Table 1.

A comparison of four of the most common DNA microarray formats

	Contact printing	Inkjet synthesis	Affymetrix	NimbleGen
Arraying method	Mechanical deposition	Phosphoramitide synthesis, piezoelectric printing	In situ DNA synthesis (photolithography)	In situ DNA synthesis (maskless photolithography)
DNA size limit	None	∼60 nt	25 nt	∼100 nt
Feature type	PCR products, oligomers	Oligomers	Oligomers	Oligomers
Features/slide	≤40 K	≤40 K	60 K–6.2 M	200–800 K
Array design	Flexible	Flexible	Fixed	Flexible
Fabrication cost	High (DNA preparation)	Moderate	High	Low
Array cost	Low	Moderate	Moderate	Moderate

While contact-printed arrays allow for unlimited customization, the initial production cost can be prohibitive compared with the relatively affordable but fixed-array designs commercially available. Maskless photolithographic arrays represent a trade-off between these platforms, allowing customized design while maintaining very high feature density.