Internal control for quality assurance of diagnostic RT-PCR

Evaluation of a commercially available synthetic RNA lipid enveloped control molecule

Detection of viral ribonucleic acid with RT PCR is a useful tool for viral detection. One of the drawbacks of this technique is the difficulty in including an internal control molecule to ensure the validity of the extraction and amplification process. In this study the potential usefulness of a novel lipid enveloped commercially available RNA control molecule is investigated. Initial optimisation of the detection assay was performed by amplification of IC (internal control) spiked into PCR water. Thirty-two clinical respiratory samples were spiked with the IC before and after extraction and RT PCR was then performed. Inefficient extraction was simulated. Inhibition of the RT PCR was achieved by serial dilution of heparin sulfate into samples post extraction. No Targets that matched the IC (Internal Control) primers were identified in 32 extracted sputum samples as determined by the absence of non specific amplification curves. The unextracted IC had an increased CT (cycle threshold) value compared to IC that had been extracted. Inefficient extraction was detected by an increased CT. Increasing concentrations of heparin inhibited the PCR in a predictable fashion. The Bioline IC molecule provides a stable RNA IC that has acceptable performance characteristics.

Preparation of His-tagged armored RNA phage particles as a control for real-time reverse transcription-PCR detection of severe acute respiratory syndrome coronavirus

Armored RNA has been increasingly used as both an external and internal positive control in nucleic acid-based assays for RNA virus. In order to facilitate armored RNA purification, a His6 tag was introduced into the loop region of the MS2 coat protein, which allows the exposure of multiple His tags on the surface during armored RNA assembly. The His-tagged armored RNA particles were purified to homogeneity and verified to be free of DNA contamination in a single run of affinity chromatography. A fragment of severe acute respiratory syndrome coronavirus (SARS-CoV) genome targeted for SARS-CoV detection was chosen for an external positive control preparation. A plant-specific gene sequence was chosen for a universal noncompetitive internal positive control preparation. Both controls were purified by Co2+ affinity chromatography and were included in a real-time reverse transcription-PCR assay for SARS-CoV. The noncompetitive internal positive control can be added to clinical samples before RNA extraction and enables the identification of potential inhibitive effects without interfering with target amplification. The external control could be used for the quantification of viral loads in clinical samples.

Minimal residual disease in melanoma

A number of specific genes encoding for melanosomal proteins are selectively expressed in melanocytes and melanomas. For detection of circulating melanoma cells, the expression of the tyrosinase gene is most widely used. Several cohorts of melanoma patients from single institutions have been analyzed by various research groups for the presence of circulating melanoma cells in all stages of disease. The percentage of patients with evidence of occult tumor dissemination has been correlated with stage of disease in several, but not all, reports. Two prospective analyses suggest that the PCR result is of prognostic value in melanoma. Several laboratories have found PCR evidence for circulating melanoma cells in the vast majority of untreated patients with stage IV disease, although other groups have reported much lower frequencies. Taken together, there is a wide range of results. Methodological differences likely account for this discrepancy. With the availability of true quantitative RT-PCR systems, such as the Light Cycler system, accurate quantification of tyrosinase transcripts over a range of 1-10,000 tumor cells per ml of blood is possible. Quantitative RT-PCR systems also dramatically improve quality control, since exact quantitation of housekeeping gene mRNA facilitates determination of sample quality.

Quantitative PCR-ELAHA for the Determination of Retroviral Vector Transduction Efficiency

Current methods to detect transduction efficiency during the routine use of integrating retroviral vectors in gene therapy applications may require the use of radioactivity and usually rely upon subjective determination of the results. We have developed two competitive quantitative assays that use an enzyme-linked, amplicon hybridization assay (ELAHA) to detect the products of PCR-amplified regions of transgene from cells transduced with Moloney murine leukemia virus vectors. The quantitative assays (PCR-ELAHA) proved to be simple, rapid, and sensitive, avoiding the need for Southern hybridization, complex histochemical stains, or often subjective and time-consuming tissue culture and immunofluorescence assays. The PCR-ELAHA systems can rapidly detect proviral DNA from any retroviral vector carrying the common selective and marker genes neomycin phosphotransferase and green fluorescent protein, and the methods described are equally applicable to other sequences of interest, providing a cheaper alternative to the evolving real-time PCR methods. The results revealed the number of copies of retrovector provirus present per stably transduced cell using vectors containing either one or both qPCR targets.

Nested quantitative real time PCR for detection of occult tumor cells

Quantification of tumor mRNA markers expressed by occult circulating tumor cells may be of prognostic value in a variety of neoplasms and disease stages. We therefore developed a novel real time nested polymerase chain reaction (PCR) assay to quantify rare transcripts using the light cycler system. Tyrosinase mRNA expressed by melanocytes and melanoma cells was used as a model. Ten-milliliter samples of ethylenediaminetetra-acetate (EDTA) blood from healthy volunteers were spiked with 10-10(4) RVH melanoma cells. Following RNA extraction and cDNA synthesis, a nested PCR with specific primers was performed. Resonance energy transfer between fluorescently labeled hybridization probes specific for the amplified portion of the tyrosinase transcript allowed continuous monitoring of the second round of PCR. The number of preamplification cycles in the first round was varied between 20 and 35. Our results show that nested PCR revealed quantitative data, regardless of the number of cycles used in the first round. The range of real time data can span four logs of target mRNA concentrations (1-10(3) tumor cells/ml of blood) and the x-intercepts of the log phases were always consistent with the amount of transcripts in the sample. These experiments indicate that nested PCR, which is much more sensitive than single-round PCR, is a useful tool for the quantification of rare transcripts--a result with important implications for the study of minimal residual disease. The assay is currently being adapted for other tumor types including leukemias as well as other solid tumors.

Simultaneous Absolute Quantification of Target and Control Templates by Real-Time Fluorescence Reverse Transcription-PCR Using 4-(4′-Dimethylaminophenylazo)benzoic Acid as a Dark Quencher Dye

Background: Despite the many advantages of real-time fluorescence reverse transcription-PCR (RT-PCR) as a quantitative analytical tool, simultaneous quantification of target and reference templates within one reaction has not been reported. We developed such an assay with an internal reference template.

Methods: For quantification of target and reference sequences, we used two fluorescent probes in one reaction vessel on an ABI PRISM 7700 SDS instrument. Fluorescent probes were labeled with either 6-carboxy-fluorescein or hexachloro-6-carboxy-fluorescein as reporter dye and 4-(4′-dimethylaminophenylazo)benzoic acid (DABCYL) as a dark quencher fluorophore. To test the sensitivity and specificity of this assay, serial dilutions of reference and target templates were analyzed in one PCR reaction. In the presence of 10 β-actin molecules as control templates, 105 bcr/abl molecules were amplified, and 105 β-actin molecules were amplified in the presence of 10 bcr/abl copies. We also performed single and duplex measurements on samples from five patients with documented Philadelphia chromosome-positive chronic myelogenous leukemia disease courses (72 samples) and three with minor bcr/abl+ acute myelogenous leukemias (26 samples).

Results: For M-bcr/abl duplex RT-PCR, the correlation coefficient (r) for starting template amounts and threshold cycle values was 0.99; for m-bcr/abl, r = 0.96, indicating a precise log-linear relation for 10–105 copies/100 ng of cDNA. In the same PCR reactions, r = 0.99 for β-actin (coamplified with M-bcr/abl or m-bcr/abl) for 103–107 copies/100 ng cDNA. The linear correlation coefficient for single and duplex measurements was 0.98 for M- and m-bcr/abl in patient samples.

Conclusions: DABCYL can be used as dark quencher fluorophore in real-time fluorescence PCR. The duplex fluorescence RT-PCR assay for bcr/abl and β-actin transcripts allows monitoring of bcr/abl+ leukemias.

Mitochondrial ATP synthase 6 as an endogenous control in the quantitative RT-PCR analysis of clinical cancer samples

BACKGROUND

Real-time polymerase chain reaction (PCR) is a powerful new technique in the evolution of quantitative reverse transcription-PCR assays. With the increased sensitivity and resolution of real-time techniques, the requirements for constitutive expression of endogenous controls have become increasingly stringent.

METHODS AND RESULTS

We compare the expression of the mitochondrial gene, adenosine triphosphate synthase 6 (ATPsy6), to the expression of other routinely used endogenous control genes (e.g., beta-actin, glyceraldehyde-3-phosphate dehydrogenase [GAPDH], ribosomal RNA 18S [18S rRNA], and cyclophilin). In a diverse assortment of tissues and across a wide range of disease stages, ATPsy6 shows a relative steady state of expression compared with other endogenous controls. ATPsy6 gene expression has been used as an endogenous control in a quantitative real-time PCR assay designed to evaluate the expression of potential cancer diagnostic leads across a diverse tissue panel.

CONCLUSION

Mitochondrial ATPsy6 serves as a good endogenous control to measure target gene expression independent of the tissue- or disease-specific variation inherent with many housekeeping genes.