The Neo count qPCR assay uses a hydrolysis probe assay (eg Applied Biosystems TaqMan technology) to determine the copy number of the Neo cassette in a sample. Homozygotes will possess two copies of Neo, heterozygotes one copy and wild type mice will show no amplification. The theory behind the calling method is discussed further here. The Neo count does not confirm the correct targeting of the allele, or that if the correct gene has been microinjected in the first place. It can however be used as a QC tool to detect multiple insertion events, problems with the internal structure of the cassette, or mixed colonies (for example if 2 copies are detected in the chimera progeny or more than two copies start being detected as the colony is established).

Neo count qPCR can be used as a routine genotyping tool once the rest of the QC has been performed. The non-gene specific nature of the assay makes it very conducive to high-throughput methods where many different genes may be present on a sample plate, and thousands of samples can be easily genotyped using this method.