Xpert(®) MTB/RIF detection of Mycobacterium tuberculosis from sputum collected in molecular transport medium.

Background: The Xpert(®) MTB/RIF assay is widely used for Mycobacterium tuberculosis detection. However, specimen transport remains a challenge. PrimeStore Molecular Transport Medium(®) (PS-MTM) inactivates specimens and stabilizes DNA/RNA at ambient temperature for subsequent molecular detection.

Performance of robust regression methods in real-time polymerase chain reaction calibration.

The ordinary least squares (OLS) method is routinely used to estimate the unknown concentration of nucleic acids in a given solution by means of calibration. However, when outliers are present it could appear sensible to resort to robust regression methods. We analyzed data from an External Quality Control program concerning quantitative real-time PCR and we found that 24 laboratories out of 40 presented outliers, which occurred most frequently at the lowest concentrations.

Short- and long-term effects of a training session on pathologists' performance: the INQAT experience for histological grading in breast cancer.

Although the introduction of the Nottingham/Tenovus classification has improved the criteria to assess the histological grading in breast cancer, several quality control studies have shown that good results in terms of reproducibility are hard to obtain. This paper reports the results obtained during an implemented quality control programme for histological grading aimed at evaluating the short- and long-term effects of a training session on pathologists' performance. The interobserver reproducibility for grading score along with its components was assessed.

An Italian program of External Quality Control for chromogranin A (CgA) assay: performance evaluation of CgA determination.

Background: Chromogranin A (CgA) is an acidic glycoprotein produced by many neuroendocrine cells and neurons. Currently, two different methods for assaying CgA, immunoradiometric assay (IRMA) and enzyme-linked immunosorbent assay (ELISA), are widely used in routine practice. Within the framework of a Ministry of Health project, an External Quality Control program was developed to investigate the state of the art of CgA determination in Italy and to monitor the performance of laboratories carrying out this assay.

[Statistical notes. Statistical significance and clinical relevance: are they the two sides of the same medal?].

The aim of this statistical note is to draw the attention of the cardiologists to the aspects pertinent to the clinical relevance of the result of a clinical controlled randomized trial. The difference between clinical relevance and statistical significance is shown by using the results of GISSI and GUSTO III clinical controlled randomized trials.

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.

[What does "p" mean at conclusion of a test of hypothesis in a randomized controlled clinical trial of superiority?].

The aim of this statistical note, the sixth in the series, is to introduce the rationale of the test of hypothesis suitable for comparing the effect of two treatments in a randomized controlled clinical trial of superiority. The presentation takes advantage of the analogy with a criminal trial debate based upon circumstantial evidence in an Italian Court. The results of three randomized controlled clinical trials: ISIS-1, AIMS and RESTORE are introduced and proper ways for their interpretation are suggested.

Axillary lymph node nanometastases are prognostic factors for disease-free survival and metastatic relapse in breast cancer patients.

Purpose: Early breast cancer presents with a remarkable heterogeneity of outcomes. Undetected, microscopic lymph node tumor deposits may account for a significant fraction of this prognostic diversity. Thus, we systematically evaluated the presence of lymph node tumor cell deposits View Article and Find Full Text PDF

[Statistical notes. Which risks do the patient incur if his own cardiologist accepts to be involved in a clinical trial without deep consideration of the a priori available evidence?].

The aim of this statistical note is to describe the results of the randomized controlled clinical trial TARGET, which compared the effect of tirofiban (new treatment) and abciximab (standard treatment) in patients who were expected to undergo coronary stenting. Primary aim of TARGET was to evaluate the non-inferiority of tirofiban with respect to abciximab, but it concluded in favor of superiority of the standard treatment. The authors of this study point out that a deep consideration regarding a priori available evidence could have avoided to expose 2398 patients randomized to tirofiban to the risk of death or non-fatal myocardial infarction.

EQUAL-quant: an international external quality assessment scheme for real-time PCR.

Background: Quantitative gene expression analysis by real-time PCR is important in several diagnostic areas, such as the detection of minimum residual disease in leukemia and the prognostic assessment of cancer patients. To address quality assurance in this technically challenging area, the European Union (EU) has funded the EQUAL project to develop methodologic external quality assessment (EQA) relevant to diagnostic and research laboratories among the EU member states. We report here the results of the EQUAL-quant program, which assesses standards in the use of TaqMan probes, one of the most widely used assays in the implementation of real-time PCR.

Artificial neural network for the joint modelling of discrete cause-specific hazards.

Objective: Artificial neural network (ANN) based regression methods have been introduced for modelling censored survival data to account for complex prognostic patterns. In the framework of ANN extensions of generalized linear models for survival data, PLANN is a partial logistic ANN, suitable for smoothed discrete hazard estimation as a function of time and covariates. An extension of PLANN for competing risks analysis (PLANNCR) is now proposed for discrete or grouped survival times, resorting to the multinomial likelihood.

Fifteen-year results of a randomized phase III trial of fenretinide to prevent second breast cancer.

Purpose: The synthetic retinoid fenretinide administered for 5 years for prevention of second breast cancer showed no difference after a median of 8 years, but a possible reduction in premenopausal women. We conducted a long-term analysis in a subgroup of women who were regularly followed up in a single center.

Patients And Methods: We analyzed data after a median follow-up of 14.

Molecular subtyping of breast cancer from traditional tumor marker profiles using parallel clustering methods.

Purpose: Recent small-sized genomic studies on the identification of breast cancer bioprofiles have led to profoundly dishomogenous results. Thus, we sought to identify distinct tumor profiles with possible clinical relevance based on clusters of immunohistochemical molecular markers measured on a large, single institution, case series.

Experimental Design: Tumor biological profiles were explored on 633 archival tissue samples analyzed by immunohistochemistry.

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.

[Statistical notes. Randomized controlled clinical trials of both superiority and non-inferiority: critical considerations].

The aim of this statistical note, the fourth in the series, is to describe and critically appraise the randomized controlled clinical trial (RCCT) GUSTO V, which combined in a single RCCT both the superiority and non-inferiority hypotheses. In this note we present the logical path that the authors have presumably followed in planning a RCCT of such a kind. The results are reported and possible critical aspects are highlighted and debated upon.

An Italian program of external quality control for quantitative assays based on real-time PCR with Taq-Man probes.

Quantitative real-time PCR techniques are increasingly being used for the measurement of nucleic acids in research applications as well as in the clinical laboratory. It is therefore important that external quality control programs (EQA) are implemented for the evaluation of the analytical aspects common to molecular tests based on quantitative PCR. The aim of this study was the development of an Italian program of external quality control for quantitative assays based on real-time PCR with Taq-Mantrade mark probes to compare the analytical performance of 42 laboratories.

[Statistical notes. Hazard curves of sudden death: their role in the cardiologist's clinical decision].

In long-term studies researchers are mainly concerned with occurrence of death during the follow-up period. This statistical note is focused on survival analysis which is the main tool to process this kind of data. Survival curve, cumulative mortality curve and hazard curve are here introduced together with an appropriate effect indicator: hazard ratio.

[Statistical notes. From superiority to non-inferiority clinical trials: a leap in the dark?].

In these "statistical notes", equivalence and non-inferiority randomized controlled clinical trials (RCCT) are considered. Equivalence trials are designed to confirm the absence of a meaningful difference between the effect of two treatments. Non-inferiority trials are designed to prove that the new treatment is no less effective than an existing one: it may be more effective or it may have a similar effect.

Picotamide, a combined inhibitor of thromboxane A2 synthase and receptor, reduces 2-year mortality in diabetics with peripheral arterial disease: the DAVID study.

Aims: Patients with diabetes are at excessive risk of mortality and cardiovascular morbidity. Previous studies suggest that aspirin may be less effective in diabetic patients. In this multi-centre, randomized, double blind trial picotamide, a dual inhibitor of thromboxane A2 synthase and receptor, was compared with aspirin for the prevention of mortality and major cardiovascular events in diabetics with peripheral arterial disease (PAD).

[Statistical notes. Absolute and relative effect measures].

The aim of these statistical notes was to give the cardiologist the suitable tools for the understanding of the statistical aspects in the reading of papers presenting the results of randomized controlled clinical trials, in the most simple and intuitive way, without any previous knowledge of basic statistics. The fundamentals of the most common tools for the comparison of two experimental treatments, are developed by getting cue from classical cardiological examples and by guiding the reader, step by step, toward the understanding and critical discussion of the proposed examples. In particular, this note focuses the attention on the main "indicators" of absolute and relative effect measures by evidencing their most important differences.

[Equivalence studies in cardiovascular diseases].

An increasing number of equivalence and non-inferiority trials appeared in recent years among randomized clinical trials, particularly for the evaluation of efficacy of treatments in cardiovascular medicine. These studies are characterized by remarkable methodological issues and important ethical implications. The aim of this review was to underscore some topic methodological problems: setting the equivalence boundary, the special logic used to establish equivalence, and the determinants of sample size.