Chip-based methods

Yuan E, Haghighi F, White S et al. A single nueleotide polymorphism chip-based method for combined genetic and epigenetic profiling validation in decitabine therapy and tumor/normal comparisons. Cancer Res 2006 66 3443-3351. 

Another class of readout measures RNA expression levels, with the three most common methods being chip-based hybridization/fluorescence techniques, realtime polymerase chain reaction (RT-PCR) and quantitative nuclease protection assays (QNPA) [48, 49]. Chip-based methods are widely used for whole-genome scans (discussed in more detail below), but have a disadvantage that they are relatively expensive and so are not really high throughput. The quantitative reproducibility and dynamic range of these chip-based methods are also lower than for the other RNA readout techniques. RT-PCR is a more quantitative technique for measuring transcript levels, and is typically run for up to 40 transcripts at a time. QNPA is another... 

Levitation of small amounts of sample can be used to avoid contact with solid walls around the sample in a gas-surrounding medium (air in most cases). Levitation provides advantages similar to those of miniaturization in chip-based methods (basically, low reagent and sample consumption). In addition, levitation avoids contamination between samples and external objects, and also adverse effects of sample-wall contact on detection [69]. 

A sequence-based approach to the identification of differentially expressed genes through comparative analysis. Allows simultaneous analysis of sequences that derive from different cell populations or tissues. This is not a chip-based method. Identification of sequences relies on completeness of public sequence databases and, therefore, can only be used to analyse known genes. 

Affinity Enrichment ChIP-based methods have been mostly combined with microarrays. These affinity-based techniques are now rapidly shifting to analysis by the next-generation techniques (56,66). As it has been described earlier, DNA immunoprecipitated with the specific methylcytosine antibody is de-cross-linked and defragmented. After ligation with specific probes, the sample is applied for on-site deep sequencing. 

Sohni, Y. R., Burke, J.R, Dyck, R J., andO Kane, D. J., Microfluidic chip-based method for genotyping microsatellites, VNTRs and insertion/deletion polymorphisms, Clin. Biochem., 36, 35, 2003. 

The current trend in analytical chemistry applied to evaluate food quality and safety leans toward user-friendly miniaturized instruments and laboratory-on-a-chip applications. The techniques applied to direct screening of colorants in a food matrix include chemical microscopy, a spatial representation of chemical information from complex aggregates inside tissue matrices, biosensor-based screening, and molec-ularly imprinted polymer-based methods that serve as chemical alternatives to the use of immunosensors. 

Because of the small volumes encountered in CE, implementing CE as a second dimension is difficult if a valve is used. More efficient, lower volume unions have been utilized in a number of cases. The main types of these interfaces include optical gating and flow gating, which are discussed below. Electrical gating is described in detail in Chapter 15. Fraction collection is also used, as discussed in Chapter 16, although this takes longer and is a less efficient method than the other comprehensive 2D schemes. Chip-based separation systems typically use some form of electrical gating and these systems will be discussed below. 

Chip-based microdevices are finally discussed, regarding fabrication methods, designs, MS interfacing, and applications. Current capabilities and limitations for future use are emphasized considering improvements in methodology and instrumentation. 

Figure 13.1 Depiction of the glass-based lab-on-a-chip fabrication method. Shown in the figure is (a) the photoresist and chrome-coated glass substrate, (b) the coated substrate exposed to UV light through a mask (black rectangle), (c) removal of the exposed photoresist, (d) removal of the exposed chrome layer, (e) removal of glass by wet chemical etching, (f) removal of the bulk photoresist, and (g) removal of the bulk chrome layer.

Dill, K., Stanker, L. H., and Young, C. R. (1999). Detection of salmonella in poultry using a silicon chip-based biosensor. J. Biochem. Biophys. Methods 41, 61-67. 

Although this section provides a brief description of most commonly nsed detectors for HPLC, most of the focus is on a few detection modes. Optical absorbance detectors remain the most widely nsed for HPLC, and are discnssed in some detail. We also focns on flnorescence, condnctivity, and electrochemical detection, as these methods were not widely nsed for HPLC in the past, bnt are especially well suited to micro- and nano-flow instrnments becanse of their high sensitivity in small sample volumes. Mass spectrometry has also come into wide and rontine nse in the last decade, but as it is the subject of another chapter, it will not be fnrther discnssed here. Miniaturization has been particularly important for capillary and chip-based electrophoresis, which often employs sub-nanoliter detection volnmes [36,37]. 

In aspect of chip-based technology, electrochemical genosensors based on different materials and transducers have been recently developed in response to clinical demand of giving promising results [18-25]. Different sensor technologies provide a unique platform in order to immobilize molecular receptors by adsorption, crosslinking or entrapment, complexation, covalent attachment, and other related methods on nanomaterials [5,7,26]. 

Zhao, W., Zhang, H., Zhu, M., Warrack, B., Ma, L., Humphreys, W. G., and Sanders, M. (2006). An integrated method for quantification and identification of radiolabeled metabolites Application of chip-based nanoelectrospray and mass defect filter techniques. In Proceedings of the 54th ASMS Conference on Mass Spectrometry and Allied Topics, Seattle, WA. 

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