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Relationships between Fragile X Mental Retardation 1 ( FMR1 ) mRNA levels in blood and intragenic  FMR1  CGG triplet expansions support the pathogenic role of RNA gain of function toxicity in premutation (PM: 55–199 CGGs) related disorders. Real-time PCR (RT-PCR) studies reporting these findings normalised  FMR1  mRNA level to a single internal control gene called  β -glucuronidase ( GUS) . This study evaluated  FMR1  mRNA-CGG correlations in 33 PM and 33 age- and IQ-matched control females using three normalisation strategies in peripheral blood mononuclear cells (PBMCs): (i)  GUS  as a single internal control; (ii) the mean of  GUS , Eukaryotic Translation Initiation Factor 4A2  (EIF4A2 ) and succinate dehydrogenase complex flavoprotein subunit A ( SDHA ); and (iii) the mean of  EIF4A2  and  SDHA  (with no contribution from  GUS ).  GUS  mRNA levels normalised to the mean of  EIF4A2  and  SDHA  mRNA levels and  EIF4A2 / SDHA  ratio were also evaluated.  FMR1 mRNA level normalised to the mean of  EIF4A2  and  SDHA  mRNA levels, with no contribution from  GUS , showed the most significant correlation with CGG size and the greatest difference between PM and control groups ( p  = 10 −11 ). Only 15% of  FMR1  mRNA PM results exceeded the maximum control value when normalised to  GUS , compared with over 42% when normalised to the mean of  EIF4A2  and  SDHA  mRNA levels. Neither  GUS  mRNA level normalised to the mean RNA levels of  EIF4A2  and  SDHA , nor to the  EIF4A2/SDHA  ratio were correlated with CGG size. However, greater variability in  GUS  mRNA levels were observed for both PM and control females across the full range of CGG repeat as compared to the  EIF4A2/SDHA  ratio. In conclusion, normalisation with multiple control genes, excluding  GUS , can improve assessment of the biological significance of  FMR1  mRNA-CGG size relationships.

β-glucuronidase use as a single internal control gene may confound analysis in FMR1 mRNA toxicity studies