Massively parallel analysis

Optical gene chips dense arrays of oligonucleotides have been successfully applied to detect transcriptional profiling and SNP discovery, where massively parallel analysis is required. However, the fluorescence-based readout of these chips involves not only highly precise and expensive instrumentation but also sophisticated numerical algorithms to interpret the data, and therefore these methods have been commonly limited to use in research laboratories. In this way, thin-film arrays of 14, 20, 25, 48 and 64 electrodes have already been fabricated [12,15,39,40,44,48], using lithographic techniques. Readout systems for these arrays based on electrical detection have also been developed. 

The practice of protein analysis of whole proteomes relies on (i) two-dimensional gel electrophoresis for separation (ii) mass spectrometry for analysis and (iii) protein arrays for achieving massively parallel analysis. 

The capabilities of antibody microarray technology are similar to those for DNA array methods selectivity of immunoreagents in complex protein lysates rapid, massively parallel analysis of proteins small sample volume requirement and automation and compatibility with DNA microarray technologies (in hardware, software, and bioinformatics) also, native proteins are analyzed, which affords information on specific structure and protein-protein interactions. Limitations of this... 

S. Nie, M. Han and X. Gao, Lab-on-a-bead optically encoded microspheres for massively parallel analysis of genes and proteins. Abstract Paper—American Chemical Society, 221st IEC-019, 2001. 

First combinations of microfiuidic integrated electrophoresis with microarrays were published in 1998 by Nanogen Inc., CA, USA [257]. This approach resulted in a 20-fold faster hybridization and more specific binding of DNA onto the microarray. This was the first step into the direction of a platform for massively parallel analysis. 

Systems for Massively Parallel Analysis Definition of massively parallel analysis ... 

Massively parallel analysis or high throughput screening allows the parallel handling of several hundred to up to billions of assays or samples within one run, and performs an according readout for each assay in parallel. Main application examples are microarrays, bead based assays and picowell-plates. 

Here, the microfluidic actuation principles that are utiziled in massively parallel analysis are outlined briefly. This is followed by some commercial application examples. Due to the similar principle, microarrays and picowell plates are presented together, followed by bead based assays. 

For high-throughput screening applications, on the contrary, a high number of assays need to be performed within an acceptable period of time. Consequently flexibility is less important, and throughput and costs are the main issues. Thus, approaches like segmented flow and systems for massively parallel analysis are interesting candidates for these applications. 

The patented Affymetrix GeneChip is a very powerful and reliable platform, allowing massively parallel analysis. However, this comes at a cost, that is frequently beyond the budget of most academic research laboratories. Home-made arrays have a much lower density of spots and also tend to be less reliable when compared to the stringent controls applied by Affymetrix. They are, however, much cheaper and can be designed specifically for each particular application. As competing companies try to fill the gap for more affordable array platforms, prices will fall and DNA arrays will find increasing use both in academic and in industrial laboratories. 

Hybridisation of matching strands of ssDNA is the underlying prinoiple of DNA arrays. Modern array platforms, such as that developed by Affymetrix Corp., are extremely miniaturised and allow massively parallel analysis for DNA sequencing and comparative studies of DNA samples. 

Microarray analysis provides a technology platform for massive, parallel analysis of protein-protein interactions (MacBeath and Schrieber, 2000 Joos et al 2002). The difficulty with protein microarray is that proteins do not behave as uniformly as nucleic acids. Protein function is dependent on a precise and fragile 3D structure that may be difficult to maintain in a microarray format A practical challenge posed by proteins derives from their relatively delicate tertiary stracture, which is susceptible to unfolding during microarray printing. In addition, the efficiency and specificity of protein-protein interactions are not nearly as standardized as nucleic acid hybridization. The use of lectin microarrays in glycoform analysis also encounters the similar problems. 

C.T. Vaughan, Structural Analysis on Massively Parallel Computers, SAND90-1706C, Sandia National Laboratories Report, Albuquerque, NM 87185, 1991. 

A number of developments have increased the importance of capillary electrophoretic methods relative to pumped column methods in analysis. Interactions of analytes with the capillary wall are better understood, inspiring the development of means to minimize wall effects. Capillary electrophoresis (CE) has been standardized to the point of being useful as a routine technique. Incremental improvements in column coating techniques, buffer preparation, and injection techniques, combined with substantive advances in miniaturization and detection have potentiated rugged operation and high capacity massive parallelism in analysis. 

Brenner S et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnol 2000 18 630-634. 

NIR-CI instrumentation is rugged and flexible, suitable for both the laboratory and manufacturing environment. Therefore analysis methods developed in the laboratory can often be tailored for implementation near-line or at-line. NIR-CI is also a massively parallel approach to NIR spectroscopy, making the technique well suited for high throughput applications. 

Brenner S, et al., Gene expression analysis by massively parallel 35. 

Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 2000 18 630-634. 

Alumbaugh, D. L., and G. A. Newman, 1997, Three-dimensional massively parallel inversion - II. Analysis of a cross-well electromagnetic experiment Geophys. J. Int., 128, 355-63. 

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