Quantitative fluorescent PCR (QF-PCR) assays are based on the amplification of DNA sequences unique for each chromosome pair and have been developed to establish the number of specific chromosomes present in a cell. These tests amplify STR or microsatellite markers with quantification of the products. QF-PCR is robust and reliable and can be completed within one working day. STR markers can confidently identify aneuploidy with tri-allelic trisomies. QF-PCR involves PCR using fluorescently labelled primers or dNTPs. The PCR reaction must be kept in the log phase by limiting the number of cycles.

The advent of fluorescent PCR technology has enabled a more sensitive determination of product length than non-fluorescent PCR. This sensitivity of fluorescent PCR is provided by laser analysis, which allows for sizing at the single base-pair level. As the number of STR markers that are analyzed increases, the determination of aneuploid status becomes more statistically significant. Compared with nested PCR, QF-PCR combines increased sensitivity and throughput, shorter turnaround time and superior precision in fragment sizing. The use of a laser system to perform automated fragment analysis with various fluorescent molecules, each with their own unique wavelength of emitted light, allows simultaneous discrimination of unrelated, similarly sized products. Furthermore, the thousand-fold increase in sensitivity compared with ethidium bromide allows a single round of PCR, potentially avoiding the contamination that can result from multiple tube openings.