlamydia and Gonorrhea). Time and motion studies estimated that the total hands-on full time employee (FTE) burden was approximately 35 min per run, of which 41% was high complexity, 29% medium complexity and 29% relatively unskilled labor. A skilled operator can easily operate four instruments for 8.5 h and generate data on 2944 results (four runs on each instrument for a total of 1472 clinical specimens) for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) analysis. Based on mean time between intervention data, the BD Viper System with XTR was estimated to be capable of operating for more than 1000 runs without system malfunction.

We determined that fully automated molecular analysis of GC and CT is possible in a core laboratory facility with significant throughput and minimal impact on labor demand using a fully automated and robust molecular diagnostics platform (such as the BD Viper System with XTR).

Development of clinical highly sensitive biosensor-based microarray system

AIM: To develop a sensitive and less instrument-dependent clinical microarray system, in which the microarray signal can be amplified in situ and identified by naked eyes.

METHODS: A group of capture probes for a specific target nucleic acid that was made according to a specific region such as hepatitis B virus (HBV) YMDD motif were arrayed on a thin-film biosensor in a well. A set of detected probes labeled with Au nanoparticle were used to take place of the fluorence labeled probes in classic microarray. The single-strand PCR product was reacted with the capture and detected probes and the deposition of capture-biotin-streptin-Au nanoparticle compound appeared on the surface of the microarray. After in situ amplification in this biosensor based system, we could read the signal on this chips by naked eyes or the digital camera. HBV YMDD mutation detection was applied to identify the sensitivity and specificity of the microarray system.

RESULTS: The signal of the biosensor microarray could be acquired by common camera or naked eyes without any instruments and we could determine the kind of mutation according to the place of the positive signal. The signal-noise ratio were high enough to make the signal absolutely yes and no both in synthesized target oligos and serum samples. The microarray could identify a single base change of selected lamivudine resistance-related mutation as well as multiple mutations at the same time with a high stability, sensitivity, and specificity. We used the biosensor system to test 23 serum samples with YMDD mutation, and the result was coincident with the sequencing result and the signal could be aquired by naked eyes.

CONCLUSION: The thin-film based microarray system which exploits nanoparticle material and biosensor technique can amplify the signal in situ that can be detected by simple instruments or even unaided eyes. Its attractive features are the nonintervention of instrumentation required to detect signal, as well as its high versatility and accuracy.

High resolution DNA separations using microchip electrophoresis

Planar microfluidic devices have emerged as effective tools for the electrophoretic separation of a variety of different DNA inputs. The advancement of this miniaturized platform was inspired initially by demands placed on electrophoretic performance metrics by the human genome project and has provided a viable alternative to slab gel and even capillary formats due to its ability to offer high resolution separations of nucleic acid materials in a fraction of the time associated with its predecessors, consumption of substantially less sample and reagents while maintaining the ability to perform many separations in parallel for realizing ultra-high throughputs. Another compelling advantage of this separation platform is that it offers the potential for integrating front-end sample preprocessing steps onto the separation device eliminating the need for manual sample handling. This review aims to compile a recent survey of various electrophoretic separations using either glass or polymer-based microchips in the areas of genotyping and DNA sequencing as well as those involving the growing field of DNA-based forensics.

Development of an integrated microsystem for injection, transport and manipulation of encoded microbeads

An integrated microsystem for injection, transport and manipulation of encoded microbeads on a single microchip is presented. The device also incorporates a customized reaction chamber to process individual, optically encoded microbeads. This research illustrates how microfabrication technologies enable convenient integration of multiple capabilities of microbeads, controlled microfluidic injection, integration of heater elements and temperature sensors and detection of microbeads in a single microfluidic chip. A practical application for the integrated microsystem is confirmed by the ability to select a specific DNA sequence of interest from a 4 x 4 cDNA library. This application emphasizes the advantages of component integration for rapid bio-assay development in a complete microsystem.

Spotting and validation of a genome wide oligonucleotide chip with duplicate measurement of each gene

The quality of DNA microarray based gene expression data relies on the reproducibility of several steps in a microarray experiment. We have developed a spotted genome wide microarray chip with oligonucleotides printed in duplicate in order to minimise undesirable biases, thereby optimising detection of true differential expression. The validation study design consisted of an assessment of the microarray chip performance using the MessageAmp and FairPlay labelling kits. Intraclass correlation coefficient (ICC) was used to demonstrate that MessageAmp was significantly more reproducible than FairPlay. Further examinations with MessageAmp revealed the applicability of the system. The linear range of the chips was three orders of magnitude, the precision was high, as 95% of measurements deviated less than 1.24-fold from the expected value, and the coefficient of variation for relative expression was 13.6%. Relative quantitation was more reproducible than absolute quantitation and substantial reduction of variance was attained with duplicate spotting. An analysis of variance (ANOVA) demonstrated no significant day-to-day variation.

Rapid, sequence-specific detection of unpurified PCR amplicons via a reusable, electrochemical sensor

We report an electrochemical method for the sequence-specific detection of unpurified amplification products of the gyrB gene of Salmonella typhimurium. Using an asymmetric PCR and the electrochemical E-DNA detection scheme, single-stranded amplicons were produced from as few as 90 gene copies and, without subsequent purification, rapidly identified. The detection is specific; the sensor does not respond when challenged with control oligonucleotides based on the gyrB genes of either Escherichia coli or various Shigella species. In contrast to existing sequence-specific optical- and capillary electrophoresis-based detection methods, the E-DNA sensor is fully electronic and requires neither cumbersome, expensive optics nor high voltage power supplies. Given these advantages, E-DNA sensors appear well suited for implementation in portable PCR microdevices directed at, for example, the rapid detection of pathogens.