The presence of a pseudogene may affect the use of HPRT as an endogenous mRNA control in RT-PCR.

Semi-quantitative reverse-transcription polymerase chain reaction (RT-PCR) has been used extensively as a tool to measure expression levels of mRNA species. Many commonly used endogenous mRNA control species are known to have genomic pseudogenes, which can confound RT-PCR results if not accounted for. The hypoxanthine phosphoribosyltransferase gene (HPRT) has previously been used as an mRNA control to circumvent these difficulties, since it was believed that no pseudogenes existed. The existence of a pseudogene of HPRT is reported, and researchers are warned that this gene cannot be used as an endogenous mRNA control without taking appropriate precautions.