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4. Comparison of some of the features of DNA microarrays
Some of the features of DNA microarrays are summarized at Table 1. The photolithographic fabrication method yields very high-density DNA microarrays (the GeneChip®), but the length of the probes is limited. The densities of the DNA microarrays fabricated by robot spotting (Stanford type) are about one-tenth those of GeneChip® but they can load very long oligonucleotides or cDNAs. The Stanford type needs self-construction of arrayers, but is flexible for custom preparation. The GeneChip® arrays are suitable for SNP studies (as described later), because DNA microarrays with a single base variation are easily fabricated by the photolithographic method. DNA microarrays with pre-synthesized probes are suitable for gene expression studies because they can load cDNA as probes. These are some of the features of both types of DNA microarrays and thus both types of DNA microarrays complemented each other.
Table 1
| Type |
GeneChip® arrays |
Stanford type microarray |
| Manufacturing method |
Photolithographic fabrication |
Robot spotting of pre-synthesized probes |
| Availability |
Readily available
(off-the-shelf products) |
Need construction or purchase of arrayers |
| Custom preparation |
Not flexible |
Flexible |
| Probes |
Oligonucleotides (limited length) |
cDNA or oligonucleotides (no limited length) |
| Density (cm-2) |
up to 500,000 22) |
up to 50,00018) |
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