Every cell in the body carries its DNA tightly organized into 46 chromosomes. A FISH probe is built from a strand of DNA that is complementary to one specific stretch of one chromosome, meaning its chemical structure fits that target the way a key fits a lock, and nowhere else in the genome. The probe carries a fluorescent dye attached to it. When the probe is mixed with a person’s cells that have been fixed onto a glass slide, it seeks out and binds tightly to its one matching target and nothing else, a process called hybridization. Under a fluorescence microscope, each bound probe appears as a single glowing dot. A typical cell has two copies of every chromosome, one from each parent, so a healthy result usually shows two dots, one for each copy. One dot instead of two suggests a piece of that region is missing; three or more dots suggest an extra copy; and a dot appearing in an unexpected position on a different chromosome suggests the region has been relocated through a rearrangement.

This test can be performed on cells caught mid-division, when chromosomes are bundled into their familiar compact shape, or on resting cells between divisions, where the DNA is more loosely spread through the nucleus. The second approach, called interphase testing, is what allows many FISH results to be ready in as little as one to two days, since it skips the several days some other tests need to grow living cells into active division.

The key difference from other chromosome tests is focus versus breadth. A karyotype photographs and sorts all 46 chromosomes under a microscope, catching large rearrangements and missing or extra whole chromosomes, but only down to a resolution of roughly five to ten million building blocks of DNA. A chromosomal microarray scans the entire genome at once for missing or duplicated material, at a much finer resolution, but cannot see a rearrangement where material has simply changed position without any being gained or lost, and does not deliver same-day results. Genome or exome sequencing reads the genetic code letter by letter, catching single-gene changes neither of the other tests can see, but is a slower, broader process not typically chosen when a fast, specific answer is needed. FISH sits apart from all three: it is fast and highly reliable for the one region it is aimed at, but it tells a family nothing about the rest of the genome, since the laboratory must already know, in advance, exactly what to look for.