Table 2.

Major advantage and disadvantages of various microarray formats for diagnostic purposes^⁎⁎.

Format	Supplier	Advantages	Disadvantages
Printed arrays	In-house manufacture by a core facility NimbleGen (Roche) Agilent	•Inexpensive •Simple to manufacture •Flexibility to change spot probes as required •Assay steps manual	•Need reliable access to a core facility(dust, humidity and temperature controlled) •Little supervision over quality control of manufacture •Requires extensive in-house probe design and manufacture •Requires expensive assay validation •Requires access to in-house bioinformatics to analyze and assess quality of the data •Can be inflexibility to change assay probes as required •Can be non-conducive to user-defined development (exception: Agilent)
In-situ synthesized oligonucleotide arrays	GeneChip®(Affymetrix)	•Custom-assay production •Automated	•Most expensive •High-density so (15,000 to >106) spot probes per assay •Complex to manufacture – probes chemically synthesized directly on quartz wafers
Electronic	NanoChip® (Nanogen)	•Electric fields promote active hybridization to nucleic acids onto a microelectronic device •Low-density (400 maximum) but adequate for diagnostic panel assays •Less expensive than high-density format •Allows flexible testing of multiple targets in a single sample or multiple samples on the same microarray cartridge	•Commercially available products discontinued (2007)
Liquid-based suspension bead-based arrays	Luminex Molecular Diagnostics	•Probes or universal sequence tags are attached to spectrally unique microspheres; bead hybridization with fluorescently labeled target DNA measured by flow cytometry •Low-density (100 maximum) but adequate for diagnostic panel assays •Less expensive than high-density format •Only FDA-approved commercial assay (xTAG Respiratory Panel) •Most flexible, practical format for clinical use •Multitude of clinical applications	•Requires careful validation of the positive fluorescent threshold for each analyte in a user-defined multiplex-bead-based assay

^⁎⁎Adapted from Miller and Tang (2009).