TABLE 1.
Comparison of microarray platformsa
| Microarray | Principle(s) | Format(s) | Density | Relative cost | Diagnostic application(s) | References |
|---|---|---|---|---|---|---|
| Printed | Glass slides are used as the solid support for printing DNA probes | For dsDNA, PCR amplicons (200-800 bp) from known genomic sequence, shotgun library clones, or cDNA are used; for oligonucleotides, 25-80-bp probes are synthesized | Moderate (∼10,000-30,000) | $$$ | No commercially available applications; pathogen detection and identification, antimicrobial resistance detection, viral discovery, molecular surveillance | 21, 32, 153, 167, 172, 195, 206-208 |
| In situ synthesized | Oligonucleotides are synthesized directly on the surface of a quartz wafer using photochemistry; multiple probe sets (one perfect-match probe and one mismatch probe) are included per target | Affymetrix GeneChips, 20-25-bp probes; Roche NimbleGen, 60-100-bp probes; Agilent, 60-bp probes | High (Affymetrix, >106; NimbleGen and Agilent, 15,000->106) | $$$$ | No commercially available applications; pathogen detection and identification, antimicrobial resistance detection, viral discovery, molecular surveillance, strain typing | 59, 117, 150, 151, 157, 200, 215 |
| High-density bead arrays | Sequence-tagged beads are randomly assorted onto fiber-optic bundles or silicon slides | SAM, 96 samples; Sentrix BeadChip; 1-16 samples | High (∼50,000-106) | $$$ | No commercially available applications; potential use in microbiology but no studies published to date | 52, 71, 146 |
| Electronic | Electric fields are used to promote active hybridization of nucleic acids on a microelectronic device; streptavidin-biotin bonds immobilize the probes on the array surface | NanoChip 400; capture probe down; amplicon down; sandwich assays | Low (400 max) | $$ | Commercially available products discontinued; pathogen detection and identification | 10, 108, 185, 226 |
| Liquid-bead suspension | Spectrally unique microspheres provide solid support for application of probes or universal sequence tags; bead hybridization with fluorescently labeled target DNA is measured using flow cytometry | Direct DNA hybridization; competitive DNA hybridization; solution-based chemistries (ASPE/TSPE, OLA, SBCE) | Low (100 max) | $$ | FDA-cleared xTAG RVP assay; pathogen detection and identification, antimicrobial resistance detection, strain typing | 18, 73, 79, 109, 112, 148, 191 |
a
Data from reference 135. $$, low-moderate cost; $$$, moderate cost; $$$$, high cost.