Biochips – fundamentals and applications - Electrochemical Sensors, Biosensors and Their Biomedical Applications - page 321

to select a commercial microarray scanner including charged coupled device (CCD)
or PMT as the detection unit, simultaneous or sequential image acquisition mode, and
confocal or non-confocal optical system. It has been controversial which is the superior
technology. Although it is generally believed PMT can deliver better data than CCD
in microarray applications, the studies by Schermer [25], Basarsky [26], and Ramdas
et al. [27] have demonstrated that the fl uorescent ratios from scanners using different
technologies were highly correlated. This means users can basically choose the scan-
ner with simultaneous or sequential scanning and a confocal or non-confocal system
with which they feel comfortable and can still obtain comparable data with others.
A scanner with two lasers for Cy3 and Cy5 labeling is fairly good enough for most
of the microarray experiments. However, multiple lasers are necessary for simulta-
neous detection of all four nucleotide polymorphisms in chip-based SNPs detection.
Besides, an extra third fl urophore attached to a sequence that specifi cally binds to a
linker region of the DNA spots could be used for spotting quality control.

11.2.5.2 Data analysis
In the microarray technology, the abundance of cDNA is measured indirectly by meas-
uring the intensity of the fl uorescent dye in order to generate more data for interpreta-
tion and analysis. A raw form a fl uorescence image of a gel-pad array biochip is shown
in Fig. 11.14 (see Plate 4 for color version). For simplifi cation, only two color dyes (red
and green) are used. The cDNAs from the control samples are labeled with a red dye,
while those from the test samples are labeled with green dyes. Hybridization of a gene
with the control will result in green spots. Likewise, hybridization of a gene with the

FIGURE 11.14 Fluorescence image of a gel-pad array biochip (see Plate 4 for color version).