microarrays

Microarrays are laboratory devices used to measure the expression or genetic variation of many genes simultaneously. They consist of a solid surface, usually glass, onto which thousands of DNA probes are fixed in a precise grid. Each probe corresponds to a known gene or genomic feature, enabling parallel interrogation of a large number of targets in a single experiment.

During a typical expression microarray experiment, RNA is isolated from two or more samples, converted to labeled cDNA or cRNA, and mixed with a reference. The labeled targets are hybridized to the array, and after washing, the slide is scanned with a laser to detect fluorescence. The resulting intensities reflect target abundance for each probe.

Arrays are categorized by design and target type. cDNA microarrays use cDNA clones as probes, while oligonucleotide arrays use short, synthesized DNA sequences. Expression microarrays compare transcript levels, whereas comparative genomic hybridization arrays assess DNA copy number. Protein microarrays and methylation arrays extend the concept to other biomolecules or epigenetic marks.

Applications include large-scale gene expression profiling, identification of disease-associated expression patterns, assessment of drug responses, and genomic copy-number analysis. Typical workflows involve quality control, normalization to remove systematic biases, and statistical analysis to identify differential signals, often with specialized software and multiple testing correction.

Limitations include dependence on predefined probes, cross-hybridization, limited dynamic range, and potential batch effects. Advances in sequencing-based methods, such as RNA sequencing, have supplanted many microarray tasks, but arrays remain practical for targeted panels or historical datasets.