At present, the most efficient method of performing massively parallel sequence interrogation is achieved through DNA array technologies. DNA arrays consist of specific probe sequences tethered to defined "addresses"; which may be a particular region of a solid support such as a glass slide or a uniquely colour-coded microsphere.
DNA arrays have predominantly been used to monitor gene expression levels as many genes can be examined simultaneously. However, arrays can also be used to detect DNA sequence changes at the single base level.
An example of one of the many platforms currently available is the Luminex Laboratory Multi-Analyte Profiling (LabMAP) system:
'With LabMAP technology, molecular reactions take place on the surface of microscopic beads called microspheres. For each reaction in a LabMAP profile, thousands of molecules are attached to the surface of colour-coded microspheres. The assigned colour-code identifies the reaction throughout the test.
The magnitude of the biomolecular reaction is measured using a second reporter molecule, which is incorporated into the target during PCR. The reporter molecule signals the extent of the reaction by hybridising to the probes on the microspheres. Because the reporter�s signal is also a colour, there are two sources of colour, the colour-code of the microsphere and the reporter colour on the surface of the microsphere'. (Luminex Corp.)
To date, 100 differently coloured bead sets are available, offering the potential to multiplex up to 100 assays simultaneously. To perform a test, the colour-coded microspheres with probes bound to their surface and the reported-labelled sample are combined. Target is allowed to hybridise to the beads during an incubation step and the mixture is then introduced into an instrument that uses microfluidics to align the microspheres in single file where lasers illuminate the dyes. Next, advanced optics capture the colour signals. Finally, digital signal processing translates the signals into real-time, quantitative data for each reaction.
Click 
for a diagram of the LabMap system (28KB)
To view a flash animation of DNA Microarray methodology follow the link:
http://www.bio.davidson.edu/courses/genomics/chip/chip.html