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Short answer
DNA microarray analysis is the reading of a chip that carries thousands to millions of known nucleic acid fragments (probes). A sample is exposed to the chip, matching sequences bind by complementary base pairing, and the bound material fluoresces so a scanner can record where binding happened. The pattern tells you either how much RNA a gene produced or which DNA variants a sample carries.
Definition and scope: what is a DNA microarray?
The NHGRI Talking Glossary defines microarray technology as a general laboratory approach that binds an array of thousands to millions of known nucleic acid fragments to a solid surface, the “chip”. The fragments on the chip are called probes. The same page notes that the approach allows genomic analysis without sequencing, which greatly lowers the cost of large studies.
What is a microarray, and what are DNA microarrays?
“Microarray” is the general term for the chip-and-probe format. “DNA microarray” (also written “DNA microarrays” in the plural) names the version whose probes are DNA, as described in the NHGRI fact sheet on DNA microarray technology: thousands of short, synthetic, single-stranded DNA sequences fixed to the chip. They are the same technology; the plural simply refers to the many chips a lab may run.
How hybridization and detection work in practice
NHGRI’s fact sheet walks through a genotype-style example. DNA from a patient and from a control is fragmented and labeled with fluorescent dye, the patient’s with green and the control’s with red. The labeled fragments are added to the chip and allowed to hybridize, meaning bind, to the synthetic DNA on it. Sample DNA without a mutation binds probes carrying the normal sequence; DNA with a mutation binds probes carrying the mutant sequence. A specialized machine then reads the fluorescence at each probe position.
The analysis step is therefore a question of which probe positions lit up, and in which colour, rather than a question of reading a sequence base by base.
Expression use versus variant use
NHGRI describes these two uses, and they differ in what is put on the chip and what is measured.
| Use | Material applied to the chip | What the signal reports | Source |
|---|---|---|---|
| Gene expression | RNA isolated from cells or tissue instead of DNA | The amount of RNA made from each gene, showing which genes are switched on or off | NHGRI fact sheet and glossary |
| Variant detection | Sample DNA | Presence of specific DNA sequences, such as single nucleotide polymorphisms (SNPs), which is useful for genome-wide association studies | NHGRI glossary |
Microarrays versus sequencing
NHGRI states that DNA microarrays are used in clinical diagnostic tests for some diseases, and that some tests that once used microarrays now use DNA sequencing instead. It also states that microarray tests still tend to be less expensive than sequencing, which is why arrays remain useful for very large studies and for some clinical tests. The practical reading for a lab is that the choice is not settled in one direction: cost favours arrays for large sample counts, while the field has moved some applications to sequencing.
Where it matters for labs and data teams
Most of the work that follows a microarray run is about the data, not the chip. These CASRAI guides cover the surrounding decisions:
- Depositing or reusing array data: Gene Expression Omnibus (GEO) and ArrayExpress.
- Deciding whether an array or an RNA-seq design suits a question: RNA-seq experimental design and analysis.
- Correcting for runs processed in different batches: ComBat batch correction, an empirical Bayes method first described for microarray expression data (Johnson, Li and Rabinovic, 2007).
- Checking input RNA before an expression experiment: RNA integrity number (RIN).
Common misunderstandings
“A microarray sequences DNA.”
It does not. NHGRI frames it as analysis without sequencing: the chip detects binding to known probes, so it reports on sequences the chip was built to look for.
“Microarrays are obsolete.”
Not according to NHGRI. Some tests have moved to sequencing, but arrays still tend to cost less, and they remain in clinical diagnostic use for some diseases.
“Expression arrays and SNP arrays are interchangeable.”
They share the hybridization principle, but one measures RNA abundance and the other detects DNA sequence variants.
Frequently asked questions
What is a DNA microarray?
A chip bearing thousands to millions of known DNA fragments (probes). Labeled sample DNA or RNA binds matching probes, and fluorescence shows where.
What is a microarray?
The general format of known nucleic acid fragments bound to a solid surface, used to analyse a sample without sequencing it.
What is DNA microarray analysis used for?
Measuring gene expression and detecting specific DNA sequences such as SNPs, including in studies such as genome-wide association studies.
Is microarray cheaper than sequencing?
NHGRI states microarray tests still tend to be less expensive than sequencing.
Sources
- National Human Genome Research Institute, Talking Glossary: https://www.genome.gov/genetics-glossary/Microarray-Technology (checked 2026-10-29).
- National Human Genome Research Institute, fact sheet: https://www.genome.gov/about-genomics/fact-sheets/DNA-Microarray-Technology (checked 2026-10-29).
- Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007: https://pubmed.ncbi.nlm.nih.gov/16632515/ (checked 2026-10-29).
