Estimates of the level of transcripts from the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) gene required to develop a CF phenotype range from 4-20% of normal. Due to the importance of obtaining reliable data on this issue for therapeutic strategies, we developed a novel polymerase chain reaction-based method to quantify CFTR transcripts and applied it to the analysis of nasal epithelium RNA of five patients with CF and the 3272-26A>G/F508del genotype. We calculated that 8.2 +/- 0.84% of the total CFTR RNA present in these five patients is normal full-length CFTR mRNA. We then demonstrated (in nasal samples from F508del carriers, n = 30) that the abundance of full-length F508del CFTR transcripts is reduced compared with wild-type transcripts, and estimated that the average ratio of F508del/wild-type transcripts is 0.87 +/- 0.06. To determine the amount of full-length transcripts relative to levels found in normal individuals, we corrected for the lower abundance of the F508del transcripts and calculated that the five patients with CF have, on average, 4.7 +/- 0.45% of the normal level of wild-type CFTR mRNA. Because these patients have mild CF compared with F508del homozygotes, this CFTR mRNA level appears to be sufficient to avoid the severe complications of the disease.

Factors other than mutations in the CFTR gene can produce phenotypes clinically indistinguishable from nonclassic cystic fibrosis caused by CFTR dysfunction.

Real-time quantitative PCR systems (Q-PCRIn an effort to evaluate the impact of CMV sequence variants in our patient population by use of a similar Q-PCR assay, we surveyed 54 isolates of CMV, each from a different patient. We detected evidence for the C630T variant in 4 of 54 (7.4%) patients. Furthermore, isolates from two additional patients were completely negative in the test. Sequencing of these false-negative isolates revealed multiple mutations within the probe hybridization sites. A Q-PCR that targeted the CMV polymerase gene instead of gB detected all 54 isolates. We suggest that Q-PCR assays for viral load be rigorously tested on large panels of viral isolates to assess the impact of sequence diversity on detection as well as quantification.Real-time quantitative PCR (Q-PCR) is currently the method of choice for the rapid detection and quantification of cytomegalovirus (CMV) in clinical specimens (10, 12). The glycoprotein B gene (gB, UL55) is, overall, one of the less variable regions of the CMV genome (11, 17), except for two variable subregions (4, 16), and has been frequently used as a target for Q-PCR assays (5,6,(8)(9)(10)19). Schaade et al. (14) described a Q-PCR assay using fluorescence energy transfer technology with two fluorophore-labeled hybridization probes within the gB gene and concluded that their assay was superior in terms of sensitivity, specificity, linear range, and efficiency to the commercially available COBAS Amplicor CMV Monitor assay (Roche), which uses the CMV DNA polymerase gene (pol) as a target. Other groups, using modifications of the assay described by Schaade et al. (14), have reported similar experiences (8, 12).However, CMV variants that could not be quantified using this Q-PCR have been reported (15). In the initial report (15), 912 clinical specimens were tested, of which 197 were positive for CMV DNA, but for 12 specimens (6.1% of the positive specimens) a viral load could not be determined. The specimens that were detected but not quantified did not produce a crossing point or any evidence of amplification during the PCR. However, in the melting curve analysis following the PCR, a signal was detected with a melting temperature of 53.1°C, which is below the 59.2°C melting temperature found for wild-type CMV. Sequence analysis revealed a single base pair mutation, C630T, in the target sequence of the downstream probe (15). This sequence variant prevented the appearance of a fluorescent signal under the cycling conditions of the assay, which included an annealing temperature of 58°C (15). The melting curve employed a lower annealing temperature (45°C), which allowed hybridization of the probe with the C630T variant (15). Thus, for the C630T gB variant, the assay developed by Schaade et al. (14) was only sufficient to provide qualitative results.To evaluate the impact of sequence variants in our patient population using a similar Q-PCR assay, we studied 54 CMV isolates, each from a different patient. We found two isolates that were not detectable. Sequence analysis o...