EQUAL-qual: a European program for external quality assessment of genomic DNA extraction and PCR amplification.

BACKGROUND: Despite the rapid transition into routine clinical practice of molecular techniques based on PCR, external quality assessment (EQA) is still not widely available. The European Union and European Communities Confederation of Clinical Chemistry have supported the EQUAL project as a series of 3 different EQA programs for the assessment of molecular methods independently from analytes. We present the results from the EQUAL-qual program designed to evaluate the analytical aspects of DNA analysis by means of a conventional qualitative PCR experiment. METHODS: The EQUAL-qual program provided DNA, blood samples, and primer sets to participant laboratories to assess DNA extraction and PCR amplification. We have developed statistical procedures to identify laboratories performing poorly in DNA extraction (quality and quantity), PCR efficiency, and data interpretation after electrophoresis. RESULTS: An application to participate was obtained from 213 laboratories (from 25 countries), and 175 (82%) of laboratories submitted results for assessment. Questionable results in terms of quality and/or quantity of DNA derived from blood extractions were returned by 27% of laboratories (46 of 166). PCR efficiency showed high variability, with 3% of laboratories (5 of 163) showing a consistently low rate of amplification and 10% (18 of 175) not reporting the expected number of bands of the amplified targets. CONCLUSIONS: The results showed considerable variability in all phases of the experiment. The approach confirms the validity of EQA as a method for evaluating analytical aspects of PCR-based tests.

Bivariate statistical approach to evaluate laboratory performance by analysis of standard curves in an External Quality Assurance program for quantitative assays based on real-time PCR with Taq-Man probes.

Recently a revolutionary technique for quantitative PCR determination was introduced in diagnostic laboratories. To determine the influence of technical variability on the reliability of the quantitative assay, it is crucial to use External Quality Assurance (EQA) programs. An EQA program was developed in Italy to check the analytical performance of real-time PCR procedures based on Taq-Mantrade mark probes. This article suggests a new statistical approach to discriminate, using a bivariate technique, laboratory performance that appears to be questionable, by separately considering the two main features of the standard curve: analytical sensitivity and efficiency. Furthermore, specific indexes to evaluate the impact of these two features on the determination of the initial number of molecules are given to help to improve the assay procedure.

Quantitative evaluation of somatostatin receptor subtype 2 expression in sporadic colorectal tumor and in the corresponding normal mucosa.

PURPOSE: The somatostatin (SS) receptor subtype 2 (sst2) is the principal mediator of the antiproliferative effects of SS and has the highest affinity for the commercially available SS analogues. The purpose of this study was to evaluate sst2 mRNA expression by quantitative reverse transcription-PCR (RT-PCR) in colon cancers and in corresponding normal tissues. EXPERIMENTAL DESIGN: The expression of sst2 mRNA was measured with a quantitative method based on real time RT-PCR with TaqMan assay in 100 colon cancers and in the corresponding normal tissues. In a limited number of patients, these results were compared with those obtained by in situ hybridization (n = 26) and by in vivo imaging with (111)In-pentetreotide (n = 17). RESULTS: Results obtained by quantitative RT-PCR on sst2 expression in colorectal cancer were significantly related to those obtained by in situ hybridization and (111)In-pentetreotide scintigraphy. Sst2 was expressed in all of the tumors investigated without any relationship with localization, grading, and stage of disease. Although the paired, unaffected mucosa tends to express a higher abundance of sst2 than the corresponding cancer samples, this difference did not reach a statistical significance. However, in patients with elevated carcinoembryonic antigen levels (>5 ng/ml) there was a significant loss of sst2 mRNA in the tumor when compared with its paired normal tissue. CONCLUSIONS: In this study we confirmed, by a quantitative method, that colorectal cancer does not express higher concentrations of sst2 mRNA than the corresponding unaffected tissue. Conversely, a loss of sst2 was found in patients with elevated preoperative concentrations of carcinoembryonic antigen, an unfavorable prognostic marker for colorectal cancer.